From 19daebb186a467744e46d74545c8301bf666047b Mon Sep 17 00:00:00 2001
From: mjwestgate <martinjwestgate@gmail.com>
Date: Mon, 5 Feb 2024 23:37:29 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20AtlasOfL?=
 =?UTF-8?q?ivingAustralia/galah-R@aac38c09a4eba6d7febec72ec1501749d28f878f?=
 =?UTF-8?q?=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                  |  2 +-
 articles/choosing_an_atlas.html           |  2 +-
 articles/download_data.html               |  2 +-
 articles/index.html                       |  2 +-
 articles/look_up_information.html         |  2 +-
 articles/narrow_your_results.html         |  2 +-
 articles/object_oriented_programming.html | 75 ++++++++++++-----------
 articles/piping.html                      |  2 +-
 articles/quick_start_guide.html           |  2 +-
 articles/spatial_filtering.html           |  4 +-
 articles/taxonomic_filtering.html         |  2 +-
 articles/temporal_filtering.html          |  6 +-
 authors.html                              | 10 +--
 index.html                                |  2 +-
 news/index.html                           | 16 ++++-
 pkgdown.yml                               |  2 +-
 reference/arrange.html                    |  2 +-
 reference/atlas_citation.html             |  2 +-
 reference/atlas_counts.html               |  2 +-
 reference/atlas_media.html                |  2 +-
 reference/atlas_occurrences.html          |  2 +-
 reference/atlas_species.html              |  2 +-
 reference/atlas_taxonomy.html             |  2 +-
 reference/collapse_galah.html             | 23 ++++---
 reference/collect_galah.html              |  6 +-
 reference/collect_media.html              |  2 +-
 reference/compute_galah.html              | 34 +++-------
 reference/deprecated-functions.html       |  2 +-
 reference/galah.html                      |  2 +-
 reference/galah_apply_profile.html        |  2 +-
 reference/galah_call.html                 |  2 +-
 reference/galah_config.html               |  2 +-
 reference/galah_filter.html               |  2 +-
 reference/galah_geolocate.html            |  2 +-
 reference/galah_group_by.html             |  2 +-
 reference/galah_identify.html             |  2 +-
 reference/galah_select.html               |  2 +-
 reference/index.html                      |  8 +--
 reference/print_galah_objects.html        | 26 ++++----
 reference/reexports.html                  |  2 +-
 reference/search_all.html                 |  2 +-
 reference/show_all.html                   |  2 +-
 reference/show_values.html                |  2 +-
 reference/slice_head.html                 |  2 +-
 reference/tidyverse_functions.html        |  2 +-
 search.json                               |  2 +-
 46 files changed, 141 insertions(+), 139 deletions(-)

diff --git a/404.html b/404.html
index a2bd09d4..0cfc6045 100644
--- a/404.html
+++ b/404.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="https://galah.ala.org.au/R/index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/choosing_an_atlas.html b/articles/choosing_an_atlas.html
index b61598b6..96d6306c 100644
--- a/articles/choosing_an_atlas.html
+++ b/articles/choosing_an_atlas.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/download_data.html b/articles/download_data.html
index aad14579..fcf09158 100644
--- a/articles/download_data.html
+++ b/articles/download_data.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 17536f85..22cc53a6 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/look_up_information.html b/articles/look_up_information.html
index 5f002df2..1526c594 100644
--- a/articles/look_up_information.html
+++ b/articles/look_up_information.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/narrow_your_results.html b/articles/narrow_your_results.html
index 7ba5aec5..fbc45d31 100644
--- a/articles/narrow_your_results.html
+++ b/articles/narrow_your_results.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/object_oriented_programming.html b/articles/object_oriented_programming.html
index 097d66dd..3b12ab5b 100644
--- a/articles/object_oriented_programming.html
+++ b/articles/object_oriented_programming.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -97,7 +97,7 @@ <h6 class="dropdown-header" data-toc-skip>Advanced</h6>
                         <h4 data-toc-skip class="author">Martin
 Westgate, Dax Kellie</h4>
             
-            <h4 data-toc-skip class="date">2023-12-14</h4>
+            <h4 data-toc-skip class="date">2024-02-02</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/AtlasOfLivingAustralia/galah-R/blob/HEAD/vignettes/object_oriented_programming.Rmd" class="external-link"><code>vignettes/object_oriented_programming.Rmd</code></a></small>
       <div class="d-none name"><code>object_oriented_programming.Rmd</code></div>
@@ -140,8 +140,8 @@ <h2 id="masked-functions">Masked functions<a class="anchor" aria-label="anchor"
 <pre><code><span><span class="co">## # A tibble: 16 × 2</span></span>
 <span><span class="co">##    species                 count</span></span>
 <span><span class="co">##    &lt;chr&gt;                   &lt;int&gt;</span></span>
-<span><span class="co">##  1 Crinia signifera        58204</span></span>
-<span><span class="co">##  2 Crinia parinsignifera   12478</span></span>
+<span><span class="co">##  1 Crinia signifera        58579</span></span>
+<span><span class="co">##  2 Crinia parinsignifera   12782</span></span>
 <span><span class="co">##  3 Crinia glauerti          3090</span></span>
 <span><span class="co">##  4 Crinia georgiana         1490</span></span>
 <span><span class="co">##  5 Crinia remota             784</span></span>
@@ -219,20 +219,24 @@ <h2 id="advanced-query-building">Advanced query building<a class="anchor" aria-l
 implemented stages of query building: <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code>,
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code>. These stages mirror
 existing <a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">functions in
-dplyr for querying databases</a>, and act in the following way</p>
+dplyr for querying databases</a>, and act in the following way:</p>
 <ul>
 <li>
-<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> converts the object to a query. This allows
-users to inspect their<br>
-API calls before they are sent</li>
+<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> converts the object to a <code>query</code>.
+This allows users to inspect<br>
+their API calls before they are sent. Depending on the request, this
+function may also call ‘supplementary’ APIs to collect required
+information, such as Taxon Concept Identifiers or field names.</li>
 <li>
-<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> sends queries to any required APIs. This
-includes sending a query for data, determining whether field names are
-valid, or finding how much data has been requested (which is necessary
-for pagination)</li>
+<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> is intended to send the query in question to
+the requested API for processing. This is particularly important for
+occurrences, where it can be useful to submit a query and retrieve it at
+a later time. If the <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> stage is not required,
+however, <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> simply converts the <code>query</code>
+to a new class (<code>computed_query</code>).</li>
 <li>
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code> retrieves the requested data into your
-workspace</li>
+workspace, returning a <code>tibble</code>.</li>
 </ul>
 <p>We can use these in sequence, or just leap ahead to the stage we
 want:</p>
@@ -244,16 +248,15 @@ <h2 id="advanced-query-building">Advanced query building<a class="anchor" aria-l
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/count.html" class="external-link">count</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## Object of class `query_set` containing 3 queries:</span></span></code></pre>
-<pre><code><span><span class="co">## • metadata/fields data: galah:::check_internal_cache()$fields</span></span>
-<span><span class="co">## • metadata/assertions data: galah:::check_internal_cache()$assertions</span></span>
-<span><span class="co">## • data/occurrences-count-groupby url: https://biocache-ws.ala.org.au/ws/occurre...</span></span></code></pre>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Object of class query with type data/occurrences-count-groupby </span></span>
 <span><span class="co">## url: https://biocache-ws.ala.org.au/ws/occurrences/facets?fq=%28genus%3A%22... </span></span>
 <span><span class="co">## arrange: species (ascending)</span></span></code></pre>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Object of class computed_query with type data/occurrences-count-groupby </span></span>
+<span><span class="co">## url: https://biocache-ws.ala.org.au/ws/occurrences/facets?fq=%28genus%3A%22... </span></span>
+<span><span class="co">## arrange: species (ascending)</span></span></code></pre>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## # A tibble: 6 × 2</span></span>
 <span><span class="co">##   species              count</span></span>
@@ -270,7 +273,7 @@ <h2 id="advanced-query-building">Advanced query building<a class="anchor" aria-l
 their query using <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code>, and download data once the
 query has finished — downloading with <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code> later —
 rather than waiting for the request to finish within R.</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Create and send query to be calculated server-side</span></span>
 <span><span class="va">request</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/galah_call.html">request_data</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/graphics/identify.html" class="external-link">identify</a></span><span class="op">(</span><span class="st">"perameles"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
@@ -288,20 +291,17 @@ <h2 id="advanced-query-building">Advanced query building<a class="anchor" aria-l
 construction prior to sending a request. For example, the query above is
 constructed with the following information, returned by
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code>.</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/galah_call.html">request_data</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/graphics/identify.html" class="external-link">identify</a></span><span class="op">(</span><span class="st">"perameles"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">&gt;</span> <span class="fl">1900</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## Object of class `query_set` containing 5 queries:</span></span></code></pre>
-<pre><code><span><span class="co">## • metadata/fields data: galah:::check_internal_cache()$fields</span></span>
-<span><span class="co">## • metadata/assertions data: galah:::check_internal_cache()$assertions</span></span>
-<span><span class="co">## • metadata/reasons data: galah:::check_internal_cache()$reasons</span></span>
-<span><span class="co">## • metadata/taxa-single url: https://api.ala.org.au/namematching/api/search?q=pe...</span></span>
-<span><span class="co">## • data/occurrences url: https://biocache-ws.ala.org.au/ws/occurrences/offline/d...</span></span></code></pre>
-<p>The <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> stage displays useful information about
-which APIs will be pinged by a query in galah when it is sent using
-<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code>.</p>
+<pre><code><span><span class="co">## Object of class query with type data/occurrences </span></span>
+<span><span class="co">## url: https://biocache-ws.ala.org.au/ws/occurrences/offline/download?fq=%28l...</span></span></code></pre>
+<p>The <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> stage includes an additional argument
+(<code>.expand</code>) that, when set to <code>TRUE</code>, shows all
+the APIs called to construct the user-requested query. This is
+especially useful for debugging.</p>
 </div>
 <div class="section level2">
 <h2 id="new-object-classes">New object classes<a class="anchor" aria-label="anchor" href="#new-object-classes"></a>
@@ -310,11 +310,12 @@ <h2 id="new-object-classes">New object classes<a class="anchor" aria-label="anch
 to a new class:</p>
 <ul>
 <li>
-<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> returns class <code>query_set</code>, which
-is a list of one or more <code>query</code> objects</li>
+<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> returns class <code>query</code>, which is a
+list containing a <code>type</code> slot and one or more
+<code>url</code>s</li>
 <li>
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> returns a single object of class
-<code>query</code>
+<code>computed_query</code>
 </li>
 <li>
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code> doesn’t add a new data class (returns class
@@ -326,7 +327,7 @@ <h2 id="new-object-classes">New object classes<a class="anchor" aria-label="anch
 To demonstrate what we mean, take the following calls, which despite
 using different syntax, all return the number of records available for
 the year 2020:</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># new syntax</span></span>
 <span><span class="fu"><a href="../reference/galah_call.html">request_data</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">year</span> <span class="op">==</span> <span class="fl">2020</span><span class="op">)</span> <span class="op">|&gt;</span></span>
@@ -345,7 +346,7 @@ <h2 id="new-object-classes">New object classes<a class="anchor" aria-label="anch
 <span>  <span class="fu"><a href="../reference/atlas_counts.html">atlas_counts</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p>Another example is to list available <code>fields</code> in the
 selected atlas:</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/galah_call.html">request_metadata</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"fields"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
@@ -355,7 +356,7 @@ <h2 id="new-object-classes">New object classes<a class="anchor" aria-label="anch
 <span></span>
 <span><span class="fu"><a href="../reference/show_all.html">show_all</a></span><span class="op">(</span><span class="va">fields</span><span class="op">)</span></span></code></pre></div>
 <p>Or to show values for states and territories:</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/galah_call.html">request_metadata</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">field</span> <span class="op">==</span> <span class="st">"cl22"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="../reference/tidyverse_functions.html">unnest</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
diff --git a/articles/piping.html b/articles/piping.html
index afcc6e51..0b54f226 100644
--- a/articles/piping.html
+++ b/articles/piping.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/quick_start_guide.html b/articles/quick_start_guide.html
index 2bf19848..3b7bb875 100644
--- a/articles/quick_start_guide.html
+++ b/articles/quick_start_guide.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/spatial_filtering.html b/articles/spatial_filtering.html
index f6a71757..e4796a20 100644
--- a/articles/spatial_filtering.html
+++ b/articles/spatial_filtering.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -1798,7 +1798,7 @@ <h4 id="large-shapefiles">Large shapefiles<a class="anchor" aria-label="anchor"
 even the bounding box doesn’t restrict the number of records to a value
 that can be downloaded easily. In this case, we recommend more nuances
 and detailed methods that can be performed using looping techniques. One
-of our ALA Labs blog posts, <a href="https://labs.ala.org.au/posts/2021-04-14_hex-maps-for-species-occurrence-data/post.html" class="external-link">Hex
+of our ALA Labs blog posts, <a href="https://labs.ala.org.au/posts/2021-04-14_hex-maps-for-species-occurrence-data/" class="external-link">Hex
 maps for species occurrence data</a>, has been written detailing how to
 approach larger problems such as this.</p>
 </div>
diff --git a/articles/taxonomic_filtering.html b/articles/taxonomic_filtering.html
index bc4b5aeb..9484e647 100644
--- a/articles/taxonomic_filtering.html
+++ b/articles/taxonomic_filtering.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/temporal_filtering.html b/articles/temporal_filtering.html
index a6909391..10dc2797 100644
--- a/articles/temporal_filtering.html
+++ b/articles/temporal_filtering.html
@@ -35,7 +35,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -226,8 +226,8 @@ <h3 id="occurrence-dates">Occurrence dates<a class="anchor" aria-label="anchor"
 recommended that greater or less than queries are used rather than exact
 matches. When used with <code><a href="../reference/galah_filter.html">galah_filter()</a></code>, we can easily
 identify how many records of the humpback whale (<em>Megaptera
-novaeangliae</em>) have occurred since the species was <a href="http://www.environment.gov.au/biodiversity/threatened/species/pubs/38-listing-advice-26022022.pdf" class="external-link">removed
-from the Australian threatened species list</a> on 26/02/2022.</p>
+novaeangliae</em>) have occurred since the species was removed from the
+Australian threatened species list on 26/02/2022.</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/galah_call.html">galah_call</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu"><a href="../reference/galah_filter.html">galah_filter</a></span><span class="op">(</span><span class="va">species</span> <span class="op">==</span> <span class="st">"Megaptera novaeangliae"</span>, </span>
diff --git a/authors.html b/authors.html
index 612eef9a..9d83ae90 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -87,15 +87,15 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/AtlasOfLivingAustralia/galah-R/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
 
-      <p>Westgate M, Stevenson M, Kellie D, Newman P (2023).
+      <p>Westgate M, Stevenson M, Kellie D, Newman P (2024).
 <em>galah: Biodiversity Data from the GBIF Node Network</em>.
-R package version 2.0.0, <a href="https://CRAN.R-project.org/package=galah" class="external-link">https://CRAN.R-project.org/package=galah</a>. 
+R package version 2.0.1, <a href="https://CRAN.R-project.org/package=galah" class="external-link">https://CRAN.R-project.org/package=galah</a>. 
 </p>
       <pre>@Manual{,
   title = {galah: Biodiversity Data from the GBIF Node Network},
   author = {Martin Westgate and Matilda Stevenson and Dax Kellie and Peggy Newman},
-  year = {2023},
-  note = {R package version 2.0.0},
+  year = {2024},
+  note = {R package version 2.0.1},
   url = {https://CRAN.R-project.org/package=galah},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index ef495ced..9fe6622b 100644
--- a/index.html
+++ b/index.html
@@ -47,7 +47,7 @@
     
     <a class="navbar-brand me-2" href="index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 679e84e3..55c98cbb 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,6 +63,20 @@ <h6 class="dropdown-header" data-toc-skip>Advanced</h6>
       <small>Source: <a href="https://github.com/AtlasOfLivingAustralia/galah-R/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2.0.1" id="galah-201">galah 2.0.1<a class="anchor" aria-label="anchor" href="#galah-201"></a></h2>
+<div class="section level4">
+<h4 id="minor-improvements-2-0-1">Minor improvements<a class="anchor" aria-label="anchor" href="#minor-improvements-2-0-1"></a></h4>
+<p><code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> now returns a <code>query</code> object, rather than a <code>query_set</code>, and gains a <code>.expand</code> argument to optionally append a <code>query_set</code> for debugging purposes (<a href="https://github.com/AtlasOfLivingAustralia/galah-R/issues/217" class="external-link">#217</a>).</p>
+</div>
+<div class="section level4">
+<h4 id="bug-fixes-2-0-1">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-2-0-1"></a></h4>
+<ul><li>Avoid triggering multiple errors when galah_identify() returns no matched taxa (<a href="https://github.com/AtlasOfLivingAustralia/galah-R/issues/219" class="external-link">#219</a>)</li>
+<li>Improve clarity of quick start guide vignette (<a href="https://github.com/AtlasOfLivingAustralia/galah-R/issues/221" class="external-link">#221</a>)</li>
+<li>show_values() no longer truncates rows to 30 (<a href="https://github.com/AtlasOfLivingAustralia/galah-R/issues/222" class="external-link">#222</a>)</li>
+<li>Column ID name returned by search_all(lists) now matches the correct field ID for galah_filter() (<a href="https://github.com/AtlasOfLivingAustralia/galah-R/issues/225" class="external-link">#225</a>)</li>
+</ul></div>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="2.0.0" id="galah-200">galah 2.0.0<a class="anchor" aria-label="anchor" href="#galah-200"></a></h2><p class="text-muted">CRAN release: 2023-11-20</p>
 <div class="section level4">
diff --git a/pkgdown.yml b/pkgdown.yml
index 928a0d66..caf9235a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
   spatial_filtering: spatial_filtering.html
   taxonomic_filtering: taxonomic_filtering.html
   temporal_filtering: temporal_filtering.html
-last_built: 2023-12-14T05:02Z
+last_built: 2024-02-05T23:36Z
 urls:
   reference: https://galah.ala.org.au/R/reference
   article: https://galah.ala.org.au/R/articles
diff --git a/reference/arrange.html b/reference/arrange.html
index 74561646..b80498f7 100644
--- a/reference/arrange.html
+++ b/reference/arrange.html
@@ -32,7 +32,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_citation.html b/reference/atlas_citation.html
index 7c539a62..eb025de0 100644
--- a/reference/atlas_citation.html
+++ b/reference/atlas_citation.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_counts.html b/reference/atlas_counts.html
index 576ee363..81e8b7ca 100644
--- a/reference/atlas_counts.html
+++ b/reference/atlas_counts.html
@@ -28,7 +28,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_media.html b/reference/atlas_media.html
index 1364c4f1..8b1175c9 100644
--- a/reference/atlas_media.html
+++ b/reference/atlas_media.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_occurrences.html b/reference/atlas_occurrences.html
index 383610ee..666ed927 100644
--- a/reference/atlas_occurrences.html
+++ b/reference/atlas_occurrences.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_species.html b/reference/atlas_species.html
index 9144c870..1ad14783 100644
--- a/reference/atlas_species.html
+++ b/reference/atlas_species.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/atlas_taxonomy.html b/reference/atlas_taxonomy.html
index c5e9428c..70da6471 100644
--- a/reference/atlas_taxonomy.html
+++ b/reference/atlas_taxonomy.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/collapse_galah.html b/reference/collapse_galah.html
index 77420b93..2277947c 100644
--- a/reference/collapse_galah.html
+++ b/reference/collapse_galah.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,13 +92,13 @@ <h6 class="dropdown-header" data-toc-skip>Advanced</h6>
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for data_request</span></span>
-<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, <span class="va">mint_doi</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, <span class="va">mint_doi</span>, .expand <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for metadata_request</span></span>
-<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, .expand <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for files_request</span></span>
-<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, thumbnail <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="va">x</span>, thumbnail <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -109,7 +109,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>...</dt>
-<dd><p>Arguments passed on to methods</p></dd>
+<dd><p>Arguments passed on to other methods</p></dd>
 
 
 <dt>mint_doi</dt>
@@ -117,6 +117,13 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 applies to <code>type = "occurrences"</code> when atlas chosen is "ALA".</p></dd>
 
 
+<dt>.expand</dt>
+<dd><p>Logical: should the <code>query_set</code> be returned? This object
+shows all the requisite data needed to process the supplied query. Defaults
+to <code>FALSE</code>; if <code>TRUE</code> will append the <code>query_set</code> to an extra slot in the
+<code>query</code> object.</p></dd>
+
+
 <dt>thumbnail</dt>
 <dd><p>Logical: should thumbnail-size images be returned? Defaults
 to <code>FALSE</code>, indicating full-size images are required.</p></dd>
@@ -126,10 +133,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>An object of class <code>query_set</code>, which is a list containing one or
-more objects of class <code>query</code>. This is valuable because it shows the set of
-queries required to correctly retrieve the requested data. Objects within a
-<code>query_set</code> are listed in the sequence in which they will be enacted.</p>
+<p>An object of class <code>query</code>, which is a list-like object containing at
+least the slots <code>type</code> and <code>url</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/collect_galah.html b/reference/collect_galah.html
index 0c991a7d..97825e76 100644
--- a/reference/collect_galah.html
+++ b/reference/collect_galah.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,10 +82,10 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="co"># S3 method for files_request</span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for query_set</span></span>
+<span><span class="co"># S3 method for query</span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, wait <span class="op">=</span> <span class="cn">TRUE</span>, file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for query</span></span>
+<span><span class="co"># S3 method for computed_query</span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, wait <span class="op">=</span> <span class="cn">TRUE</span>, file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
diff --git a/reference/collect_media.html b/reference/collect_media.html
index e9969523..7edd24fb 100644
--- a/reference/collect_media.html
+++ b/reference/collect_media.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/compute_galah.html b/reference/compute_galah.html
index 1fe5cd81..f41863ab 100644
--- a/reference/compute_galah.html
+++ b/reference/compute_galah.html
@@ -1,19 +1,9 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="compute() is useful for several purposes. It's original
 purpose is to send a request for data, which can then be processed by the
-server and retrieved at a later time (via collect()). However, because
-query-altering functions (such as filter() and select()) are evaluated
-lazily from galah version 2.0 onwards, compute() is also the function where
-all objects within the query_set are evaluated, and any checks run using
-that information. Therefore it is possible for invalid queries to be built
-using collapse(), but fail at compute()."><title>Compute a query — compute_galah • galah</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Source_Code_Pro-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Compute a query — compute_galah"><meta property="og:description" content="compute() is useful for several purposes. It's original
+server and retrieved at a later time (via collect())."><title>Compute a query — compute_galah • galah</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Source_Code_Pro-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Compute a query — compute_galah"><meta property="og:description" content="compute() is useful for several purposes. It's original
 purpose is to send a request for data, which can then be processed by the
-server and retrieved at a later time (via collect()). However, because
-query-altering functions (such as filter() and select()) are evaluated
-lazily from galah version 2.0 onwards, compute() is also the function where
-all objects within the query_set are evaluated, and any checks run using
-that information. Therefore it is possible for invalid queries to be built
-using collapse(), but fail at compute()."><meta property="og:image" content="https://galah.ala.org.au/R/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+server and retrieved at a later time (via collect())."><meta property="og:image" content="https://galah.ala.org.au/R/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -24,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -81,12 +71,7 @@ <h6 class="dropdown-header" data-toc-skip>Advanced</h6>
     <div class="ref-description section level2">
     <p><code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> is useful for several purposes. It's original
 purpose is to send a request for data, which can then be processed by the
-server and retrieved at a later time (via <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code>). However, because
-query-altering functions (such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code>) are evaluated
-lazily from galah version 2.0 onwards, <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> is also the function where
-all objects within the <code>query_set</code> are evaluated, and any checks run using
-that information. Therefore it is possible for invalid queries to be built
-using <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code>, but fail at <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code>.</p>
+server and retrieved at a later time (via <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code>).</p>
     </div>
 
     <div class="section level2">
@@ -100,9 +85,6 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="co"># S3 method for files_request</span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for query_set</span></span>
-<span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
-<span></span>
 <span><span class="co"># S3 method for query</span></span>
 <span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -111,7 +93,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
     <dl><dt>x</dt>
 <dd><p>An object of class <code>data_request</code>, <code>metadata_request</code> or
-<code>files_request</code> (i.e. constructed using a pipe) or <code>query</code> or <code>query_set</code>
+<code>files_request</code> (i.e. constructed using a pipe) or <code>query</code>
 (i.e. constructed by <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code>)</p></dd>
 
 
@@ -123,9 +105,9 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>An object of class <code>query</code> containing a checked, valid query
-for the selected atlas. In the case of occurrence data, also contains
-information on the status of the request.</p>
+<p>An object of class <code>computed_query</code>, which is identical to class
+<code>query</code> except for occurrence data, where it also contains information on the
+status of the request.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/deprecated-functions.html b/reference/deprecated-functions.html
index 89acd9f6..4a264a36 100644
--- a/reference/deprecated-functions.html
+++ b/reference/deprecated-functions.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah.html b/reference/galah.html
index 4181fe6b..e2dab961 100644
--- a/reference/galah.html
+++ b/reference/galah.html
@@ -34,7 +34,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_apply_profile.html b/reference/galah_apply_profile.html
index 9444670c..69a13d05 100644
--- a/reference/galah_apply_profile.html
+++ b/reference/galah_apply_profile.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_call.html b/reference/galah_call.html
index 809f6e71..d17a27aa 100644
--- a/reference/galah_call.html
+++ b/reference/galah_call.html
@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_config.html b/reference/galah_config.html
index f77c3a2f..818f187f 100644
--- a/reference/galah_config.html
+++ b/reference/galah_config.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_filter.html b/reference/galah_filter.html
index 93205093..80a2dd28 100644
--- a/reference/galah_filter.html
+++ b/reference/galah_filter.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_geolocate.html b/reference/galah_geolocate.html
index 4bcdde02..591dbfa3 100644
--- a/reference/galah_geolocate.html
+++ b/reference/galah_geolocate.html
@@ -34,7 +34,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_group_by.html b/reference/galah_group_by.html
index dec20c2f..071bd592 100644
--- a/reference/galah_group_by.html
+++ b/reference/galah_group_by.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_identify.html b/reference/galah_identify.html
index bd62508f..2155d996 100644
--- a/reference/galah_identify.html
+++ b/reference/galah_identify.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/galah_select.html b/reference/galah_select.html
index 5674d5ea..f32702d7 100644
--- a/reference/galah_select.html
+++ b/reference/galah_select.html
@@ -28,7 +28,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index d2337c1a..2c9f6b66 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -85,17 +85,17 @@ <h2 id="piping-functions">Piping functions<a class="anchor" aria-label="anchor"
         <dd>Generate a query</dd>
       </dl><dl><dt>
           
-          <code><a href="compute_galah.html">compute(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;query_set&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;query&gt;</i>)</a></code> 
+          <code><a href="compute_galah.html">compute(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="compute_galah.html">compute(<i>&lt;query&gt;</i>)</a></code> 
         </dt>
         <dd>Compute a query</dd>
       </dl><dl><dt>
           
-          <code><a href="collect_galah.html">collect(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;query_set&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;query&gt;</i>)</a></code> 
+          <code><a href="collect_galah.html">collect(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;query&gt;</i>)</a></code> <code><a href="collect_galah.html">collect(<i>&lt;computed_query&gt;</i>)</a></code> 
         </dt>
         <dd>Retrieve a database query</dd>
       </dl><dl><dt>
           
-          <code><a href="print_galah_objects.html">print(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;query&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;query_set&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;galah_config&gt;</i>)</a></code> 
+          <code><a href="print_galah_objects.html">print(<i>&lt;data_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;files_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;metadata_request&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;query&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;computed_query&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;query_set&gt;</i>)</a></code> <code><a href="print_galah_objects.html">print(<i>&lt;galah_config&gt;</i>)</a></code> 
         </dt>
         <dd>Print galah objects</dd>
       </dl></div><div class="section level2">
diff --git a/reference/print_galah_objects.html b/reference/print_galah_objects.html
index cfbf3849..23e0ddd0 100644
--- a/reference/print_galah_objects.html
+++ b/reference/print_galah_objects.html
@@ -2,15 +2,15 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="As of version 2.0, galah supports several bespoke object types. Classes
 data_request, metadata_request and files_request are for starting pipes
 to download different types of information. These objects are parsed using
-collapse() into a query_set object, which contains a set of query
-objects, each describing one API call. These are then enacted using
+collapse() into a query object, which contains one or more URLs necessary
+to return the requested information. This object is then passed to
 compute() and/or collect(). Finally, galah_config() creates an object
 of class galah_config which (unsurprisingly) stores configuration
 information."><title>Print galah objects — print_galah_objects • galah</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Source_Code_Pro-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Print galah objects — print_galah_objects"><meta property="og:description" content="As of version 2.0, galah supports several bespoke object types. Classes
 data_request, metadata_request and files_request are for starting pipes
 to download different types of information. These objects are parsed using
-collapse() into a query_set object, which contains a set of query
-objects, each describing one API call. These are then enacted using
+collapse() into a query object, which contains one or more URLs necessary
+to return the requested information. This object is then passed to
 compute() and/or collect(). Finally, galah_config() creates an object
 of class galah_config which (unsurprisingly) stores configuration
 information."><meta property="og:image" content="https://galah.ala.org.au/R/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,8 +82,8 @@ <h6 class="dropdown-header" data-toc-skip>Advanced</h6>
     <p>As of version 2.0, <code>galah</code> supports several bespoke object types. Classes
 <code>data_request</code>, <code>metadata_request</code> and <code>files_request</code> are for starting pipes
 to download different types of information. These objects are parsed using
-<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> into a <code>query_set</code> object, which contains a set of <code>query</code>
-objects, each describing one API call. These are then enacted using
+<code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse()</a></code> into a <code>query</code> object, which contains one or more URLs necessary
+to return the requested information. This object is then passed to
 <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">compute()</a></code> and/or <code><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect()</a></code>. Finally, <code><a href="galah_config.html">galah_config()</a></code> creates an object
 of class <code>galah_config</code> which (unsurprisingly) stores configuration
 information.</p>
@@ -103,6 +103,9 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span><span class="co"># S3 method for query</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
+<span><span class="co"># S3 method for computed_query</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
 <span><span class="co"># S3 method for query_set</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -155,15 +158,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/count.html" class="external-link">count</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collapse</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">Object of class </span><span style="color: #BB0000;">`query_set` </span><span style="color: #555555;">containing 3 queries:</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> <span style="color: #000000;">metadata/fields</span> <span style="color: #555555;">url: https://biocache-ws.ala.org.au/ws/index/fields</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> <span style="color: #000000;">metadata/assertions</span> <span style="color: #555555;">url: https://biocache-ws.ala.org.au/ws/assertions/codes</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> <span style="color: #000000;">data/occurrences-count</span> <span style="color: #555555;">url: https://biocache-ws.ala.org.au/ws/occurrences/sea...</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">Object of class</span> <span style="color: #BB0000;">query</span> <span style="color: #555555;">with type</span> <span style="color: #000000;">data/occurrences-count</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">url: https://biocache-ws.ala.org.au/ws/occurrences/search?fq=%28year%3A%5B2...</span>  </span>
 <span class="r-in"><span>  </span></span>
 <span class="r-in"><span><span class="co"># Each `query_set` contains one or more `query` objects</span></span></span>
 <span class="r-in"><span><span class="va">x</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">Object of class</span> <span style="color: #BB0000;">query</span> <span style="color: #555555;">with type</span> <span style="color: #000000;">data/occurrences-count</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">url: https://biocache-ws.ala.org.au/ws/occurrences/search?fq=%28year%3A%5B2...</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "totalRecords"</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/reexports.html b/reference/reexports.html
index 134837bf..15d66d0c 100644
--- a/reference/reexports.html
+++ b/reference/reexports.html
@@ -40,7 +40,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/search_all.html b/reference/search_all.html
index 7931813e..58745493 100644
--- a/reference/search_all.html
+++ b/reference/search_all.html
@@ -30,7 +30,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/show_all.html b/reference/show_all.html
index cb5b5cc5..00a644ef 100644
--- a/reference/show_all.html
+++ b/reference/show_all.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/show_values.html b/reference/show_values.html
index a5ed5565..2b104c28 100644
--- a/reference/show_values.html
+++ b/reference/show_values.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/slice_head.html b/reference/slice_head.html
index a66ecc26..607a310f 100644
--- a/reference/slice_head.html
+++ b/reference/slice_head.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tidyverse_functions.html b/reference/tidyverse_functions.html
index fa8d821a..7467387c 100644
--- a/reference/tidyverse_functions.html
+++ b/reference/tidyverse_functions.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">galah</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">2.0.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index bfd69fb7..2573987b 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"set-organisation","dir":"Articles","previous_headings":"","what":"Set Organisation","title":"Choosing an atlas","text":"Set atlas want use changing atlas argument galah_config(). atlas argument can accept full name, acronym, region select given atlas, available via show_all(atlases). value provided, automatically update galah’s server configuration selected atlas. default atlas Australia. intend download records, may need register user profile relevant atlas first.","code":"galah_config(atlas = \"GBIF.es\", email = \"your_email_here\")"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"look-up-information","dir":"Articles","previous_headings":"","what":"Look up Information","title":"Choosing an atlas","text":"can use look-functions find useful information Atlas set. Available information may vary Living Atlas.","code":"galah_config(atlas = \"Guatemala\") ## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala] show_all(datasets) ## # A tibble: 1,283 × 3 ##    id     name                                                                                                                     uri   ##    <chr>  <chr>                                                                                                                    <chr> ##  1 dr1440 A catalogue of the Heteroptera (Hemiptera) or true bugs of Argentina                                                     http… ##  2 dr1436 A cybercatalogue of American sand fly types (Diptera, Psychodidae, Phlebotominae) deposited at the Natural History Muse… http… ##  3 dr1226 A distinctive new species of biting midge in the subgenus Euprojoannisia Brèthes from Mexico with new records of Neotro… http… ##  4 dr321  A Distribution and Taxonomic Reference Dataset of Geranium (Geraniaceae) in the New World                                http… ##  5 dr1285 A geographic distribution database of the cassava whitefly complex (Hemiptera, Aleyrodidae) and their associated parasi… http… ##  6 dr12   A global database for the distributions of crop wild relatives                                                           http… ##  7 dr467  A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera Tenebrionidae)                                    http… ##  8 dr1061 A Monographic Revision of the Genus Hoplopyga Thomson, 1880 (Coleoptera: Scarabaeidae: Cetoniinae: Gymnetini)            http… ##  9 dr1570 A new Anomiopus Westwood (Coleoptera: Scarabaeidae: Scarabaeinae) from the Mayan Biosphere Reserve, Petén, Guatemala     http… ## 10 dr1177 A new Central American genus of pleasing fungus beetles (Coleoptera: Erotylidae) from the Ischyrus-Megischyrus complex   http… ## # ℹ 1,273 more rows show_all(fields) ## # A tibble: 127 × 3 ##    id                   description        type   ##    <chr>                <chr>              <chr>  ##  1 all_image_url        <NA>               fields ##  2 assertion_user_id    Assertions by user fields ##  3 assertions           Record issues      fields ##  4 assertions_missing   <NA>               fields ##  5 assertions_passed    <NA>               fields ##  6 assertions_unchecked <NA>               fields ##  7 basis_of_record      Record type        fields ##  8 catalogue_number     Catalogue Number   fields ##  9 cl10011              <NA>               fields ## 10 class                Class              fields ## # ℹ 117 more rows search_all(fields, \"year\") ## # A tibble: 2 × 3 ##   id              description      type   ##   <chr>           <chr>            <chr>  ## 1 year            Year             fields ## 2 occurrence_year Date (by decade) fields search_taxa(\"lagomorpha\") ## # A tibble: 1 × 8 ##   search_term scientific_name taxon_concept_id rank  kingdom  phylum   class    order      ##   <chr>       <chr>           <chr>            <chr> <chr>    <chr>    <chr>    <chr>      ## 1 lagomorpha  Lagomorpha      785              order Animalia Chordata Mammalia Lagomorpha"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"download-data","dir":"Articles","previous_headings":"","what":"Download data","title":"Choosing an atlas","text":"can build queries normally galah. taxonomic queries, use search_taxa() make sure searches returning correct taxonomic data. Download species occurrence records atlases atlas_occurrences()","code":"galah_config(atlas = \"United Kingdom\") ## Atlas selected: National Biodiversity Network (NBN) [United Kingdom] search_taxa(\"vlps\")   # Returns no data due to misspelling ## # A tibble: 0 × 0 search_taxa(\"vulpes\") # Returns data ## # A tibble: 1 × 12 ##   search_term scientific_name scientific_name_authorship taxon_concept_id rank  kingdom  phylum   class    order family genus superclass ##   <chr>       <chr>           <chr>                      <chr>            <chr> <chr>    <chr>    <chr>    <chr> <chr>  <chr> <chr>      ## 1 vulpes      Vulpes          Frisch, 1775               NBNSYS0000138878 genus Animalia Chordata Mammalia Carn… Canid… Vulp… Tetrapoda galah_call() |>   galah_identify(\"vulpes\") |>   galah_filter(year > 2010) |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 124167 galah_config(atlas = \"Guatemala\") ## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala] galah_call() |>   galah_identify(\"Lagomorpha\") |>   galah_filter(year <= 1980) |>   galah_select(taxon_name, year) |>   atlas_occurrences() ## # A tibble: 4 × 2 ##   taxon_name                       year ##   <chr>                           <dbl> ## 1 Erinnyis ello subsp. ello        1973 ## 2 Manduca rustica Fabricius, 1775  1930 ## 3 Manduca rustica Fabricius, 1775  1930 ## 4 Aellopos titan Burmeister, 1856  1971"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"complex-queries-with-multiple-atlases","dir":"Articles","previous_headings":"","what":"Complex queries with multiple Atlases","title":"Choosing an atlas","text":"also possible create complex queries return data multiple Living Atlases. example, setting atlases within loop galah_config() purrr::map() allows us return total number species records Living Atlas one table.","code":"library(purrr) library(tibble) library(dplyr) library(gt)  atlases <- show_all(atlases)  counts <- map(atlases$region,    function(x){     galah_config(atlas = x)     atlas_counts() })  atlases |>     select(region, institution) |>     bind_cols(bind_rows(counts)) |>     arrange(desc(count)) |>     gt() |>     fmt_number(column = count)"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"record-counts","dir":"Articles","previous_headings":"","what":"Record counts","title":"Download data","text":"atlas_counts() provides summary counts records specified atlas, without needing download records. addition filter arguments, optional group_by argument, provides counts binned requested field.","code":"galah_config(atlas = \"Australia\") # Total number of records in the ALA atlas_counts() ## # A tibble: 1 × 1 ##       count ##       <int> ## 1 132342396 galah_call() |>   galah_group_by(kingdom) |>   atlas_counts() ## # A tibble: 11 × 2 ##    kingdom       count ##    <chr>         <int> ##  1 Animalia  101442503 ##  2 Plantae    26136825 ##  3 Fungi       2293753 ##  4 Chromista   1021828 ##  5 Protista     352983 ##  6 Bacteria     113118 ##  7 Eukaryota      8826 ##  8 Protozoa       4765 ##  9 Archaea        4119 ## 10 Virus          2307 ## 11 Viroid          103"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"species-lists","dir":"Articles","previous_headings":"","what":"Species lists","title":"Download data","text":"common use case atlas data identify species occur specified region, time period, taxonomic group. atlas_species() similar search_taxa, returns taxonomic information unique identifiers tibble. differs able return information taxonomic levels species; also flexible supporting filtering:","code":"species <- galah_call() |>   galah_identify(\"Rodentia\") |>   galah_filter(stateProvince == \"Northern Territory\") |>   atlas_species()    species |> head() ## # A tibble: 6 × 10 ##   kingdom  phylum   class    order    family  genus        species                     author            species_guid    vernacular_name ##   <chr>    <chr>    <chr>    <chr>    <chr>   <chr>        <chr>                       <chr>             <chr>           <chr>           ## 1 Animalia Chordata Mammalia Rodentia Muridae Pseudomys    Pseudomys delicatulus       (Gould, 1842)     https://biodiv… Delicate Mouse  ## 2 Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Mesembriomys gouldii        (J.E. Gray, 1843) https://biodiv… Black-footed T… ## 3 Animalia Chordata Mammalia Rodentia Muridae Zyzomys      Zyzomys argurus             (Thomas, 1889)    https://biodiv… Common Rock-rat ## 4 Animalia Chordata Mammalia Rodentia Muridae Pseudomys    Pseudomys hermannsburgensis (Waite, 1896)     https://biodiv… Sandy Inland M… ## 5 Animalia Chordata Mammalia Rodentia Muridae Melomys      Melomys burtoni             (Ramsay, 1887)    https://biodiv… Grassland Melo… ## 6 Animalia Chordata Mammalia Rodentia Muridae Notomys      Notomys alexis              Thomas, 1922      https://biodiv… Spinifex Hoppi…"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"occurrence-data","dir":"Articles","previous_headings":"","what":"Occurrence data","title":"Download data","text":"download occurrence data need specify email galah_config(). email must associated active ALA account. See information config section Download occurrence records Eolophus roseicapilla","code":"galah_config(email = \"your_email@email.com\", atlas = \"Australia\") occ <- galah_call() |>   galah_identify(\"Eolophus roseicapilla\") |>   galah_filter(     stateProvince == \"Australian Capital Territory\",     year >= 2010,     profile = \"ALA\"   ) |>   galah_select(institutionID, group = \"basic\") |>   atlas_occurrences() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. ## Retrying in 8 seconds. occ |> head() ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 0000a928-d756-42… Eolophus rose… https://biodi…           -35.6             149. 2017-04-19 09:11:00 PRESENT          eBird Australia  ## 2 0001bc78-d2e9-48… Eolophus rose… https://biodi…           -35.2             149. 2019-08-13 15:13:00 PRESENT          eBird Australia  ## 3 0002064f-08ea-42… Eolophus rose… https://biodi…           -35.3             149. 2014-03-16 06:48:00 PRESENT          eBird Australia  ## 4 00022dd2-9f85-48… Eolophus rose… https://biodi…           -35.3             149. 2022-05-08 08:20:00 PRESENT          eBird Australia  ## 5 0002cc35-8d5a-4d… Eolophus rose… https://biodi…           -35.3             149. 2015-11-01 08:00:00 PRESENT          eBird Australia  ## 6 00030a8c-082f-44… Eolophus rose… https://biodi…           -35.3             149. 2022-01-06 11:47:00 PRESENT          eBird Australia  ## # ℹ 1 more variable: institutionID <lgl>"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"media-metadata","dir":"Articles","previous_headings":"","what":"Media metadata","title":"Download data","text":"addition text data describing individual occurrences attributes, ALA stores images, sounds videos associated given record. Metadata records can downloaded R using atlas_media() set filters data download functions. actually download media files computer, use [collect_media()].","code":"media_data <- galah_call() |>   galah_identify(\"Eolophus roseicapilla\") |>   galah_filter(     year == 2020,     cl22 == \"Australian Capital Territory\") |>   atlas_media() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. media_data |> head() ## # A tibble: 6 × 19 ##   media_id recordID scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>    <chr>    <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 ff8322d… 003a192… Eolophus rose… https://biodi…           -35.3             149. 2020-09-12 06:11:00 PRESENT          iNaturalist Aus… ## 2 c66fc81… 015ee7c… Eolophus rose… https://biodi…           -35.4             149. 2020-08-09 05:11:00 PRESENT          iNaturalist Aus… ## 3 fe6d7b9… 05e86b7… Eolophus rose… https://biodi…           -35.4             149. 2020-11-13 22:29:00 PRESENT          NatureMapr       ## 4 2f4d32c… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## 5 7340741… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## 6 89171c4… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## # ℹ 10 more variables: multimedia <chr>, images <chr>, videos <lgl>, sounds <lgl>, creator <chr>, license <chr>, mimetype <chr>, ## #   width <int>, height <int>, image_url <chr>"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"taxonomic-trees","dir":"Articles","previous_headings":"","what":"Taxonomic trees","title":"Download data","text":"atlas_taxonomy provides way build taxonomic trees one clade another using service’s internal taxonomy. Specify taxonomic level tree go galah_filter() using rank argument.","code":"galah_call() |>   galah_identify(\"chordata\") |>   galah_filter(rank == class) |>   atlas_taxonomy() ## # A tibble: 19 × 4 ##    name            rank      parent_taxon_concept_id                                                   taxon_concept_id                  ##    <chr>           <chr>     <chr>                                                                     <chr>                             ##  1 Chordata        phylum    <NA>                                                                      https://biodiversity.org.au/afd/… ##  2 Cephalochordata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  3 Tunicata        subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  4 Appendicularia  class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  5 Ascidiacea      class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  6 Thaliacea       class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  7 Vertebrata      subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  8 Agnatha         informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/… ##  9 Myxini          informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/… ## 10 Petromyzontida  informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/… ## 11 Gnathostomata   informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/… ## 12 Amphibia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 13 Aves            class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 14 Mammalia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 15 Pisces          informal  https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 16 Actinopterygii  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 17 Chondrichthyes  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 18 Sarcopterygii   class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 19 Reptilia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"configuring-galah","dir":"Articles","previous_headings":"","what":"Configuring galah","title":"Download data","text":"Various aspects galah package can customized.","code":""},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"email","dir":"Articles","previous_headings":"Configuring galah","what":"Email","title":"Download data","text":"download occurrence records, need provide email address registered service want use (e.g. ALA can create account ). email registered, stored config:","code":"galah_config(email = \"myemail@gmail.com\")"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"setting-your-directory","dir":"Articles","previous_headings":"Configuring galah","what":"Setting your directory","title":"Download data","text":"default, galah stores downloads temporary folder, meaning local files automatically deleted R session ended. behaviour can altered downloaded files preserved setting directory non-temporary location.","code":"galah_config(directory = \"example/dir\")"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"setting-the-download-reason","dir":"Articles","previous_headings":"Configuring galah","what":"Setting the download reason","title":"Download data","text":"ALA requires provide reason downloading occurrence data (via galah atlas_occurrences() function). reason set “scientific research” default, can change using galah_config(). See show_all_reasons() valid download reasons.","code":"galah_config(download_reason_id = your_reason_id)"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"debugging","dir":"Articles","previous_headings":"Configuring galah","what":"Debugging","title":"Download data","text":"things aren’t working expected, detail (particularly web requests caching behaviour) can obtained setting verbose configuration option:","code":"galah_config(verbose = TRUE)"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_all-search_all","dir":"Articles","previous_headings":"","what":"show_all() & search_all()","title":"Look up information","text":"galah 1.5.0, two simplified functions look information: show_all() search_all(). individual functions able return types information one place, rather using specific sub-functions look information. example, show available Living Atlases supported: search specific available Living Atlas: show fields: search specific field: list information types can used show_all() search_all():","code":"show_all(atlases) ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk search_all(atlases, \"Spain\") ## # A tibble: 1 × 4 ##   region institution acronym url                 ##   <chr>  <chr>       <chr>   <chr>               ## 1 Spain  GBIF Spain  GBIF.es https://www.gbif.es show_all(fields) ## # A tibble: 646 × 3 ##    id                  description               type   ##    <chr>               <chr>                     <chr>  ##  1 _nest_parent_       <NA>                      fields ##  2 _nest_path_         <NA>                      fields ##  3 _root_              <NA>                      fields ##  4 abcdTypeStatus      <NA>                      fields ##  5 acceptedNameUsage   Accepted name             fields ##  6 acceptedNameUsageID Accepted name             fields ##  7 accessRights        Access rights             fields ##  8 annotationsDoi      <NA>                      fields ##  9 annotationsUid      Referenced by publication fields ## 10 assertionUserId     Assertions by user        fields ## # ℹ 636 more rows search_all(fields, \"australian states\") ## # A tibble: 2 × 3 ##   id     description                            type   ##   <chr>  <chr>                                  <chr>  ## 1 cl2013 ASGS Australian States and Territories fields ## 2 cl22   Australian States and Territories      fields"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_all_-subfunctions","dir":"Articles","previous_headings":"","what":"show_all_ subfunctions","title":"Look up information","text":"show_all useful variety cases, can still call underlying subfunctions prefer. functions - prefix show_all_ - return tibble exactly ; showing possible values category specified. functions include: show_all_fields show_all_atlases show_all_ranks show_all_profiles show_all_reasons show_all_ functions require arguments. Simply call function return accepted values tibble:","code":"show_all_atlases() ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk show_all_reasons() ## # A tibble: 13 × 2 ##       id name                             ##    <int> <chr>                            ##  1     1 biosecurity management/planning  ##  2    11 citizen science                  ##  3     5 collection management            ##  4     0 conservation management/planning ##  5     7 ecological research              ##  6     3 education                        ##  7     2 environmental assessment         ##  8    12 restoration/remediation          ##  9     4 scientific research              ## 10     8 systematic research/taxonomy     ## 11    13 species modelling                ## 12     6 other                            ## 13    10 testing"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"search_-subfunctions","dir":"Articles","previous_headings":"","what":"search_ subfunctions","title":"Look up information","text":"second subset lookup subfunctions use search_ prefix, differ show_all_ require query work. used search detailed information can’t summarised across whole atlas, include: search_taxa search_identifiers search_fields show_values Search single taxon multiple taxa name search_taxa. Alternatively, search_identifiers partner function search_taxa. already know taxonomic identifier, can search taxa identifier belongs search_identifiers: Sifting output show_all_fields find specific field can inefficient. Instead, might wish use search_fields look specific fields match search. search_taxa, search_fields requires query work.","code":"search_taxa(\"reptilia\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_taxa(\"reptilia\", \"aves\", \"mammalia\", \"pisces\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_identifiers(\"urn:lsid:biodiversity.org.au:afd.taxon:682e1228-5b3c-45ff-833b-550efd40c399\") ## # A tibble: 1 × 15 ##   search_term    success scientific_name taxon_concept_id rank  rank_id   lft   rgt match_type kingdom kingdom_id phylum phylum_id class ##   <chr>          <lgl>   <chr>           <chr>            <chr>   <int> <int> <int> <chr>      <chr>   <chr>      <chr>  <chr>     <chr> ## 1 urn:lsid:biod… TRUE    REPTILIA        https://biodive… class    3000 46718 49924 taxonIdMa… Animal… https://b… Chord… https://… Rept… ## # ℹ 1 more variable: class_id <chr> search_fields(\"date\") |> head() ## # A tibble: 6 × 3 ##   id             description     type   ##   <chr>          <chr>           <chr>  ## 1 eventDate      Event Date      fields ## 2 lastLoadDate   lastLoadDate    fields ## 3 datePrecision  Date precision  fields ## 4 eventDateEnd   <NA>            fields ## 5 dateIdentified Date Identified fields ## 6 raw_eventDate  <NA>            fields"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_values-search_values","dir":"Articles","previous_headings":"","what":"show_values() & search_values()","title":"Look up information","text":"desired field found, can use show_values understand information contained within field, e.g. provides information need pass meaningful queries galah_filter. works types query, data profiles:","code":"search_all(fields, \"basis\") |> show_values() ## ! Search returned 2 matched fields. ## • Showing values for 'basisOfRecord'. ## # A tibble: 9 × 1 ##   basisOfRecord       ##   <chr>               ## 1 Human observation   ## 2 Preserved specimen  ## 3 Observation         ## 4 Occurrence          ## 5 Machine observation ## 6 Material Sample     ## 7 Living specimen     ## 8 Material Citation   ## 9 Fossil specimen galah_call() |>    galah_filter(basisOfRecord == \"LIVING_SPECIMEN\") |>    atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 126135 search_all(profiles, \"ALA\") |>    show_values() |>    head() ## • Showing values for 'ALA'. ## # A tibble: 6 × 5 ##      id enabled description                                                                                          filter displayOrder ##   <int> <lgl>   <chr>                                                                                                <chr>         <int> ## 1    94 TRUE    \"Exclude all records where spatial validity is \\\"false\\\"\"                                            \"-spa…            1 ## 2    96 TRUE    \"Exclude all records with an assertion that the scientific name provided does not match any of the … \"-ass…            1 ## 3    97 TRUE    \"Exclude all records with an assertion that the scientific name provided is not structured as a val… \"-ass…            2 ## 4    98 TRUE    \"Exclude all records with an assertion that the name and classification supplied can't be used to c… \"-ass…            3 ## 5    99 TRUE    \"Exclude all records with an assertion that kingdom provided doesn't match a known kingdom e.g. Ani… \"-ass…            4 ## 6   100 TRUE    \"Exclude all records with an assertion that the scientific name provided in the record does not mat… \"-ass…            5"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_identify-search_taxa","dir":"Articles","previous_headings":"","what":"galah_identify & search_taxa","title":"Narrow your results","text":"Perhaps unsurprisingly, search_taxa searches taxonomic information. uses fuzzy matching work lot like search bar Atlas Living Australia website, can use search taxa scientific name. Finding desired taxon search_taxa important step using taxonomic information download data galah. example, search reptiles, first need identify whether correct query: want specific providing additional taxonomic information search_taxa, can provide tibble (data.frame) containing levels taxonomic hierarchy: know search matches correct taxon taxa, can use galah_identify narrow results queries: ’re using international atlas, search_taxa automatically switch using local name-matching service. example, Portugal uses GBIF taxonomic backbone, integrates seamlessly standard workflow. Conversely, UK’s National Biodiversity Network (NBN), ’ taxonomic backbone, supported using function call.","code":"search_taxa(\"Reptilia\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 Reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_taxa(tibble(genus = \"Eolophus\", kingdom = \"Aves\")) ## # A tibble: 1 × 13 ##   search_term   scientific_name scientific_name_autho…¹ taxon_concept_id rank  match_type kingdom phylum class order family genus issues ##   <chr>         <chr>           <chr>                   <chr>            <chr> <chr>      <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  ## 1 Eolophus_Aves Eolophus        Bonaparte, 1854         https://biodive… genus exactMatch Animal… Chord… Aves  Psit… Cacat… Eolo… noIss… ## # ℹ abbreviated name: ¹​scientific_name_authorship galah_call() |>   galah_identify(\"Reptilia\") |>   atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 1682010 taxa <- search_taxa(tibble(genus = \"Eolophus\", kingdom = \"Aves\"))  galah_call() |>  galah_identify(taxa) |>  atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 1093469 galah_config(atlas = \"Portugal\") ## Atlas selected: GBIF Portugal (GBIF.pt) [Portugal] galah_call() |>    galah_identify(\"Lepus\") |>    galah_group_by(species) |>    atlas_counts() ## # A tibble: 5 × 2 ##   species           count ##   <chr>             <int> ## 1 Lepus granatensis  1378 ## 2 Lepus microtis       64 ## 3 Lepus europaeus      10 ## 4 Lepus saxatilis       2 ## 5 Lepus capensis        1 galah_config(atlas = \"United Kingdom\") ## Atlas selected: National Biodiversity Network (NBN) [United Kingdom] galah_call() |>    galah_filter(genus == \"Bufo\") |>    galah_group_by(species) |>    atlas_counts() ## # A tibble: 3 × 2 ##   species       count ##   <chr>         <int> ## 1 Bufo bufo     94517 ## 2 Bufo spinosus    88 ## 3 Bufo marinus      1"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_filter","dir":"Articles","previous_headings":"","what":"galah_filter","title":"Narrow your results","text":"Perhaps important function galah galah_filter, used filter rows queries: find available fields corresponding valid values, use field lookup functions show_all(fields), search_all(fields) & show_values(). Finally, special case galah_filter make complex taxonomic queries possible using search_taxa. using taxonConceptID field, possible build queries exclude certain taxa, example. can useful paraphyletic concepts invertebrates:","code":"galah_config(atlas = \"Australia\") ## Atlas selected: Atlas of Living Australia (ALA) [Australia] # Get total record count since 2000 galah_call() |>   galah_filter(year > 2000) |>   atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 90875204 # Get total record count for iNaturalist in 2021 galah_call() |>   galah_filter(     year > 2000,     dataResourceName == \"iNaturalist Australia\") |>   atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 5850806 galah_call() |>   galah_filter(      taxonConceptID == search_taxa(\"Animalia\")$taxon_concept_id,      taxonConceptID != search_taxa(\"Chordata\")$taxon_concept_id   ) |>   galah_group_by(class) |>   atlas_counts() ## # A tibble: 30 × 2 ##    class          count ##    <chr>          <int> ##  1 Insecta      5887288 ##  2 Gastropoda    940371 ##  3 Maxillopoda   793499 ##  4 Arachnida     701320 ##  5 Malacostraca  657455 ##  6 Polychaeta    276460 ##  7 Bivalvia      225965 ##  8 Anthozoa      218244 ##  9 Cephalopoda   145902 ## 10 Demospongiae  118515 ## # ℹ 20 more rows"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_apply_profile","dir":"Articles","previous_headings":"","what":"galah_apply_profile","title":"Narrow your results","text":"working ALA, notable feature ability specify profile remove records suspect way. see full list data quality profiles, use show_all(profiles).","code":"galah_call() |>   galah_filter(year > 2000) |>   galah_apply_profile(ALA) |>   atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 80883916"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_group_by","dir":"Articles","previous_headings":"","what":"galah_group_by","title":"Narrow your results","text":"Use galah_group_by group record counts summarise counts specified fields:","code":"# Get record counts since 2010, grouped by year and basis of record galah_call() |>   galah_filter(year > 2015 & year <= 2020) |>   galah_group_by(year, basisOfRecord) |>   atlas_counts() ## # A tibble: 36 × 3 ##    year  basisOfRecord         count ##    <chr> <chr>                 <int> ##  1 2020  Human observation   6553463 ##  2 2020  Occurrence           419842 ##  3 2020  Preserved specimen    84298 ##  4 2020  Machine observation   39643 ##  5 2020  Observation           24887 ##  6 2020  Material Sample        1677 ##  7 2020  Living specimen          62 ##  8 2019  Human observation   5735637 ##  9 2019  Occurrence           290610 ## 10 2019  Preserved specimen   165505 ## # ℹ 26 more rows"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_select","dir":"Articles","previous_headings":"","what":"galah_select","title":"Narrow your results","text":"Use galah_select choose columns returned downloading records: can also use dplyr functions work dplyr::select() galah_select()","code":"# Get *Reptilia* records from 1930, but only 'eventDate' and 'kingdom' columns occurrences <- galah_call() |>   galah_identify(\"reptilia\") |>   galah_filter(year == 1930) |>   galah_select(kingdom, species, eventDate) |>   atlas_occurrences()  occurrences |> head() ## # A tibble: 6 × 3 ##   kingdom  species                 eventDate           ##   <chr>    <chr>                   <dttm>              ## 1 Animalia Gehyra variegata        1930-11-30 00:00:00 ## 2 Animalia Intellagama lesueurii   1930-01-01 00:00:00 ## 3 Animalia Lampropholis guichenoti 1930-10-02 00:00:00 ## 4 Animalia Acanthophis antarcticus 1930-01-01 00:00:00 ## 5 Animalia <NA>                    1930-04-23 00:00:00 ## 6 Animalia Pseudechis porphyriacus 1930-01-01 00:00:00 occurrences <- galah_call() |>   galah_identify(\"reptilia\") |>   galah_filter(year == 1930) |>   galah_select(starts_with(\"accepted\") | ends_with(\"record\")) |>   atlas_occurrences()  occurrences |> head() ## # A tibble: 6 × 6 ##   acceptedNameUsage acceptedNameUsageID basisOfRecord      raw_basisOfRecord OCCURRENCE_STATUS_INFERRED_FROM_BASIS…¹ userDuplicateRecord ##   <chr>             <lgl>               <chr>              <chr>             <lgl>                                   <lgl>               ## 1 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 2 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 3 <NA>              NA                  PRESERVED_SPECIMEN Museum specimen   FALSE                                   FALSE               ## 4 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 5 <NA>              NA                  PRESERVED_SPECIMEN PreservedSpecimen FALSE                                   FALSE               ## 6 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## # ℹ abbreviated name: ¹​OCCURRENCE_STATUS_INFERRED_FROM_BASIS_OF_RECORD"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_geolocate","dir":"Articles","previous_headings":"","what":"galah_geolocate","title":"Narrow your results","text":"Use galah_geolocate specify geographic area region limit search:","code":"# Get list of perameles species only in area specified: # (Note: This can also be specified by a shapefile) wkt <- \"POLYGON((131.36328125 -22.506468769126,135.23046875 -23.396716654542,134.17578125 -27.287832521411,127.40820312499 -26.661206402316,128.111328125 -21.037340349154,131.36328125 -22.506468769126))\"  galah_call() |>   galah_identify(\"perameles\") |>   galah_geolocate(wkt) |>   atlas_species() ## # A tibble: 1 × 10 ##   kingdom  phylum   class    order           family      genus     species            author        species_guid         vernacular_name ##   <chr>    <chr>    <chr>    <chr>           <chr>       <chr>     <chr>              <chr>         <chr>                <chr>           ## 1 Animalia Chordata Mammalia Peramelemorphia Peramelidae Perameles Perameles eremiana Spencer, 1897 https://biodiversit… Desert Bandico…"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"masked-functions","dir":"Articles","previous_headings":"","what":"Masked functions","title":"Object-Oriented Programming in galah","text":"default method building queries galah first use galah_call() create query object called data_request. object class specific galah. object class data_request, galah can trigger functions use specific methods object class, even function name used another package. example, users can use filter() group_by() functions dplyr instead galah_filter() galah_group_by() construct query. Consequently, following queries synonymous: Thanks object-oriented programming, galah “masks” filter() group_by() functions use methods defined data_request objects instead. full list masked functions : arrange() (dplyr) count() (dplyr) identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() Note functions evaluated lazily; amend underlying object, amend nature data call evaluated. actually build run query, ’ll need use one different set dplyr verbs: collapse(), compute() collect().","code":"galah_call() |>   galah_filter(genus == \"Crinia\") |>   class() ## [1] \"data_request\" galah_call() |>   galah_filter(genus == \"Crinia\", year == 2020) |>   galah_group_by(species) |>   atlas_counts() galah_call() |>    filter(genus == \"Crinia\", year == 2020) |>   group_by(species) |>   atlas_counts() ## # A tibble: 16 × 2 ##    species                 count ##    <chr>                   <int> ##  1 Crinia signifera        58204 ##  2 Crinia parinsignifera   12478 ##  3 Crinia glauerti          3090 ##  4 Crinia georgiana         1490 ##  5 Crinia remota             784 ##  6 Crinia sloanei            644 ##  7 Crinia insignifera        536 ##  8 Crinia tinnula            417 ##  9 Crinia deserticola        278 ## 10 Crinia pseudinsignifera   236 ## 11 Crinia tasmaniensis       189 ## 12 Crinia bilingua            75 ## 13 Crinia subinsignifera      45 ## 14 Crinia riparia             10 ## 15 Crinia flindersensis        3 ## 16 Crinia nimba                1"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"advanced-query-building","dir":"Articles","previous_headings":"","what":"Advanced query building","title":"Object-Oriented Programming in galah","text":"usual way begin query request data galah using galah_call(). version 2.0, make galah flexible modular, underlying architecture galah_call() divided several types request_ functions. can begin pipe one dedicated request_ functions (rather galah_call()) depending type data want collect. example, want download occurrences, use request_data(): ’ll notice query differs slightly typical query structure users galah familiar . desired data type, \"occurrences\", specified beginning query within request_data() rather end using atlas_occurrences(). Specifying data type start allows users make use advanced query building using three newly implemented stages query building: collapse(), compute() collect(). stages mirror existing functions dplyr querying databases, act following way collapse() converts object query. allows users inspect API calls sent compute() sends queries required APIs. includes sending query data, determining whether field names valid, finding much data requested (necessary pagination) collect() retrieves requested data workspace can use sequence, just leap ahead stage want: benefit using collapse(), compute() collect() queries modular. particularly useful large data requests galah. Users can send query using compute(), download data query finished — downloading collect() later — rather waiting request finish within R. Additionally, functions modular generally easier interrogate debug. Previously functions several different things, making difficult know APIs called, , purpose. Partitioning queries three distinct stages much transparent, allows users check query construction prior sending request. example, query constructed following information, returned collapse(). collapse() stage displays useful information APIs pinged query galah sent using compute().","code":"x <- request_data(\"occurrences\") |> # note that \"occurrences\" is the default `type`   filter(species == \"Crinia tinnula\",           year == 2010) |>   collect() x <- request_data() |>   filter(genus == \"Crinia\", year == 2020) |>   group_by(species) |>   arrange(species) |>   count()  collapse(x) ## Object of class `query_set` containing 3 queries: ## • metadata/fields data: galah:::check_internal_cache()$fields ## • metadata/assertions data: galah:::check_internal_cache()$assertions ## • data/occurrences-count-groupby url: https://biocache-ws.ala.org.au/ws/occurre... compute(x) ## Object of class query with type data/occurrences-count-groupby  ## url: https://biocache-ws.ala.org.au/ws/occurrences/facets?fq=%28genus%3A%22...  ## arrange: species (ascending) collect(x) |> head() ## # A tibble: 6 × 2 ##   species              count ##   <chr>                <int> ## 1 Crinia bilingua         75 ## 2 Crinia deserticola     278 ## 3 Crinia flindersensis     3 ## 4 Crinia georgiana      1490 ## 5 Crinia glauerti       3090 ## 6 Crinia insignifera     536 # Create and send query to be calculated server-side request <- request_data() |>   identify(\"perameles\") |>   filter(year > 1900) |>   compute()    # Download data request |>   collect() request_data() |>   identify(\"perameles\") |>   filter(year > 1900) |>   collapse() ## Object of class `query_set` containing 5 queries: ## • metadata/fields data: galah:::check_internal_cache()$fields ## • metadata/assertions data: galah:::check_internal_cache()$assertions ## • metadata/reasons data: galah:::check_internal_cache()$reasons ## • metadata/taxa-single url: https://api.ala.org.au/namematching/api/search?q=pe... ## • data/occurrences url: https://biocache-ws.ala.org.au/ws/occurrences/offline/d..."},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"new-object-classes","dir":"Articles","previous_headings":"","what":"New object classes","title":"Object-Oriented Programming in galah","text":"hood, different query-building verbs amend object new class: collapse() returns class query_set, list one query objects compute() returns single object class query collect() doesn’t add new data class (returns class tibble) can called directly, via method type arguments galah_call(), specify dedicated request_ function data type return. demonstrate mean, take following calls, despite using different syntax, return number records available year 2020: Another example list available fields selected atlas: show values states territories: Although little reason use request_metadata() rather show_all() time, cases larger databases like GBIF return huge data.frames metadata. galah allows users use collapse(), compute() collect() types requests, meaning users able download large metadata queries using process detailed “Advanced query building” get around issue.","code":"# new syntax request_data() |>   filter(year == 2020) |>   count() |>   collect()  # similar, but using `galah_call()` galah_call(method = \"data\",            type = \"occurrences-count\") |>   filter(year == 2020) |>   collect()  # original syntax galah_call() |>   galah_filter(year == 2020) |>   atlas_counts() request_metadata(type = \"fields\") |>   collect()  galah_call(method = \"metadata\",             type = \"fields\") |>   collect()  show_all(fields) request_metadata() |>   filter(field == \"cl22\") |>   unnest() |>   collect()  galah_call(method = \"metadata\",             type = \"fields-unnest\") |>   galah_filter(id == \"cl22\") |>   collect()  search_all(fields, \"cl22\") |>   show_values()"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"do-i-need-to-use-advanced-query-building","dir":"Articles","previous_headings":"","what":"Do I need to use advanced query building?","title":"Object-Oriented Programming in galah","text":"Despite benefits, plans require new syntax; functions prefixed galah_ atlas_ going away. Indeed, perfect redundancy old new syntax cases, others serve different purposes. atlas_media() example, several calls made joined way reduces number steps required user. hood, however, atlas_ functions now entirely built using syntax.","code":""},{"path":"https://galah.ala.org.au/R/articles/piping.html","id":"piping-with-galah_call","dir":"Articles","previous_headings":"","what":"Piping with galah_call()","title":"Piping in galah","text":"may noticed examples dplyr pipes begin data, galah pipes begin galah_call() (sure add parentheses!). function tells galah using pipes construct query. Follow preferred pipe (|> base %>% magrittr). can narrow query line--line using galah_ functions. Finally, end atlas_ function identify type data want query. example using counts bandicoot records: second example, download occurrence records bandicoots 2021, also include information records zero coordinates: Note order galah_ functions added doesn’t matter, long galah_call() goes first, atlas_ function comes last.","code":"galah_call() |>   galah_identify(\"perameles\") |>   galah_filter(year >= 2020) |>   galah_group_by(species, year) |>   atlas_counts() ## # A tibble: 15 × 3 ##    species                year  count ##    <chr>                  <chr> <int> ##  1 Perameles nasuta       2021   3475 ##  2 Perameles nasuta       2022   1701 ##  3 Perameles nasuta       2020   1576 ##  4 Perameles nasuta       2023    714 ##  5 Perameles gunnii       2023    122 ##  6 Perameles gunnii       2021     71 ##  7 Perameles gunnii       2022     64 ##  8 Perameles gunnii       2020     49 ##  9 Perameles bougainville 2021     84 ## 10 Perameles bougainville 2022     72 ## 11 Perameles bougainville 2020      1 ## 12 Perameles pallescens   2022     30 ## 13 Perameles pallescens   2023     26 ## 14 Perameles pallescens   2021     25 ## 15 Perameles pallescens   2020     11 galah_call() |>   galah_identify(\"perameles\") |>   galah_filter(year == 2021) |>   galah_select(group = \"basic\", ZERO_COORDINATE) |>   atlas_occurrences() |>   head() ## Retrying in 1 seconds. ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 00108221-afc6-42… Perameles nas… https://biodi…           -28.8             153. 2021-09-29 00:00:00 PRESENT          NSW BioNet Atlas ## 2 001e914d-0281-41… Perameles nas… https://biodi…           -33.8             151. 2021-04-19 00:00:00 PRESENT          NSW BioNet Atlas ## 3 00233c1e-66df-4d… Perameles nas… https://biodi…           -33.8             151. 2021-02-27 00:00:00 PRESENT          NSW BioNet Atlas ## 4 003064b3-490a-49… Perameles nas… https://biodi…           -27.5             152. 2021-11-05 12:06:00 PRESENT          iNaturalist Aus… ## 5 004fd28b-a899-4a… Perameles nas… https://biodi…           -33.8             151. 2021-07-24 00:00:00 PRESENT          NSW BioNet Atlas ## 6 0068547b-b091-4a… Perameles nas… https://biodi…           -33.8             151. 2021-01-28 00:00:00 PRESENT          NSW BioNet Atlas ## # ℹ 1 more variable: ZERO_COORDINATE <lgl>"},{"path":"https://galah.ala.org.au/R/articles/piping.html","id":"using-dplyr-functions-in-galah","dir":"Articles","previous_headings":"","what":"Using dplyr functions in galah","title":"Piping in galah","text":"version 1.5.1, possible call dplyr functions natively within galah amend queries processed, .e.: full list masked functions : identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() count() (dplyr) synonym atlas_counts()","code":"# galah syntax galah_call() |>   galah_filter(year >= 2020) |>   galah_group_by(year) |>   atlas_counts() ## # A tibble: 4 × 2 ##   year    count ##   <chr>   <int> ## 1 2022  8409790 ## 2 2021  8254306 ## 3 2020  7124140 ## 4 2023  3446001 # dplyr syntax galah_call() |>   filter(year >= 2020) |>   group_by(year) |>   count() ## Object of type `data_request` containing: ## • type occurrences-count ## • filter year >= 2020 ## • group_by year"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"about","dir":"Articles","previous_headings":"","what":"About","title":"Quick start guide","text":"galah R interface biodiversity data hosted ‘living atlases’; set organisations share common codebase, act nodes Global Biodiversity Information Facility (GBIF). organisations collate store observations individual life forms, using ‘Darwin Core’ data standard. galah enables users locate download species observations, taxonomic information, record counts, associated media images sounds. Users can restrict queries particular taxa locations specifying columns rows returned query, restricting results observations meet particular quality-control criteria. functions return tibble standard format.","code":""},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Quick start guide","text":"install CRAN: install development version GitHub: Load package","code":"install.packages(\"galah\") install.packages(\"remotes\") remotes::install_github(\"AtlasOfLivingAustralia/galah\") library(galah)"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"choosing-an-atlas","dir":"Articles","previous_headings":"","what":"Choosing an atlas","title":"Quick start guide","text":"default, galah downloads information Atlas Living Australia (ALA). show full list Atlases currently supported galah, use show_all(atlases). Use galah_config() set Atlas use. automatically populate server configuration selected Atlas. default, atlas Australia.","code":"show_all(atlases) ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk galah_config(atlas = \"United Kingdom\")"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"building-queries","dir":"Articles","previous_headings":"","what":"Building queries","title":"Quick start guide","text":"Functions return data chosen atlas prefix atlas_; e.g. find total number records atlas, use: pass complex queries, start galah_call() function pipe additional arguments modify query. modifying functions galah_ prefix support non-standard evaluation (NSE). Alternatively, can use subset dplyr verbs pipe queries, assuming start galah_call(). narrow search particular taxonomic group, use galah_identify() identify. Note function accepts scientific names case sensitive. ’s good practice first use search_taxa() check taxa provide returns correct taxonomic results.","code":"galah_config(atlas = \"ALA\") atlas_counts() ## # A tibble: 1 × 1 ##       count ##       <int> ## 1 132342396 galah_call() |>    galah_filter(year >= 2020) |>    atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 27234237 galah_call() |>   filter(year >= 2020) |>    group_by(year) |>   count() |>   collect() ## # A tibble: 4 × 2 ##   year    count ##   <chr>   <int> ## 1 2022  8409790 ## 2 2021  8254306 ## 3 2020  7124140 ## 4 2023  3446001 search_taxa(\"reptilia\") # Check whether taxonomic info is correct ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… galah_call() |>   galah_filter(year >= 2020) |>    galah_identify(\"reptilia\") |>    atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 226794"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"downloading-records","dir":"Articles","previous_headings":"","what":"Downloading records","title":"Quick start guide","text":"common use case galah download ‘occurrence’ records; observations plants animals made contributors atlas. download, first register relevant atlas, provide registration email. GBIF queries, need provide email, username, password registered GBIF. Search fields field IDs filter query. can customise records require query atlas question. Check vignettes detail use functions.","code":"galah_config(email = \"email@email.com\") search_all(fields, \"australian states\") ## # A tibble: 2 × 3 ##   id     description                            type   ##   <chr>  <chr>                                  <chr>  ## 1 cl2013 ASGS Australian States and Territories fields ## 2 cl22   Australian States and Territories      fields result <- galah_call() |>   galah_identify(\"Litoria\") |>   galah_filter(year >= 2020, cl22 == \"Tasmania\") |>   galah_select(basisOfRecord, group = \"basic\") |>   atlas_occurrences() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. result |> head() ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 00250163-ec50-4e… Litoria        https://biodi…           -41.2             147. 2023-08-23 01:49:28 PRESENT          iNaturalist Aus… ## 2 003e0f63-9f95-4a… Litoria ewing… https://biodi…           -42.9             148. 2022-12-23 19:27:00 PRESENT          iNaturalist Aus… ## 3 00410554-5289-41… Litoria ewing… https://biodi…           -41.7             147. 2021-05-06 00:00:00 PRESENT          FrogID           ## 4 0081e7ef-459b-42… Litoria ewing… https://biodi…           -43.2             147. 2020-08-02 00:00:00 PRESENT          FrogID           ## 5 0086def1-8415-4b… Litoria ewing… https://biodi…           -41.2             147. 2020-12-31 00:00:00 PRESENT          FrogID           ## 6 00b40ee7-074b-4d… Litoria ewing… https://biodi…           -41.5             147. 2020-11-01 00:00:00 PRESENT          FrogID           ## # ℹ 1 more variable: basisOfRecord <chr>"},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"contextual-and-spatial-layers","dir":"Articles","previous_headings":"","what":"Contextual and spatial layers","title":"Spatial filtering","text":"Often want filter results commonly defined spatial regions, states, LGAs IBRA/IMCRA regions. ALA contains large range (>100) contextual spatial layers, -built searchable queriable fields. denoted names beginning \"cl\", followed identifying number may 6 digits long. fields based shapefiles, contain names regions layers record lies . strongly recommend using search_fields() check whether contextual layer already exists ALA matches require proceeding methods spatial filtering. fields able queried galah_filter()generally easier use. Suppose interested querying records Red-Necked Avocet (Recurvirostra novaehollandiae) particular protected wetlands, Coorong wetlands South Australia. can search ALA fields wetlands. search identifies layer cl901 seems match looking . can either view possible values field show_values(), search particular field. can filter occurrences exact matches value, \"Lake Eyre\". galah query can built follows:","code":"library(galah) library(tidyverse) library(gt) library(sf) galah_config(email = \"your_email_here\", verbose = FALSE) search_fields(\"wetlands\") ## # A tibble: 1 × 3 ##   id    description                     type   ##   <chr> <chr>                           <chr>  ## 1 cl901 Directory of Important Wetlands fields search_fields(\"cl901\") |> search_values(\"coorong\") ## • Showing values for 'cl901'. ## # A tibble: 1 × 1 ##   cl901                                       ##   <chr>                                       ## 1 The Coorong, Lake Alexandrina & Lake Albert galah_call() |>   galah_identify(\"Recurvirostra novaehollandiae\") |>   galah_filter(cl901 == \"The Coorong, Lake Alexandrina & Lake Albert\") |>   atlas_occurrences() |>   head(5) |>   gt::gt() ## Retrying in 1 seconds."},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"galah_geolocate","dir":"Articles","previous_headings":"","what":"galah_geolocate()","title":"Spatial filtering","text":"server-side spatial information useful, likely cases shapefile region wish query pre-loaded contextual layer ALA. case, shapefiles can introduced filtering process using {sf} package galah_geolocate() function. Shapefiles can provided sf object, whether importing sf::st_read() taking POLYGON MULTIPOLYGON character string transforming sf::st_as_sfc(). instance, might interested species occurrences King George Square, Brisbane. can take MULTIPOLYGON object square (sourced Brisbane City Council) transform sfc sf objects. can provide MULTIPOLYGON filter argument galah_geolocate() assess species recorded King George Square. second argument galah_geolocate() called type, defaults value \"polygon\". setting type argument \"bbox\", provided POLYGON MULTIPOLYGON converted smallest bounding box (rectangle) contains POLYGON. case, records included may exactly lie inside provided shape.","code":"king_george_sq <- \"MULTIPOLYGON(((153.0243 -27.46886, 153.0242 -27.46896, 153.0236 -27.46837, 153.0239 -27.46814, 153.0239 -27.46813, 153.0242 -27.46789, 153.0244 -27.46805, 153.0245 -27.46821, 153.0246 -27.46828, 153.0247 -27.46835, 153.0248 -27.46848, 153.0246 -27.4686, 153.0246 -27.46862, 153.0245 -27.46871, 153.0243 -27.46886)))\" |>   sf::st_as_sfc() |>    sf::st_as_sf() galah_call() |>   galah_filter() |>   galah_geolocate(king_george_sq) |>   galah_select(decimalLatitude, decimalLongitude, eventDate, scientificName, vernacularName) |>   atlas_occurrences() |>    head(10) |>   gt::gt() galah_call() |>   galah_filter() |>   galah_geolocate(king_george_sq, type = \"bbox\") |>   galah_select(decimalLatitude, decimalLongitude, eventDate, scientificName, vernacularName) |>   atlas_occurrences() |>   head(10) |>   gt::gt() ## Data returned for bounding box: ## xmin = 153.0236 xmax = 153.0248 ymin = -27.46896 ymax = -27.46789"},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"large-shapefiles","dir":"Articles","previous_headings":"galah_geolocate()","what":"Large shapefiles","title":"Spatial filtering","text":"type argument option \"bbox\" provided sf objects >500 vertices accepted ALA. event large shapefile, using type = \"bbox\" least enable initial reduction data downloaded, finer filtering actual shapefile obtain desired set occurrences. Alternatively, one can also perform \"bbox\" reduction passing shape galah_geolocate() using sf::st_bbox(). common situation occur shapefile multiple shapes provided, interested grouping results shape. mock workflow using subset shapefile 2,184 Brisbane parks. Let’s say interested knowing parks Brisbane postcode 4075 occurrences Scaly-Breasted Lorikeet, Trichoglossus chlorolepidotus, since 2020. can download entire shapefile link, perform filtering summarising follows: shapefiles cover large geographic areas caveat even bounding box doesn’t restrict number records value can downloaded easily. case, recommend nuances detailed methods can performed using looping techniques. One ALA Labs blog posts, Hex maps species occurrence data, written detailing approach larger problems .","code":"brisbane_parks <- sf::st_read(\"path/to/Park___Locations.shp\") |>   sf::st_make_valid() |>   filter(POST_CODE == 4075) # Convert shapefile to a bounding box brisbane_parks_bbox <- brisbane_parks |> sf::st_bbox()  # Find all occurrences of Trichoglossus chlorolepidotus in the bounding box in 2022 lorikeet_brisbane <- galah_call() |>   galah_filter(scientificName == \"Trichoglossus chlorolepidotus\",                 year >= 2020) |>   galah_geolocate(brisbane_parks_bbox, type = \"bbox\") |>   atlas_occurrences() ## Data returned for bounding box: ## xmin = 152.96331 xmax = 152.99668 ymin = -27.57737 ymax = -27.51606 # Filter records down to only those in the shapefile polygons lorikeet_brisbane |>   # Create a point geometry based on the occurrence coordinates   sf::st_as_sf(coords = c(\"decimalLongitude\", \"decimalLatitude\"), crs = sf::st_crs(brisbane_parks), remove = FALSE) |>   # identify which park each occurrence sits in with st_intersects()   mutate(intersection = sf::st_intersects(geometry, brisbane_parks) |> as.integer(),          park = ifelse(is.na(intersection), NA, brisbane_parks$PARK_NAME[intersection])) |>   # Filter out occurrences that did not occur in a park   filter(!is.na(park)) |>   # Drop the geometry column   sf::st_drop_geometry() |>   # Summarise the top 10 parks for lorikeet sightings in 2022   group_by(park) |>   summarise(counts = n()) |>   arrange(desc(counts)) |>   head(10) ## # A tibble: 10 × 2 ##    park                           counts ##    <chr>                           <int> ##  1 SHERWOOD ARBORETUM                276 ##  2 NYUNDARE-BA PARK                  271 ##  3 FAULKNER PARK                      51 ##  4 STRICKLAND TERRACE PARK            33 ##  5 FORT ROAD BUSHLAND                 31 ##  6 GRACEVILLE RIVERSIDE PARKLANDS     31 ##  7 BENARRAWA RESERVE                  19 ##  8 NOSWORTHY PARK                     16 ##  9 HORACE WINDOW RESERVE               9 ## 10 GRACEVILLE AVENUE PARK              6"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"search_taxa","dir":"Articles","previous_headings":"","what":"search_taxa()","title":"Taxonomic filtering","text":"search_taxa() enables users look taxonomic names downloading data, allows disambiguating homonyms checking search term matches taxon name ALA . search_taxa() returns scientific name, authorship, rank, full classification taxon matched provided search term.","code":"search_taxa(\"Petroica boodang\") |> gt::gt() # Muscicapa chrysoptera is a synonym for the Flame Robin, Petroica phoenicea # Guniibuu is the Yuwaalaraay Indigenous name for the Red-Capped Robin, Petroica goodenovii search_taxa(\"Muscicapa chrysoptera\", \"Guniibuu\") |> gt::gt() search_taxa(\"Morganella\") |> gt::gt() ## Warning: Search returned multiple taxa due to a homonym issue. ## ℹ Please provide another rank in your search to clarify taxa. ## ℹ Use a `tibble` to clarify taxa, see `?search_taxa`. ## ✖ Homonym issue with \"Morganella\". search_taxa(tibble(kingdom = \"Fungi\", genus = \"Morganella\")) |> gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_identify","dir":"Articles","previous_headings":"","what":"galah_identify()","title":"Taxonomic filtering","text":"galah_identify() similar search_taxa(), except can used within piped workflow retrieve counts, species, records e.g. recommend using search_taxa() prior calling galah_identify() workflow confirm validity provided search term. Setting search = TRUE passes results search_taxa() galah_identify(), also speeds query.","code":"galah_call() |>   galah_identify(\"Petroica boodang\") |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 118998 galah_call() |>   galah_identify(\"Muscicapa chrysoptera\", \"Guniibuu\") |>   atlas_species() |>    gt::gt() galah_call() |>   galah_identify(tibble(kingdom = \"Fungi\", genus = \"Morganella\")) |>   atlas_occurrences() |>   head() |>    gt::gt() robins <- search_taxa(\"Muscicapa chrysoptera\", \"Guniibuu\")   galah_call() |>   galah_identify(robins$taxon_concept_id, search = FALSE) |>   atlas_counts() ## Error: ## ! The `search` argument of `galah_identify()` was deprecated in galah 2.0.0 and is now defunct. ## ℹ `galah_identify()` now always does a search to verify search terms. To pass identifiers, please use `filter(lsid == ##   'identifier_here') instead."},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_filter","dir":"Articles","previous_headings":"","what":"galah_filter()","title":"Taxonomic filtering","text":"galah_filter() subsets records searching exact matches expression, may also used taxonomic filtering e.g. can useful searching paraphyletic polyphyletic groups, done using galah_identify(). example, get counts non-chordates:","code":"galah_call() |>   galah_filter(species == \"Petroica boodang\") |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 118998 aus_petroica <- c(\"Petroica boodang\", \"Petroica goodenovii\",                    \"Petroica phoenicea\", \"Petroica rosea\",                   \"Petroica rodinogaster\", \"Petroica multicolor\")  galah_call() |>   galah_filter(species == aus_petroica) |>   galah_group_by(species, vernacularName) |>   atlas_counts() |>    gt::gt() galah_call() |>   galah_filter(kingdom == \"Animalia\", phylum != \"Chordata\") |>   galah_group_by(phylum) |>   atlas_counts() |>   head() |>    gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_filter-galah_identify-and-taxonomic-ranks","dir":"Articles","previous_headings":"","what":"galah_filter(), galah_identify(), and taxonomic ranks","title":"Taxonomic filtering","text":"Deciding using galah_filter() galah_identify() query comes record classified, whether correct unique name classification taxa interest. ALA fields primary taxonomic ranks (kingdom, phylum, class, order, family, genus, species) secondary ranks (e.g. subfamily, subgenus), may used galah_filter() galah_identify(). Additionally, field named scientificName, refers lowest taxonomic rank record identified e.g. , instance, correct species subspecies name, searching matches species subspecies fields, respectively, provide precise results. field scientificName may include subgenera. ’ve used search_taxa() get ALA-matched name taxon want records identified particular level classification, searching matches scientificName recommended. Paraphyletic polyphyletic groups may contain taxa identified different taxonomic levels. case, simpler use search_taxa() galah_identify() rather galah_filter(). example , search_taxa() matches terms one genus, three species, two subspecies. can used piped workflow galah_identify().","code":"galah_call() |>   galah_identify(tibble(genus = \"Pitta\")) |>   galah_group_by(scientificName, taxonRank) |>   atlas_counts() |>   filter(!is.na(scientificName)) |>   gt::gt() tas_endemic <- c(\"Sarcophilus\", # Tasmanian Devil                  \"Bettongia gaimardi\", # Tasmanian Bettong                  \"Melanodryas vittata\", # Dusky Robin                  \"Platycercus caledonicus\",# Green Rosella                  \"Aquila audax fleayi\", # Tasmanian Wedge-Tailed Eagle                  \"Tyto novaehollandiae castanops\") # Tasmanian Masked Owl  search_taxa(tas_endemic) |> gt::gt() galah_call() |>   galah_identify(tas_endemic) |>   galah_group_by(scientificName) |>   atlas_counts() |>   arrange(scientificName) |>   gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"year-month-and-day","dir":"Articles","previous_headings":"","what":"Year, Month and Day","title":"Temporal filtering","text":"ALA contains -built year, month, day fields every record. queried numeric fields (.e. July = 7) can used quick data exploration filtering. fields useful date limits query can easily defined year, month /day. instance, can get monthly counts amphibians 2021 using year month fields. also important observe outputted month column type character even though values numeric. case year, month day fields. However, can queried either numeric character values within galah_filter(). One limitation using fields queries galah_filter() independence; used query within windows bounded two dates day month filters applied universally. instance, consider native perennial Australian wildflower Chamaescilla corymbosa, whose known growth flowering times August–October. might interested number records species first week spring (.e. September) last 10 years. following query provide results 1/9/2013 7/9/2023. Rather, return results fall within 3 windows .","code":"library(galah) library(tidyverse) library(gt) library(lubridate) galah_config(email = \"your_email_here\", verbose = FALSE) galah_call() |>   galah_filter(class == \"Amphibia\", year == 2021) |>   galah_group_by(month) |>   atlas_counts() ## # A tibble: 12 × 2 ##    month     count ##    <chr>     <int> ##  1 October   52816 ##  2 September 42206 ##  3 January   32825 ##  4 August    26252 ##  5 March     25423 ##  6 February  23473 ##  7 November  23389 ##  8 July      12301 ##  9 April     10005 ## 10 June       9217 ## 11 May        8083 ## 12 December   3998 galah_call() |>   galah_filter(species == \"Chamaescilla corymbosa\",                year >= 2013, year <= 2023, month == 9, day >= 1, day <= 7) |>   galah_group_by(year) |>   atlas_counts() |>   arrange(year) ## # A tibble: 11 × 2 ##    year  count ##    <chr> <int> ##  1 2013      8 ##  2 2014     13 ##  3 2015      8 ##  4 2016      7 ##  5 2017      1 ##  6 2018      9 ##  7 2019      5 ##  8 2020     20 ##  9 2021     36 ## 10 2022     25 ## 11 2023     52"},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"occurrence-dates","dir":"Articles","previous_headings":"","what":"Occurrence dates","title":"Temporal filtering","text":"bespoke way query exact dates records, users can use eventDate field. field contains exact date time information records enables specific time windows queried easily. caveat time/date must provided specific format galah_filter() ALA query work. required format dates eventDate ISO 8601 International Date Standard format. requires dates times form “YYYY-MM-DDTHH:MM:SSZ”. Note T middle actual letter “T” delimit date time components, “Z” officially denotes time queried UTC (Greenwich Meridian) time. Timezones can confusing best times, however easiest remember ALA records recorded local time location, times treated effectively UTC times. upshot specific formatting , instance, time writing paragraph, 4:26pm 2nd August 2023, represented \"2023-08-02T16:26:44Z\" ALA, even though officially timezone \"+0930\". eventDate specifies time seconds, recommended greater less queries used rather exact matches. used galah_filter(), can easily identify many records humpback whale (Megaptera novaeangliae) occurred since species removed Australian threatened species list 26/02/2022. can unintuitive provide dates format. Luckily, simple convert standard R dates {lubridate} dates format already required “YYYY-MM-DD” form. took date (26/02/2022), converted form using base R lubridate follows: sending query, outputted eventDate values returned galah query date class \"POSIXct\".","code":"galah_call() |>   galah_filter(species == \"Megaptera novaeangliae\",                 eventDate >= \"2022-02-26T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1   542 humpback_date <- \"26/02/2022\" # Base R paste0(as.Date(humpback_date, format = \"%d/%m/%Y\"), \"T00:00:00Z\") ## [1] \"2022-02-26T00:00:00Z\" # lubridate paste0(dmy(humpback_date), \"T00:00:00Z\") ## [1] \"2022-02-26T00:00:00Z\""},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"upload-dates","dir":"Articles","previous_headings":"","what":"Upload dates","title":"Temporal filtering","text":"important date field present ALA pertains date record provided ALA. field called firstLoadedDate formatted exactly manner eventDate. Different data providers provide batches records ALA different intervals. iNaturalist Australia provide weekly uploads data, eBird provides yearly uploads. firstLoadedDate can especially useful finding new records ALA provided since last checked. instance, can use see many observations Sulphur-Crested Cockatoos recorded first week 2023 actually loaded ALA following week: Note lower bound required firstLoadedDate eventDate imposes proxy (records can’t uploaded ’ve occurred).","code":"# Total records of Cactua galerita in Jan 1-7 galah_call() |>   galah_filter(species == \"Cacatua galerita\",                eventDate >= \"2023-01-07T00:00:00Z\",                 eventDate < \"2023-01-08T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1   388 # Records of Cactua galerita uploaded in Jan 1-14 galah_call() |>   galah_filter(species == \"Cacatua galerita\",                eventDate >= \"2023-01-07T00:00:00Z\",                 eventDate < \"2023-01-08T00:00:00Z\",                firstLoadedDate < \"2023-01-15T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1     6"},{"path":"https://galah.ala.org.au/R/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Martin Westgate. Author, maintainer. Matilda Stevenson. Author. Dax Kellie. Author. Peggy Newman. Author.","code":""},{"path":"https://galah.ala.org.au/R/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Westgate M, Stevenson M, Kellie D, Newman P (2023). galah: Biodiversity Data GBIF Node Network. R package version 2.0.0, https://CRAN.R-project.org/package=galah.","code":"@Manual{,   title = {galah: Biodiversity Data from the GBIF Node Network},   author = {Martin Westgate and Matilda Stevenson and Dax Kellie and Peggy Newman},   year = {2023},   note = {R package version 2.0.0},   url = {https://CRAN.R-project.org/package=galah}, }"},{"path":[]},{"path":"https://galah.ala.org.au/R/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Biodiversity Data from the GBIF Node Network","text":"galah R interface biodiversity data hosted Global Biodiversity Information Facility (GBIF) members GBIF node network maintain APIs (.e. ‘living atlases’). organisations collate store observations individual life forms, using ‘Darwin Core’ data standard. galah built maintained Science & Decision Support Team Atlas Living Australia (ALA). galah enables users locate download species occurrence records (observations, specimens, eDNA records, etc.), taxonomic information, associated media images sounds, restrict queries particular taxa locations. Users can specify columns returned query, restrict results occurrences meet particular data-quality criteria. functions return tibble standard format. package named bird name (Eolophus roseicapilla), widely-distributed endemic Australian species. logo designed Ian Brennan. comments, questions suggestions, please contact us.","code":""},{"path":"https://galah.ala.org.au/R/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Biodiversity Data from the GBIF Node Network","text":"quick start guide provides introduction package functions. outline package structure, list available functions, run ?galah view reference page.","code":""},{"path":"https://galah.ala.org.au/R/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Biodiversity Data from the GBIF Node Network","text":"Install CRAN: Install development version GitHub: galah depends sf location-based searches. install galah need make sure system meets sf system requirements, specified .","code":"install.packages(\"galah\") install.packages(\"remotes\") remotes::install_github(\"AtlasOfLivingAustralia/galah-R\")"},{"path":[]},{"path":"https://galah.ala.org.au/R/index.html","id":"citations","dir":"","previous_headings":"","what":"Citations","title":"Biodiversity Data from the GBIF Node Network","text":"generate citation package version using, can run ’re using occurrence data downloaded galah publication, please generate DOI cite . request DOI download occurrence record, set mint_doi = TRUE call atlas_occurrences(). generate citation downloaded occurrence records, pass tibble generated atlas_citation().","code":"citation(package = \"galah\") # Download occurrence records with a DOI  occ <- atlas_occurrences(..., mint_doi = TRUE)  # See DOI attr(occ, \"doi\")  # Generate citation atlas_citation(occ)"},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange rows of a query — arrange.data_request","title":"Arrange rows of a query — arrange.data_request","text":"arrange.data_request() arranges rows query server side, meaning prior sending query, query constructed way information arranged query processed. data returned query rows already pre-arranged. benefit using arrange() within galah_call() faster process arranging rows server side arranging rows locally downloaded data, especially dataset large complex. arrange() can used within galah_call() pipe, queries  type = \"occurrences-count\". galah_call() pipe must include count() finish collect() (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange rows of a query — arrange.data_request","text":"","code":"# S3 method for data_request arrange(.data, ...)  # S3 method for metadata_request arrange(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange rows of a query — arrange.data_request","text":".data object class data_request ... Either count index","code":""},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange rows of a query — arrange.data_request","text":"","code":"if (FALSE) {  # Arrange grouped counts by ascending year galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(year) |>   count() |>   collect()    # Arrange grouped counts by ascending record count galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(count) |>   count() |>   collect()  # Arrange grouped counts by descending year galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(desc(year)) |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a citation for occurrence data — atlas_citation","title":"Generate a citation for occurrence data — atlas_citation","text":"data.frame generated using atlas_occurrences(), mint_doi argument set TRUE, DOI associated dataset appended resulting data.frame attribute. function simply formats DOI citation can included scientific publication. Please also consider citing package, using information citation(\"galah\").","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a citation for occurrence data — atlas_citation","text":"","code":"atlas_citation(data)"},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a citation for occurrence data — atlas_citation","text":"data data.frame: occurrence data generated atlas_occurrences()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a citation for occurrence data — atlas_citation","text":"string containing citation dataset.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a citation for occurrence data — atlas_citation","text":"","code":"if (FALSE) { atlas_citation(doi) }"},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Return a count of records — atlas_counts","title":"Return a count of records — atlas_counts","text":"Prior downloading data often valuable estimate many records available, deciding query feasible, estimating long take download. Alternatively, kinds reporting, count observations may required, example understanding observations growing shrinking particular locations, particular taxa. end, atlas_counts() takes arguments format atlas_occurrences(), provides either total count records matching criteria, data.frame counts matching criteria supplied group_by argument.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return a count of records — atlas_counts","text":"","code":"atlas_counts(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL,   group_by = NULL,   limit = NULL,   type = c(\"occurrences\", \"species\") )  # S3 method for data_request count(x, ..., wt, sort, name)"},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return a count of records — atlas_counts","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile() group_by data.frame: object class galah_group_by, returned galah_group_by(). Alternatively vector field names (see search_all(fields) show_all(fields). limit numeric: maximum number categories return, defaulting 100. limit NULL, results returned. categories take . type string: one c(\"occurrences-count\", \"species-count\"). Defaults \"occurrences-count\", returns number records match selected criteria; alternatively returns number species. Formerly accepted arguments (\"records\" \"species\") deprecated remain functional. x object class data_request, created using galah_call() ... currently ignored wt currently ignored sort currently ignored name currently ignored","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return a count of records — atlas_counts","text":"object class tbl_df data.frame (aka tibble) returning: single number, group_by specified , summary counts grouped field(s), group_by specified","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return a count of records — atlas_counts","text":"","code":"if (FALSE) { # classic syntax: galah_call() |>   galah_filter(year == 2015) |>   atlas_counts()  # synonymous with: request_data() |>   filter(year == 2015) |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":null,"dir":"Reference","previous_headings":"","what":"Get metadata on images, sounds and videos — atlas_media","title":"Get metadata on images, sounds and videos — atlas_media","text":"addition text data describing individual occurrences attributes, ALA stores images, sounds videos associated given record. atlas_media displays metadata media types.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get metadata on images, sounds and videos — atlas_media","text":"","code":"atlas_media(   request = NULL,   identify = NULL,   filter = NULL,   select = NULL,   geolocate = NULL,   data_profile = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get metadata on images, sounds and videos — atlas_media","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() select list: generated call galah_select() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get metadata on images, sounds and videos — atlas_media","text":"object class tbl_df data.frame (aka tibble) metadata requested media.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get metadata on images, sounds and videos — atlas_media","text":"atlas_media() works first finding occurrence records matching filter contain media, downloading metadata media. actually download files , use collect_media(). may beneficial requesting large number records show progress bar setting verbose = TRUE galah_config().","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get metadata on images, sounds and videos — atlas_media","text":"","code":"if (FALSE) { # Download Regent Honeyeater records with multimedia attached galah_call() |>   galah_identify(\"Regent Honeyeater\") |>   galah_filter(year == 2011) |>   atlas_media()  # Download multimedia galah_call() |>   galah_identify(\"Regent Honeyeater\") |>   galah_filter(year == 2011) |>   atlas_media() |>   collect_media(path = \"folder/your-directory\")  # Specify a single media type to download galah_call() |>   galah_identify(\"Eolophus Roseicapilla\") |>   galah_filter(multimedia == \"Sound\") |>   atlas_media()  # It's good to check how many records have media files before downloading galah_call() |>   galah_filter(multimedia == c(\"Image\", \"Sound\", \"Video\")) |>   galah_group_by(multimedia) |>   atlas_counts()       # post version 2.0, it is possible to run all steps in sequence # first, get occurrences, making sure to include media fields: occurrences_df <- request_data() |>   identify(\"Regent Honeyeater\") |>   filter(!is.na(images), year == 2011) |>   select(group = \"media\") |>   collect()   # second, get media metadata media_info <- request_metadata() |>   filter(media == occurrences_df) |>   collect()    # the two steps above + `right_join()` are synonmous with `atlas_media()` # third, get images request_files() |>   filter(media == media_df) |>   collect(thumbnail = TRUE)    # step three is synonymous with `collect_media()` }"},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect a set of occurrences — atlas_occurrences","title":"Collect a set of occurrences — atlas_occurrences","text":"common form data stored living atlases observations individual life forms, known 'occurrences'. function allows user search occurrence records match specific criteria, return tibble analysis. Optionally, user can also request DOI given download facilitate citation re-use specific data resources.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect a set of occurrences — atlas_occurrences","text":"","code":"atlas_occurrences(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL,   select = NULL,   mint_doi = FALSE,   doi = NULL,   file = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect a set of occurrences — atlas_occurrences","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile() select data.frame: generated call galah_select() mint_doi logical: default DOI generated. Set TRUE intend use data publication similar. doi string: (optional) DOI download. provided overrides arguments. available ALA. file string: (Optional) file name. given, set data date time added. file path (directory) always given galah_config()$package$directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect a set of occurrences — atlas_occurrences","text":"object class tbl_df data.frame (aka tibble) occurrences, containing columns specified galah_select().","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Collect a set of occurrences — atlas_occurrences","text":"Note unless care taken, queries can particularly large. cases simply take long time process, number requested records >50 million, call return data. Users can test whether threshold reached first calling atlas_counts() using arguments intend pass atlas_occurrences(). may also beneficial requesting large number records show progress bar setting verbose = TRUE galah_config(), use compute() run call collecting later collect().","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect a set of occurrences — atlas_occurrences","text":"","code":"if (FALSE) { # Download occurrence records for a specific taxon galah_config(email = \"your_email_here\") galah_call() |>   galah_identify(\"Reptilia\") |>   atlas_occurrences()  # Download occurrence records in a year range galah_call() |>   galah_identify(\"Litoria\") |>   galah_filter(year >= 2010 & year <= 2020) |>   atlas_occurrences()    # Or identically with alternative syntax request_data() |>   identify(\"Litoria\") |>   filter(year >= 2010 & year <= 2020) |>   collect()    # Download occurrences records in a WKT-specified area polygon <- \"POLYGON((146.24960 -34.05930,                      146.37045 -34.05930,                      146.37045 -34.152549,                      146.24960 -34.15254,                      146.24960 -34.05930))\" galah_call() |>    galah_identify(\"Reptilia\") |>   galah_filter(year >= 2010, year <= 2020) |>   galah_geolocate(polygon) |>   atlas_occurrences()    }"},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect the set of species observed within the specified filters — atlas_species","title":"Collect the set of species observed within the specified filters — atlas_species","text":"reasons users may need check every record meeting search criteria (.e. using atlas_occurrences()), common use case simply identify species occur specified region, time period, taxonomic group. function returns data.frame one row per species, columns giving associated taxonomic information.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect the set of species observed within the specified filters — atlas_species","text":"","code":"atlas_species(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect the set of species observed within the specified filters — atlas_species","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect the set of species observed within the specified filters — atlas_species","text":"object class tbl_df data.frame (aka tibble), returning matching species data.frame object attributes listing user-supplied arguments data_request (.e., identify, filter, geolocate, columns)","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Collect the set of species observed within the specified filters — atlas_species","text":"primary use case function extract species-level information given set criteria defined search_taxa(), galah_filter() galah_geolocate(). purpose simply get taxonomic information restricted filtering, search_taxa() efficient. Similarly, counts required include filter without returning taxonomic detail, atlas_counts() efficient (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect the set of species observed within the specified filters — atlas_species","text":"","code":"if (FALSE) { # First register a valid email address galah_config(email = \"ala4r@ala.org.au\")  # Get a list of species within genus \"Heleioporus\" # (every row is a species with associated taxonomic data) galah_call() |>   galah_identify(\"Heleioporus\") |>   atlas_species()  # Get a list of species within family \"Peramelidae\" galah_call() |>   galah_identify(\"peramelidae\") |>   atlas_species()    # Or alternatively request_data(type = \"species\") |>   identify(\"peramelidae\") |>   collect()  # It's good idea to find how many species there are before downloading galah_call() |>   galah_identify(\"Heleioporus\") |>   atlas_counts(type = \"species\") # Or alternatively request_data(type = \"species\") |>   identify(\"Heleioporus\") |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Search taxonomic trees — atlas_taxonomy","title":"Search taxonomic trees — atlas_taxonomy","text":"ALA ' internal taxonomy derived authoritative sources. atlas_taxonomy provides means query taxonomy, returning tibble showing child nodes parent derived .","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search taxonomic trees — atlas_taxonomy","text":"","code":"atlas_taxonomy(   request = NULL,   identify = NULL,   filter = NULL,   constrain_ids = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search taxonomic trees — atlas_taxonomy","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter(rank == \"chosen_rank\"). identity clade downwards search stop. constrain_ids string: Optional string limit taxon_concept_id's returned. useful restricting taxonomy particular authoritative sources. Default \"biodiversity.org.au\" Australia (can overridded setting constrain_ids = NULL) NULL otherwise. Powered grepl() meaning supports regular expressions.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search taxonomic trees — atlas_taxonomy","text":"tibble containing taxon names, ranks parent/child IDs","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search taxonomic trees — atlas_taxonomy","text":"approach used function recursive, meaning becomes slow large queries atlas_taxonomy(search_taxa(\"Plantae\"), down_to = galah_down_to(species)). Although inputs search_taxa down_to case-insensitive, node names always returned title case.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search taxonomic trees — atlas_taxonomy","text":"","code":"if (FALSE) { # Get a taxonomic tree of *Chordata* down to the class level galah_call() |>    galah_identify(\"chordata\") |>   galah_filter(rank == class) |>   atlas_taxonomy() }"},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a query — collapse_galah","title":"Generate a query — collapse_galah","text":"collapse() constructs valid query can inspected sent. typically occurs end pipe, traditionally begun galah_call(), used define query. version 2.0, objects class data_request (created using request_data()), metadata_request (request_metadata()) files_request (request_files()) supported collapse(). objects can created using galah_call() via method argument.","code":""},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a query — collapse_galah","text":"","code":"# S3 method for data_request collapse(x, ..., mint_doi)  # S3 method for metadata_request collapse(x, ...)  # S3 method for files_request collapse(x, ..., thumbnail = FALSE)"},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a query — collapse_galah","text":"x object class data_request, metadata_request files_request ... Arguments passed methods mint_doi Logical: DOI minted download? applies type = \"occurrences\" atlas chosen \"ALA\". thumbnail Logical: thumbnail-size images returned? Defaults FALSE, indicating full-size images required.","code":""},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a query — collapse_galah","text":"object class query_set, list containing one objects class query. valuable shows set queries required correctly retrieve requested data. Objects within query_set listed sequence enacted.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve a database query — collect_galah","title":"Retrieve a database query — collect_galah","text":"collect() attempts retrieve result query selected API.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve a database query — collect_galah","text":"","code":"# S3 method for data_request collect(x, ..., wait = TRUE, file = NULL)  # S3 method for metadata_request collect(x, ...)  # S3 method for files_request collect(x, ...)  # S3 method for query_set collect(x, ..., wait = TRUE, file = NULL)  # S3 method for query collect(x, ..., wait = TRUE, file = NULL)"},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve a database query — collect_galah","text":"x object class data_request, metadata_request files_request (galah_call()); oject class query_set query (collapse() compute()) ... Arguments passed methods wait logical; galah wait response? Defaults FALSE. applies type = \"occurrences\" \"species\". file (Optional) file name. given, set data date time added. file path (directory) always given galah_config()$package$directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve a database query — collect_galah","text":"cases, collect() returns tibble containing requested data. requested data yet ready (.e. occurrences wait set FALSE), function returns object class query can used recheck download later time.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect media files — collect_media","title":"Collect media files — collect_media","text":"function downloads full-sized thumbnail images media files using information atlas_media local directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect media files — collect_media","text":"","code":"collect_media(df, thumbnail = FALSE, path)"},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect media files — collect_media","text":"df tibble: returned atlas_media() pipe starting request_data(type = \"media\"). thumbnail logical: TRUE download small thumbnail-sized images, rather full size images (default). path string:  Use galah_config(directory = \"path--directory)\" instead. Supply path local folder/directory downloaded media saved .","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect media files — collect_media","text":"Invisibly returns tibble listing number files downloaded, grouped HTML status codes. Primarily called side effect downloading available image & media files user local directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect media files — collect_media","text":"","code":"if (FALSE) { # Use `atlas_media()` to return a `tibble` of records that contain media x <- galah_call() |>    galah_identify(\"perameles\") |>   galah_filter(year == 2015) |>   atlas_media()  # To download media files, add `collect_media()` to the end of a query  galah_config(directory = \"media_files\") collect_media(x) }"},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute a query — compute_galah","title":"Compute a query — compute_galah","text":"compute() useful several purposes. original purpose send request data, can processed server retrieved later time (via collect()). However, query-altering functions (filter() select()) evaluated lazily galah version 2.0 onwards, compute() also function objects within query_set evaluated, checks run using information. Therefore possible invalid queries built using collapse(), fail compute().","code":""},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute a query — compute_galah","text":"","code":"# S3 method for data_request compute(x, ...)  # S3 method for metadata_request compute(x, ...)  # S3 method for files_request compute(x, ...)  # S3 method for query_set compute(x, ...)  # S3 method for query compute(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute a query — compute_galah","text":"x object class data_request, metadata_request files_request (.e. constructed using pipe) query query_set (.e. constructed collapse()) ... Arguments passed methods","code":""},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute a query — compute_galah","text":"object class query containing checked, valid query selected atlas. case occurrence data, also contains information status request.","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated functions — galah_down_to","title":"Deprecated functions — galah_down_to","text":"include: galah_down_to() favour galah_filter()","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated functions — galah_down_to","text":"","code":"galah_down_to(...)"},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated functions — galah_down_to","text":"... name single taxonomic rank","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated functions — galah_down_to","text":"string named rank","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deprecated functions — galah_down_to","text":"","code":"if (FALSE) { # Return a taxonomic tree of *Chordata* down to the class level galah_call() |>     galah_identify(\"Vertebrata\") |>     galah_down_to(class) |>     atlas_taxonomy() }"},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Biodiversity Data from the GBIF Node Network — galah","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Global Biodiversity Information Facility (GBIF; https://www.gbif.org) provides tools enable users find, access, combine visualise biodiversity data. galah enables R community directly access data resources hosted GBIF several subsidiary organisations, known 'nodes'. basic unit observation stored infrastructures occurrence record, based Darwin Core' data standard (https://dwc.tdwg.org); however galah also enables users locate download taxonomic information, associated media images sounds, restricting queries particular taxa locations. Users can specify columns returned query, restrict results observations meet particular quality-control criteria. outside Australia, 'galah' common name Eolophus roseicapilla, widely-distributed Australian bird species.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Piping functions galah_call() request_() et al.  Start build data query collapse() Generate query compute() Compute query collect() Retrieve database query Lazy data manipulation identify() galah_identify() Search taxonomic identifiers filter() galah_filter()Filter records select() galah_select()Fields report information group_by() galah_group_by() Fields group counts st_crop() galah_geolocate() Specify location apply_profile() galah_apply_profile() Restrict data pass predefined checks (ALA ) slice_head() Choose first n rows download arrange() Arrange rows query server side Download data atlas_occurrences() Download occurrence records atlas_counts() count() Count number records species returned query atlas_species() Download species lists atlas_taxonomy() Return section ALA taxonomic tree atlas_media() View images sounds available download collect_media() Download images sounds Look information search_taxa() Search taxa using text-search search_identifiers() Search taxa using taxonomic identifiers show_all() & search_all() Data generating filter queries show_values() & search_values() Show search values within fields, profiles, lists, collections, datasets providers Configure session galah_config() Package configuration options Cite atlas_citation() Citation dataset","code":""},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"terminology","dir":"Reference","previous_headings":"","what":"Terminology","title":"Biodiversity Data from the GBIF Node Network — galah","text":"get value galah, helpful understand terminology. occurrence record contains taxonomic information, usually information observation , location. addition record-specific information, living atlases append contextual information record, particularly data spatial layers reflecting climate gradients political boundaries. also run number quality checks record, resulting assertions attached record. piece information associated given occurrence record stored field, corresponds column imported R data.frame. See show_all(fields) view valid fields, layers assertions, conduct search using search_all(fields). Data fields important provide means filter occurrence records;  .e. return information need, . Consequently, much architecture galah designed make filtering simple possible. easiest way start pipe galah_call() follow relevant dplyr function; starting filter(), also including select(), group_by() others. Functions without relevant dplyr synonym include galah_identify()/identify() choosing taxon, galah_geolocate()/ st_crop() choosing specific location. combining different filters, possible build complex queries return valuable information given problem. notable extension filtering approach remove records low 'quality'. living atlases perform quality control checks records store. checks used generate new fields, can used filter records unsuitable particular applications. However, many possible data quality checks, always clear appropriate given instance. Therefore, galah supports data quality profiles, can passed galah_apply_profile() quickly remove undesirable records. full list data quality profiles returned show_all(profiles). Note service currently available Australian atlas (ALA).","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Maintainer: Martin Westgate martin.westgate@csiro.au Authors: Matilda Stevenson Dax Kellie dax.kellie@csiro.au Peggy Newman peggy.newman@csiro.au","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a data quality profile — galah_apply_profile","title":"Apply a data quality profile — galah_apply_profile","text":"'profile' group filters pre-applied ALA. Using data profile allows query filtered quickly relevant quality-assured data fit--purpose. example, \"ALA\" profile designed exclude lower quality records, whereas profiles apply filters specific species distribution modelling (e.g. CDSM).","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a data quality profile — galah_apply_profile","text":"","code":"galah_apply_profile(...)  apply_profile(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a data quality profile — galah_apply_profile","text":"... profile name. string - name abbreviation data quality profile apply query. Valid values can seen using show_all(profiles) .data object class data_request","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply a data quality profile — galah_apply_profile","text":"tibble containing valid data profile value.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Apply a data quality profile — galah_apply_profile","text":"Note one profile can loaded time; multiple profiles given, first valid profile used. bespoke editing filters within profile, use galah_filter()","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply a data quality profile — galah_apply_profile","text":"","code":"if (FALSE) { # Apply a data quality profile to a query galah_call() |>    galah_identify(\"reptilia\") |>   galah_filter(year == 2021) |>   galah_apply_profile(ALA) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Start building a query — galah_call","title":"Start building a query — galah_call","text":"download data selected atlas, one must construct query. query tells atlas API data download return, well filtered. Using galah_call() allows build piped query download data, way wrangle data dplyr tidyverse. Since version 2.0, galah_call() wrapper group underlying request_ functions. functions can begin piped query end collapse(), compute() collect(). underlying request_ #' functions useful allow galah separate different types requests perform better. example, filter.data_request translates filters R solr, whereas filter.metadata_request searches using search term. details see object-oriented programming vignette: vignette(\"object_oriented_programming\", package = \"galah\")","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start building a query — galah_call","text":"","code":"galah_call(method = c(\"data\", \"metadata\", \"files\"), type, ...)  request_data(   type = c(\"occurrences\", \"occurrences-count\", \"occurrences-doi\", \"species\",     \"species-count\"),   ... )  request_metadata(type)  request_files(type = c(\"media\"))"},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start building a query — galah_call","text":"method string: request function called. one \"data\" (default), \"metadata\" \"files\" type string: form data returned? Acceptable values specified corresponding request function ... Zero arguments alter query. See 'details'.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start building a query — galah_call","text":"sub-function returns different object class: request_data() returns data_request. request_metadata returns metadata_request, request_files() returns files_request.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start building a query — galah_call","text":"atlas several types data can chosen. Currently supported \"occurrences\" (default), \"species\" \"media\" (latter currently ALA). also possible use type = \"occurrences-count\" type = \"species-count\"; practice synonymous galah_call() |> count(), therefore practically useful debugging (via collapse() compute()). named arguments supported via .... practice, functions galah_ prefix S3 methods ported dplyr assign information correct slots internally. Overwriting user-defined alternatives possible, advised. Accepted arguments : filter (accepts galah_filter() filter()) select (accepts galah_select() select) group_by (accepts galah_group_by() group_by()) identify (accepts galah_identify() identify()) geolocate (accepts galah_geolocate(), galah_polygon() galah_bbox() st_crop()) limit (accepts slice_head()) doi (accepts sting listing valid DOI, specific collect() type = \"doi\") Unrecognised names ignored collect() related functions.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Start building a query — galah_call","text":"","code":"if (FALSE) {  # Begin your query with `galah_call()`, then pipe using `%>%` or `|>`  # Get number of records of *Aves* from 2001 to 2004 by year galah_call() |>   galah_identify(\"Aves\") |>   galah_filter(year > 2000 & year < 2005) |>   galah_group_by(year) |>   atlas_counts()    # Get information for all species in *Cacatuidae* family galah_call() |>   galah_identify(\"Cacatuidae\") |>   atlas_species()    # Download records of genus *Eolophus* from 2001 to 2004 galah_config(email = \"your-email@email.com\")  galah_call() |>   galah_identify(\"Eolophus\") |>   galah_filter(year > 2000 & year < 2005) |>   atlas_occurrences()   # ---------- # Since galah 2.0.0, a pipe can start with a `request_` function. # This allows users to use `collapse()`, `compute()` and `collect()`.  # Get number of records of *Aves* from 2001 to 2004 by year request_data(type = \"occurrences-count\") |>   galah_identify(\"Aves\") |>   galah_filter(year > 2000 & year < 2005) |>   galah_group_by(year) |>   collect()  # Get information for all species in *Cacatuidae* family request_data(type = \"species\") |>   galah_identify(\"Cacatuidae\") |>   collect()    # Get metadata information about supported atlases in galah request_metadata(type = \"atlases\") |>   collect()  }"},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Get or set configuration options that control galah behaviour — galah_config","title":"Get or set configuration options that control galah behaviour — galah_config","text":"galah package supports large data downloads, also interfaces ALA requires users services provide registered email address reason downloading data. galah_config function provides way manage issues simply possible.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get or set configuration options that control galah behaviour — galah_config","text":"","code":"galah_config(...)"},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get or set configuration options that control galah behaviour — galah_config","text":"... Options can defined using form name = \"value\". Valid arguments : api-key string: registered API key (currently unused). atlas string: Living Atlas point , Australia default. Can organisation name, acronym, region (see show_all_atlases() admissible values) directory string: directory use cache. default temporary directory, means results cached within R session cleared automatically user exits R. user may wish set non-temporary directory caching across sessions. directory must exist file system. download_reason_id numeric string: \"download reason\" required. ALA services, either numeric ID (currently 0--13) string (see show_all(reasons) list valid ID codes names). default NA. ALA services require valid download_reason_id code, either specified directly associated R function. email string: email address registered chosen atlas. ALA, can register address. password string: registered password (GBIF ) run_checks logical: galah run checks filters columns. making lots requests sequentially, checks can slow process lead HTTP 500 errors, turned . Defaults TRUE. send_email logical: receive email query atlas_occurrences()? Defaults FALSE; can useful instances, example tracking DOIs assigned specific downloads later citation. username string: registered username (GBIF ) verbose logical: galah give verbose progress bars? Defaults FALSE.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get or set configuration options that control galah behaviour — galah_config","text":"galah_config(), list options. galah_config(...) called arguments, nothing returned configuration set.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get or set configuration options that control galah behaviour — galah_config","text":"","code":"if (FALSE) { # To download occurrence records, enter your email in `galah_config()`.  # This email should be registered with the atlas in question.  galah_config(email = \"your-email@email.com\")   # Turn on caching in your session galah_config(caching = TRUE)   # Some ALA services require that you add a reason for downloading data.  # Add your selected reason using the option `download_reason_id` galah_config(download_reason_id = 0)  # To look up all valid reasons to enter, use `show_all(reasons)` show_all(reasons)  # Make debugging in your session easier by setting `verbose = TRUE` galah_config(verbose = TRUE) }"},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query by specifying filters — galah_filter","title":"Narrow a query by specifying filters — galah_filter","text":"\"Filters\" arguments form field logical value used narrow number records returned specific query. example, common users request records particular year (year == 2020), return records except fossils (basisOfRecord != \"FossilSpecimen\"). result galah_filter() can passed filter argument atlas_occurrences(), atlas_species(), atlas_counts() atlas_media().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query by specifying filters — galah_filter","text":"","code":"galah_filter(..., profile = NULL)  # S3 method for data_request filter(.data, ...)  # S3 method for metadata_request filter(.data, ...)  # S3 method for files_request filter(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query by specifying filters — galah_filter","text":"... filters, form field logical value profile Use galah_apply_profile instead. .data object class files_request, created using request_files()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query by specifying filters — galah_filter","text":"tibble containing filter values.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query by specifying filters — galah_filter","text":"galah_filter uses non-standard evaluation (NSE), designed compatible possible dplyr::filter() syntax. statements passed galah_filter() (except profile argument) take form field - logical - value. Permissible examples include: = == (e.g. year = 2020) !=, e.g. year != 2020) > >= (e.g. year >= 2020) < <= (e.g. year <= 2020) statements (e.g. year == 2018 | year == 2020) statements (e.g. year >= 2000 & year <= 2020) cases R fail parse inputs single equals sign (=), particularly statements separated & |. problem can avoided using double-equals (==) instead. Notes behaviour Separating statements comma equivalent statement; Ergo galah_filter(year >= 2010 & year < 2020) galah_filter(year >= 2010, year < 2020). statements must include field name; galah_filter(year == 2010 | year == 2021) works, galah_filter(year == c(2010, 2021)), galah_filter(year == 2010 | 2021) fails. possible use object specify required values, e.g. year_value <- 2010; galah_filter(year > year_value) solr supports range queries text well numbers; valid: galah_filter(cl22 >= \"Tasmania\")","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query by specifying filters — galah_filter","text":"","code":"if (FALSE) { # Filter query results to return records of interest galah_call() |>   galah_filter(year >= 2019,                basisOfRecord == \"HumanObservation\") |>   atlas_counts()  # Alternatively, the same call using `dplyr` functions: request_data() |>   filter(year >= 2019,                basisOfRecord == \"HumanObservation\") |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query to within a specified area — galah_bbox","title":"Narrow a query to within a specified area — galah_bbox","text":"Restrict results specified area using galah_geolocate(). Areas can specified either polygons bounding boxes, depending type. Alternatively, users can call underlying functions directly via galah_bbox() galah_polygon(). Finally, possible use sf syntax calling st_crop(), synonymous galah_polygon(). calling galah_geolocate(), default type \"polygon\", narrows queries within area supplied POLYGON. Polygons must specified either sf object, 'well-known text' (WKT) string, shapefile. Shapefiles must simple accepted ALA. Alternatively, set type = \"bbox\" narrow queries within bounding box. Bounding boxes can extracted supplied sf object shapefile. bounding box can also supplied bbox object (via sf::st_bbox()) tibble/data.frame.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query to within a specified area — galah_bbox","text":"","code":"galah_bbox(...)  galah_geolocate(..., type = c(\"polygon\", \"bbox\"))  galah_polygon(...)  # S3 method for data_request st_crop(x, y, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query to within a specified area — galah_bbox","text":"... single sf object, WKT string shapefile. Bounding boxes can supplied tibble/data.frame bbox type string: one c(\"polygon\", \"bbox\"). Defaults \"polygon\". type = \"polygon\", multipolygon built via galah_polygon(). type = \"bbox\", multipolygon built via galah_bbox(). multipolygon used narrow query ALA. x object class data_request, created using galah_call() y valid Well-Known Text string (wkt), POLYGON MULTIPOLYGON","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query to within a specified area — galah_bbox","text":"length-1 string (class character) containing multipolygon WKT string representing area provided.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query to within a specified area — galah_bbox","text":"type = \"polygon\", WKT strings longer 10000 characters sf objects 500 vertices accepted ALA. polygons  may need simplified. type = \"bbox\", sf objects shapefiles converted bounding box query ALA.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query to within a specified area — galah_bbox","text":"","code":"if (FALSE) { # Search for records within a polygon using a shapefile location <- sf::st_read(\"path/to/shapefile.shp\") galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location) |>   atlas_counts()    # Search for records within the bounding box of a shapefile location <- sf::st_read(\"path/to/shapefile.shp\") galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location, type = \"bbox\") |>   atlas_counts()  # Search for records within a polygon using an `sf` object location <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" |>  sf::st_as_sfc() galah_call() |>   galah_identify(\"reptilia\") |>   galah_polygon(location) |>   atlas_counts()    # Alternatively, we can use `st_crop()` as a synonym for `galah_polygon()`.  # Hence the above example can be rewritten as: request_data() |>   identify(\"reptilia\") |>   st_crop(location) |>   count() |>   collect()     # Search for records using a Well-known Text string (WKT) wkt <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(wkt) |>   atlas_counts()  # Search for records within the bounding box extracted from an `sf` object location <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" |>   sf::st_as_sfc() galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location, type = \"bbox\") |>   atlas_counts()  # Search for records using a bounding box of coordinates b_box <- sf::st_bbox(c(xmin = 143, xmax = 148, ymin = -29, ymax = -28),                       crs = sf::st_crs(\"WGS84\")) galah_call() |>   galah_identify(\"reptilia\") |>   galah_geolocate(b_box, type = \"bbox\") |>   atlas_counts()  # Search for records using a bounding box in a `tibble` or `data.frame` b_box <- tibble::tibble(xmin = 148, ymin = -29, xmax = 143, ymax = -21) galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(b_box, type = \"bbox\") |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify fields to group when downloading record counts — galah_group_by","title":"Specify fields to group when downloading record counts — galah_group_by","text":"count.data_request() atlas_counts() support server-side grouping data. Grouping can used return record counts grouped multiple, valid fields (found search_all(fields)).","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify fields to group when downloading record counts — galah_group_by","text":"","code":"galah_group_by(...)  # S3 method for data_request group_by(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify fields to group when downloading record counts — galah_group_by","text":"... zero individual column names include .data object class data_request","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify fields to group when downloading record counts — galah_group_by","text":"arguments provided, returns data.frame columns name type, per select.data_request().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specify fields to group when downloading record counts — galah_group_by","text":"","code":"if (FALSE) { galah_call() |>    galah_group_by(basisOfRecord) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query by passing taxonomic identifiers — galah_identify","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"conducting search creating data query, common identify known taxon group taxa narrow records results returned.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"","code":"galah_identify(..., search = NULL)  # S3 method for data_request identify(x, ...)  # S3 method for metadata_request identify(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"... One scientific names. search galah_identify() now always search verify search terms; ergo argument ignored. x object class metadata_request, created using request_metadata()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"tibble containing identified taxa.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"galah_identify() used identify taxa want returned search data query. Users pass scientific names taxonomic identifiers pipes provide data biological group interest. good use search_taxa() search_identifiers() first check taxa provide galah_identify() return correct results.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"","code":"if (FALSE) { # Specify a taxon. A valid taxon will return an identifier. galah_identify(\"reptilia\")  # Specify more than one taxon at a time. galah_identify(\"reptilia\", \"mammalia\", \"aves\", \"pisces\")  # Use `galah_identify()` to narrow your queries galah_call() |>    galah_identify(\"Eolophus\") |>   atlas_counts()  # Within a pipe, `identify()` and `galah_identify()` are synonymous. # hence the following is identical to the previous example: request_data() |>   identify(\"Eolophus\") |>   count() |>   collect()  # If you know a valid taxon identifier, use `galah_filter()` instead. # (This was formerly supported by `galah_identify()` with `search = FALSE`) id <- \"https://biodiversity.org.au/afd/taxa/009169a9-a916-40ee-866c-669ae0a21c5c\" galah_call() |>    galah_filter(lsid == id) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify fields for occurrence download — galah_select","title":"Specify fields for occurrence download — galah_select","text":"GBIF partner nodes store content hundreds different fields, users often require thousands millions records time. reduce time taken download data, limit complexity resulting tibble, sensible restrict fields returned atlas_occurrences(). function allows easy selection fields, commonly-requested groups columns, following syntax shared dplyr::select(). full list available fields can viewed show_all(fields). Note select() galah_select() supported atlases allow downloads, exception GBIF, columns returned.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify fields for occurrence download — galah_select","text":"","code":"galah_select(..., group)  # S3 method for data_request select(.data, ..., group)"},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify fields for occurrence download — galah_select","text":"... zero individual column names include group string: (optional) name one column groups include. Valid options \"basic\", \"event\" \"assertions\" .data object class data_request, created using galah_call()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify fields for occurrence download — galah_select","text":"tibble specifying name type column include call atlas_counts() atlas_occurrences().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Specify fields for occurrence download — galah_select","text":"Calling argument group = \"basic\" returns following columns: decimalLatitude decimalLongitude eventDate scientificName taxonConceptID recordID dataResourceName occurrenceStatus Using group = \"event\" returns following columns: eventRemarks eventTime eventID eventDate samplingEffort samplingProtocol Using group = \"media\" returns following columns: multimedia multimediaLicence images videos sounds Using group = \"assertions\" returns quality assertion-related columns. list assertions shown show_all_assertions().","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specify fields for occurrence download — galah_select","text":"","code":"if (FALSE) { # Download occurrence records of *Perameles*,  # Only return scientificName and eventDate columns galah_config(email = \"your-email@email.com\") galah_call() |>   galah_identify(\"perameles\")|>   galah_select(scientificName, eventDate) |>   atlas_occurrences()  # Only return the \"basic\" group of columns and the basisOfRecord column galah_call() |>   galah_identify(\"perameles\") |>   galah_select(basisOfRecord, group = \"basic\") |>   atlas_occurrences()    # When used in a pipe, `galah_select()` and `select()` are synonymous. # Hence the previous example can be rewritten as: request_data() |>   identify(\"perameles\") |>   select(basisOfRecord, group = \"basic\") |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"Print galah objects — print_galah_objects","title":"Print galah objects — print_galah_objects","text":"version 2.0, galah supports several bespoke object types. Classes data_request, metadata_request files_request starting pipes download different types information. objects parsed using collapse() query_set object, contains set query objects, describing one API call. enacted using compute() /collect(). Finally, galah_config() creates object class galah_config (unsurprisingly) stores configuration information.","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print galah objects — print_galah_objects","text":"","code":"# S3 method for data_request print(x, ...)  # S3 method for files_request print(x, ...)  # S3 method for metadata_request print(x, ...)  # S3 method for query print(x, ...)  # S3 method for query_set print(x, ...)  # S3 method for galah_config print(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print galah objects — print_galah_objects","text":"x object appropriate class ... Arguments passed methods","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print galah objects — print_galah_objects","text":"Print return object; instead prints description object console","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print galah objects — print_galah_objects","text":"","code":"# The most common way to start a pipe is with `galah_call()` # later functions update the `data_request` object galah_call() |> # same as calling `request_data()`   filter(year >= 2020) |>   group_by(year) |>   count() #> Object of type `data_request` containing: #> • type occurrences-count #> • filter year >= 2020 #> • group_by year  # Metadata requests are formatted in a similar way request_metadata() |>   filter(field == basisOfRecord) |>   unnest() #> Object of type `metadata_request` containing: #> • type fields-unnest #> • filter field == basisOfRecord  # Queries are converted into a `query_set` by `collapse()` x <- galah_call() |> # same as calling `request_data()`   filter(year >= 2020) |>   count() |>   collapse() print(x) #> Object of class `query_set` containing 3 queries: #> • metadata/fields url: https://biocache-ws.ala.org.au/ws/index/fields #> • metadata/assertions url: https://biocache-ws.ala.org.au/ws/assertions/codes #> • data/occurrences-count url: https://biocache-ws.ala.org.au/ws/occurrences/sea...    # Each `query_set` contains one or more `query` objects x[[3]] #> Object of class query with type data/occurrences-count  #> url: https://biocache-ws.ala.org.au/ws/occurrences/search?fq=%28year%3A%5B2..."},{"path":"https://galah.ala.org.au/R/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. dplyr arrange, collapse, collect, compute, count, filter, group_by, select, slice_head graphics identify sf st_crop","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Search for record information — search_all","title":"Search for record information — search_all","text":"living atlases store huge amount information, beyond occurrence records main output. galah, one way users can investigate information searching specific option category type information interested . Functions prefixed search_ , displaying matches search term within valid options information specified suffix. search_all() helper function can searches within multiple types information search_ sub-functions. See Details () accepted values.","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search for record information — search_all","text":"","code":"search_all(type, query)  search_assertions(query)  search_apis(query)  search_atlases(query)  search_collections(query)  search_datasets(query)  search_fields(query)  search_identifiers(...)  search_licences(query)  search_lists(query)  search_profiles(query)  search_providers(query)  search_ranks(query)  search_reasons(query)  search_taxa(...)"},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search for record information — search_all","text":"type string specify type parameters searched. query string specifying search term. Searches case-sensitive. ... set strings tibble queried","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search for record information — search_all","text":"object class tbl_df data.frame (aka tibble) containing data match search query.","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search for record information — search_all","text":"five categories information, specific sub-functions look-type information. available types information search_all() :","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Search for record information — search_all","text":"Darwin Core terms https://dwc.tdwg.org/terms/","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search for record information — search_all","text":"","code":"if (FALSE) { # Search for fields that include the word \"date\" search_all(fields, \"date\")  # Search for fields that include the word \"marine\" search_all(fields, \"marine\")  # Search using a single taxonomic term # (see `?search_taxa()` for more information) search_all(taxa, \"Reptilia\") # equivalent  # Look up a unique taxon identifier # (see `?search_identifiers()` for more information) search_all(identifiers,             \"https://id.biodiversity.org.au/node/apni/2914510\")  # Search for species lists that match \"endangered\" search_all(lists, \"endangered\") # equivalent  # Search for a valid taxonomic rank, \"subphylum\" search_all(ranks, \"subphylum\")  # An alternative is to download the data and then `filter` it. This is  # largely synonymous, and allows greater control over which fields are searched. request_metadata(type = \"fields\") |>  collect() |>  dplyr::filter(grepl(\"date\", id)) }"},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Show valid record information — show_all","title":"Show valid record information — show_all","text":"living atlases store huge amount information, beyond occurrence records main output. galah, one way users can investigate information showing available options categories type information interested . Functions prefixed show_all_ , displaying valid options information specified suffix. show_all() helper function can display multiple types information show_all_ sub-functions.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show valid record information — show_all","text":"","code":"show_all(..., limit = NULL)  show_all_apis(limit = NULL)  show_all_assertions(limit = NULL)  show_all_atlases(limit = NULL)  show_all_collections(limit = NULL)  show_all_datasets(limit = NULL)  show_all_fields(limit = NULL)  show_all_licences(limit = NULL)  show_all_lists(limit = NULL)  show_all_profiles(limit = NULL)  show_all_providers(limit = NULL)  show_all_ranks(limit = NULL)  show_all_reasons(limit = NULL)"},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show valid record information — show_all","text":"... String showing type information requested. See Details () accepted values. limit Optional number values return. Defaults NULL, .e. records","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show valid record information — show_all","text":"object class tbl_df data.frame (aka tibble) containing data interest.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show valid record information — show_all","text":"five categories information, specific sub-functions look-type information. available types information show_all_ :","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Show valid record information — show_all","text":"Darwin Core terms https://dwc.tdwg.org/terms/","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show valid record information — show_all","text":"","code":"if (FALSE) { # See all supported atlases show_all(atlases)  # Show a list of all available data quality profiles show_all(profiles)  # Show a listing of all accepted reasons for downloading occurrence data show_all(reasons)  # Show a listing of all taxonomic ranks show_all(ranks)  # `show_all()` is synonymous with `request_metadata() |> collect()` request_metadata(type = \"fields\") |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Show or search for values within a specified field — show_values","title":"Show or search for values within a specified field — show_values","text":"Users may wish see specific values within chosen field, profile list narrow queries understand information interest. show_values() provides users values. search_values() allows users search specific values within specified field.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show or search for values within a specified field — show_values","text":"","code":"show_values(df)  search_values(df, query)"},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show or search for values within a specified field — show_values","text":"df search result search_fields(), search_profiles() search_lists(). query string specifying search term. case sensitive.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show or search for values within a specified field — show_values","text":"tibble values specified field, profile list.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show or search for values within a specified field — show_values","text":"Field contains categorical numeric values. example: field \"year\" contains values 2021, 2020, 2019, etc. field \"stateProvince\" contains values New South Wales, Victoria, Queensland, etc. used narrow queries galah_filter(). Profile consists many individual quality filters. example, \"ALA\" profile consists values: Exclude records spatial validity FALSE Exclude records latitude value zero Exclude records longitude value zero List contains list species, usually taxonomic name. example, Endangered Plant species list contains values: Acacia curranii (Curly-bark Wattle) Brachyscome papillosa (Mossgiel Daisy) Solanum karsense (Menindee Nightshade)","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show or search for values within a specified field — show_values","text":"","code":"if (FALSE) { # Show values in field 'cl22' search_fields(\"cl22\") |>    show_values()  # This is synonymous with `request_metadata() |> unnest()`. # For example, the previous example can be run using: request_metadata() |>   filter(field == \"cl22\") |>   unnest() |>   collect()   # Search for any values in field 'cl22' that match 'tas' search_fields(\"cl22\") |>    search_values(\"tas\")  # See items within species list \"dr19257\" search_lists(\"dr19257\") |>    show_values() }"},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset first rows of data_request — slice_head.data_request","title":"Subset first rows of data_request — slice_head.data_request","text":"simple function set limit argument atlas_counts() using dplyr syntax. galah 2.0.0, slice_head() supported queries type occurrences-count(), metadata requests. Note also slice_head() lazily evaluated; affects query run compute() (likely) collect().","code":""},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset first rows of data_request — slice_head.data_request","text":"","code":"# S3 method for data_request slice_head(.data, ..., n, prop, by = NULL)  # S3 method for metadata_request slice_head(.data, ..., n, prop, by = NULL)"},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset first rows of data_request — slice_head.data_request","text":".data object class data_request, created using galah_call() ... currently ignored n number rows returned. data grouped (using group_by), operation performed group. prop currently ignored, added later currently ignored","code":""},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset first rows of data_request — slice_head.data_request","text":"","code":"if (FALSE) { # Limit number of rows returned to 3. # In this case, our query returns the top 3 years with most records. galah_call() |>   identify(\"perameles\") |>   filter(year > 2010) |>   group_by(year) |>   count() |>   slice_head(n = 3) |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Non-generic tidyverse functions — tidyverse_functions","title":"Non-generic tidyverse functions — tidyverse_functions","text":"Several useful functions tidyverse packages generic, meaning can define class-specific versions functions implement galah; examples include filter(), select() group_by(). However, also functions defined within tidyverse packages generic. cases re-implemented functions galah. consequence supporting consistent syntax tidyverse, cost potentially introducing conflicts. can avoided using :: operator required (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Non-generic tidyverse functions — tidyverse_functions","text":"","code":"desc(...)  unnest(.query)"},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Non-generic tidyverse functions — tidyverse_functions","text":"... column order .query object class metadata_request","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Non-generic tidyverse functions — tidyverse_functions","text":"galah::desc() returns tibble used arrange.data_request() arrange rows query. galah::unnest() returns object class metadata_request.","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Non-generic tidyverse functions — tidyverse_functions","text":"following functions included: desc() (dplyr): Use within arrange() specify arrangement descending unnest() (tidyr): Use 'drill ' nested information fields, lists, profiles, taxa galah versions use lazy evaluation.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Non-generic tidyverse functions — tidyverse_functions","text":"","code":"if (FALSE) { # Arrange grouped record counts by descending year galah_call() |>   identify(\"perameles\") |>   filter(year > 2019) |>   count() |>   arrange(galah::desc(year)) |>   collect()  # Return values of field `basisOfRecord` request_metadata() |>    galah::unnest() |>    filter(field == basisOfRecord) |>    collect()    # Using `galah::unnest()` in this way is equivalent to: show_all(fields, \"basisOfRecord\") |>    show_values() }"},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-200","dir":"Changelog","previous_headings":"","what":"galah 2.0.0","title":"galah 2.0.0","text":"CRAN release: 2023-11-20","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"object-oriented-programming-2-0-0","dir":"Changelog","previous_headings":"","what":"Object-oriented programming","title":"galah 2.0.0","text":"galah 2.0.0 now built around object-oriented programming principles. architectural change makes query building galah modular transparent. result, galah 2.0.0 allows easier debugging gives users options advanced query building (information, see “Object-oriented programming” vignette galah website) (#183).","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"collapse-compute-collect-2-0-0","dir":"Changelog","previous_headings":"","what":"collapse(), compute(), collect()","title":"galah 2.0.0","text":"New underlying architecture behind every function pings API galah separates query building 3 stages: Convert object query_set lists APIs pinged (collapse()), send queries required APIs (compute()), return data tibble (collect()) (#183). New architecture solves timing-issue downloading large numbers records (#180, #192) galah_filter(), galah_select() related functions now evaluated lazily; API calls made compute() called, meaning earlier programming stages faster easier debug.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"major-improvements-to-galah_filter-2-0-0","dir":"Changelog","previous_headings":"","what":"Major improvements to galah_filter()","title":"galah 2.0.0","text":"galah_filter() upgraded use hierarchical parsing architecture suggested Advanced R. result, galah_filter() faster evaluates expressions consistently (#196, #169) galah_filter() now supports .na, !, c() & %% (#196)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-2-0-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 2.0.0","text":"potions package underlies galah_config() better options management (#193) Addition slice_head() desc() masked functions use galah atlas_counts() query. New vignettes added advanced taxonomic, spatial temporal filtering (#42)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-2-0-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 2.0.0","text":"Fixed parsing | galah_filter() (#169) show_values() errors nicely API (#184) Sporadic atlas$region error loading galah fixed potions package implementation (#178) DOI longer missing attribute atlas_occurrences(mint_doi = TRUE) (#182) Fixed bug order fields group_by() sometimes caused error (#201) Fixed parsing ampersands (&) query results (#203) galah builds correct data_request object wrapped function (#207)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-154","dir":"Changelog","previous_headings":"","what":"galah 1.5.4","title":"galah 1.5.4","text":"CRAN release: 2023-10-14 Patch release fix minor issues devel systems CRAN.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-153","dir":"Changelog","previous_headings":"","what":"galah 1.5.3","title":"galah 1.5.3","text":"CRAN release: 2023-07-01 Minor release address CRAN issues. Last release 2.0.0.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-152","dir":"Changelog","previous_headings":"","what":"galah 1.5.2","title":"galah 1.5.2","text":"CRAN release: 2023-03-10 Minor release resolve issues CRAN, recent bugs.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.5.2","text":"Prevent error providing tibble input search_taxa() (e.g., resolve homonyms, #168) Better error message email address required, given (#179) Add informative message users call galah_select() atlas = GBIF (supported; #181) Ensure DOIs added downloads requested (#182) Improve tests avoid flagging issues CRAN one atlases (#184) Resolve problem queries replaced ... galah_filter() (#186)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-151","dir":"Changelog","previous_headings":"","what":"galah 1.5.1","title":"galah 1.5.1","text":"CRAN release: 2023-01-13","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"mask-function-names-from-other-packages-1-5-1","dir":"Changelog","previous_headings":"","what":"Mask function names from other packages","title":"galah 1.5.1","text":"experimental feature version 1.5.1 ability call functions packages (#161), synonyms galah_ functions. : identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() count() (dplyr) synonym atlas_counts() implemented S3 methods objects class data_request, created galah_call(). Hence new function names work piped galah_call().","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"experimental-support-for-gbif-queries-1-5-1","dir":"Changelog","previous_headings":"","what":"Experimental support for GBIF queries","title":"galah 1.5.1","text":"Global Biodiversity Information Facility (GBIF) umbrella organisation atlases supply data. Hence logical able query GBIF ’s “nodes” (.e. living atlases) via common API. Supported functions : search_taxa galah_identify name matching show_all(fields) show_all(assertions) show_all() calls give ‘collections’ information limited 20 records default, GBIF datasets often huge. search_all() generally reliable show_values() GBIF field galah_filter galah_group_by (therefore filter group_by(), see ), galah_select. atlas_counts() (therefore count(), see ) atlas_occurrences() & atlas_species(); implemented via ‘downloads’ system, meaning queries can larger, may slow current implementation experimental back-end changes expected future. Users require stable implementation use {rgbif} package.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-5-1","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.5.1","text":"galah_config() gains print function, now uses fuzzy matching atlas field match region, organisation acronym (defined show_all(atlases)). example use case match organisations via acronyms, e.g. galah_config(atlas = \"ALA\"). Improved support data Spain via gbif.es (name-matching, lists, spatial) Swapped provider data France; formerly gbif.fr, now OpenObs, per advice maintainers Reading data disk now uses readr::read_csv place utils::read.csv improved speed show_all (associated sub-functions) gain limit argument, set NULL (.e. limit) default galah longer imports data.table, since function previously used package (rbindlist) duplicated dplyr::bind_rows Help files now built without markdown improved speed (mainly building)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-1","dir":"Changelog","previous_headings":"","what":"Bug fixes:","title":"galah 1.5.1","text":"New function url_paginate() handle cases pagination needed, total data length unknown (e.g. show_all_lists(), #170). galah_select(group = \"assertions\") always enacted properly atlas_occurrences, won’t lead overly long urls (#137). called without field names, recordID added avoid triggering ‘default’ set columns. atlas_species works minor changes API; requires registered email function","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-150","dir":"Changelog","previous_headings":"","what":"galah 1.5.0","title":"galah 1.5.0","text":"CRAN release: 2022-10-27","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"expanded-support-for-querying-other-international-living-atlases-1-5-0","dir":"Changelog","previous_headings":"","what":"Expanded support for querying other International Living Atlases","title":"galah 1.5.0","text":"Support complex queries 10 Living Atlases, including France, Guatemala Sweden. Complex queries can constructed using galah_call(), filtered galah_ functions, downloaded atlas_ functions. Previously, functionality possible queries ALA (#126)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"collect_media-1-5-0","dir":"Changelog","previous_headings":"","what":"collect_media()","title":"galah 1.5.0","text":"Show available media: atlas_media() returns tibble available media files Download media: collect_media() downloads list media atlas_media() local machine Download image thumbnails specifying type = \"thumbnails\" collect_media() (#140)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"updates-to-galah_geolocate-1-5-0","dir":"Changelog","previous_headings":"","what":"Updates to galah_geolocate()","title":"galah 1.5.0","text":"galah_geolocate() now supports filtering queries using polygons bounding boxes. Overall improvements bug fixes galah_geolocate() new internal functions galah_polygon() galah_bbox() (#125)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"show_all-search_all--show_values-search_values-1-5-0","dir":"Changelog","previous_headings":"","what":"show_all(), search_all() & show_values(), search_values()","title":"galah 1.5.0","text":"Experimental functions show_all() search_all() flexible look-functions can search information {galah}, rather separate search_/show_all_ functions (e.g. search_fields(), search_atlases(), show_all_fields(), show_all_reasons(), etc) (#127, #132) Added look-support collections, data providers, data resources, licenses, APIs species lists (e.g. list endangered species) (#126, #127, #132, #151) Checking valid values within fields, profiles species lists improved functions show_values() & search_values() (#131)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-5-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.5.0","text":"Apply data quality profiles pipe galah_apply_profile() function (#130) Improved internal consistency galah_ functions (#133) galah_geolocate() longer depends archived {wellknown} package (#141) Added support queries exclude/include missing values (e.g. galah_filter(species != \"\") galah_filter(species == \"\") (#143) Re-download previously-minted DOI collect_doi() (#140) checks ensure galah fails gracefully API fails (#157)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.5.0","text":"galah_select() longer adds “basic” group columns automatically (#128) galah_config() doesn’t display incorrect preserve = TRUE message (#136) Fixes error selecting assertion columns galah_select() (#137) atlas_counts() atlas_occurrences() longer return different record numbers field empty (#138) atlas_media() results longer differ results returned galah_filter() & atlas_counts() (#151)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-140","dir":"Changelog","previous_headings":"","what":"galah 1.4.0","title":"galah 1.4.0","text":"CRAN release: 2022-01-24","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"revamped-syntax-1-4-0","dir":"Changelog","previous_headings":"","what":"Revamped syntax","title":"galah 1.4.0","text":"ala_ functions renamed use prefix atlas_. change reflects functionality international atlases (.e., atlas_occurrences, atlas_counts, atlas_species, atlas_media, atlas_taxonomy, atlas_citation) (#103) select_taxa replaced 3 functions: galah_identify, search_taxa search_identifiers. galah_identify used building data queries, whereas search_taxa search_identifiers now exclusively used search taxonomic information. Syntax changes intended reflect usage expected output (#112, #122) select_ functions renamed use prefix galah_. Specifically, galah_filter, galah_select galah_geolocate replace select_filters, select_columns select_locations. syntax changes reflect move towards consistency dplyr naming functionality (#101, #108) find_ functions provide listing possible values renamed show_all_ (.e., show_all_profiles, show_all_ranks, show_all_atlases, show_all_cached_files, show_all_fields, show_all_reasons). find_ functions require input return specific results renamed search_ (.e., search_field_values, search_profile_attributes) (#112, #113)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_group_by-1-4-0","dir":"Changelog","previous_headings":"","what":"galah_group_by","title":"galah 1.4.0","text":"Group fields using galah_group_by(), groups summarises record counts based categorical field values, similar dplyr::group_by() (#90, #95)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_down_to-1-4-0","dir":"Changelog","previous_headings":"","what":"galah_down_to","title":"galah 1.4.0","text":"Select taxonomic level taxonomic tree go galah_down_to() + atlas_taxonomy(), uses tidy evaluation like galah_ functions (#101, #120)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"pipe-queries-using-galah_call-1-4-0","dir":"Changelog","previous_headings":"","what":"Pipe queries using galah_call","title":"galah 1.4.0","text":"Build data queries using piping syntax (.e., |>, %>%) first using galah_call(), narrowing queries galah_ functions finishing queries atlas_ function (#60, #120). S3 methods now implemented functions allow piping (#40)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-4-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.4.0","text":"Improved error messages using {glue} {rlang} (#117) Revamped syntax functions return output tibbles (#110, #118) Pass vectors galah_filter (#91, #92) Cache valid fields faster field look (#73, #116) New vignettes updated syntax (#104, #105), plus improvements previous vignettes. Updated R Markdown-style documentation added warnings deprecated functions (#113, #121)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-4-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.4.0","text":"galah longer returns error ALA system /API fails (#102, #119) search_taxa returns correct IDs search terms parentheses (#96) search_taxa returns best-fit taxonomic result ranks specified data.frame tibble (#115)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-131","dir":"Changelog","previous_headings":"","what":"galah 1.3.1","title":"galah 1.3.1","text":"CRAN release: 2021-08-21","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"search_taxonomy-renamed-to-ala_taxonomy-1-3-1","dir":"Changelog","previous_headings":"","what":"search_taxonomy() renamed to ala_taxonomy()","title":"galah 1.3.1","text":"bug fix: ala_taxonomy longer fails nodes ranked informal unranked (#86) function now returns tree built using data.tree package change function name required greater consistency data-providing functions galah","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"vignettes-1-3-1","dir":"Changelog","previous_headings":"","what":"Vignettes","title":"galah 1.3.1","text":"vignettes now pre-compiled avoid failing CRAN (#85) expanded vignette navigating taxonomic information (#42)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-130","dir":"Changelog","previous_headings":"","what":"galah 1.3.0","title":"galah 1.3.0","text":"CRAN release: 2021-08-06","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_config-1-3-0","dir":"Changelog","previous_headings":"","what":"galah_config()","title":"galah 1.3.0","text":"ala_config() renamed galah_config() improve internal consistency (#68)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"search_taxonomy-1-3-0","dir":"Changelog","previous_headings":"","what":"search_taxonomy()","title":"galah 1.3.0","text":"search_taxonomy() provides means search taxonomic names check results ‘correct’ proceeding download data via ala_occurrences(), ala_species() ala_counts() (e.g., ambiguous homonymous) (#64 #75) search_taxonomy() returns information author authority taxonomic names (#79) search_taxonomy() consistently orders column names, including correct taxonomic order rank (#81)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"caching-helper-functions-1-3-0","dir":"Changelog","previous_headings":"","what":"Caching helper functions","title":"galah 1.3.0","text":"find_cached_files() lists user cached files stored metadata (#57) clear_cached_files() removes previously cached files stored metadata (#71) ala_counts(), ala_occurrences(), ala_media() ala_species() now refresh_cache argument remove previously cached files replace current query (#71)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-3-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.3.0","text":"Cache files saved RDS format, making query attributes easier find, including data DOI, search url (#55, #32, #28) ala_media() caches media metadata galah_config(caching = TRUE) search_fields() allows user pass qid argument (#59) Users can now optionally skip filter count validation checks spatial biocache web services setting galah_config(run_checks = FALSE). helps users avoid slowing data request download speeds many requests made quick succession via galah_filter() ala_occurrences() (#61, #80) ala_counts(), select_columns() search_fields() now use match.arg approximate strings fuzzy matching (#66) Better handling cache errors improved error messages (#70)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-3-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.3.0","text":"select_columns(group = 'assertions') now sends qa = includeall ALA web service API return assertion columns (#48) ala_occurrences() returns data DOI ala_occurrences(mint_doi = TRUE) re-downloads data called multiple times (#56) ala_occurrences() longer converts field names -CAPS camelCase (#62)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-120","dir":"Changelog","previous_headings":"","what":"galah 1.2.0","title":"galah 1.2.0","text":"CRAN release: 2021-07-02","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"living-atlases-1-2-0","dir":"Changelog","previous_headings":"","what":"Living Atlases","title":"galah 1.2.0","text":"ala_config() allows users specify international Atlas download data (#21)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-2-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.2.0","text":"ala_media() includes file path downloaded media returned metadata (#22) Data returned ala_occurrences() contains search_url used download records; takes user website search page (#32) ala_species() provides helpful error species found (#39) Data quality filters created using specific web service argument, rather constructing filters attributes (#37) select_taxa() optional all_ranks argument return intermediate rank information (#35)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-2-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.2.0","text":"R > 4.0.0 now required (#43, #45) select_taxa() behaves expected character strings 32 36 characters provided (#23) Caching functionality ala_occurrences() uses columns expected (#30) galah_filter() negates assertion filters required, fixing issue assertion values ignored (#27) select_taxa() longer throws error queries one term differing number columns return value (#41) ala_counts() returns data.frame consistent column classes group_by parameter called multiple times ala_config(caching = TRUE) (#47) ala_ functions fail gracefully non-id character string passed (#49)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-110","dir":"Changelog","previous_headings":"","what":"galah 1.1.0","title":"galah 1.1.0","text":"CRAN release: 2021-05-05","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"downloading-media-1-1-0","dir":"Changelog","previous_headings":"","what":"Downloading media","title":"galah 1.1.0","text":"ala_media() now takes select_ arguments ala_ functions (#18) Filtering media metadata e.g. licence type possible (#19) search_fields now media type argument option Performance improvement download times (#13) Progress bar displayed downloads verbose == TRUE (#8) media download types supported","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"select_-functions-1-1-0","dir":"Changelog","previous_headings":"","what":"select_ functions","title":"galah 1.1.0","text":"galah_location auto-detects type argument provided takes single argument, query, place sf wkt (#17) select_taxa auto-detects type argument provided takes single argument, query, place term term_type (#16)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-1-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.1.0","text":"Provide useful error message empty occurrence download (#7) ala_counts uses group_by field name returned data.frame column name (#6) ala_occurrences sends sourceId parameter ALA (#5) search_fields provides helpful error invalid types (#11)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-100","dir":"Changelog","previous_headings":"","what":"galah 1.0.0","title":"galah 1.0.0","text":"CRAN release: 2021-04-06 First version galah, built earlier functionality ALA4R package.","code":""}]
+[{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"set-organisation","dir":"Articles","previous_headings":"","what":"Set Organisation","title":"Choosing an atlas","text":"Set atlas want use changing atlas argument galah_config(). atlas argument can accept full name, acronym, region select given atlas, available via show_all(atlases). value provided, automatically update galah’s server configuration selected atlas. default atlas Australia. intend download records, may need register user profile relevant atlas first.","code":"galah_config(atlas = \"GBIF.es\", email = \"your_email_here\")"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"look-up-information","dir":"Articles","previous_headings":"","what":"Look up Information","title":"Choosing an atlas","text":"can use look-functions find useful information Atlas set. Available information may vary Living Atlas.","code":"galah_config(atlas = \"Guatemala\") ## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala] show_all(datasets) ## # A tibble: 1,283 × 3 ##    id     name                                                                                                                     uri   ##    <chr>  <chr>                                                                                                                    <chr> ##  1 dr1440 A catalogue of the Heteroptera (Hemiptera) or true bugs of Argentina                                                     http… ##  2 dr1436 A cybercatalogue of American sand fly types (Diptera, Psychodidae, Phlebotominae) deposited at the Natural History Muse… http… ##  3 dr1226 A distinctive new species of biting midge in the subgenus Euprojoannisia Brèthes from Mexico with new records of Neotro… http… ##  4 dr321  A Distribution and Taxonomic Reference Dataset of Geranium (Geraniaceae) in the New World                                http… ##  5 dr1285 A geographic distribution database of the cassava whitefly complex (Hemiptera, Aleyrodidae) and their associated parasi… http… ##  6 dr12   A global database for the distributions of crop wild relatives                                                           http… ##  7 dr467  A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera Tenebrionidae)                                    http… ##  8 dr1061 A Monographic Revision of the Genus Hoplopyga Thomson, 1880 (Coleoptera: Scarabaeidae: Cetoniinae: Gymnetini)            http… ##  9 dr1570 A new Anomiopus Westwood (Coleoptera: Scarabaeidae: Scarabaeinae) from the Mayan Biosphere Reserve, Petén, Guatemala     http… ## 10 dr1177 A new Central American genus of pleasing fungus beetles (Coleoptera: Erotylidae) from the Ischyrus-Megischyrus complex   http… ## # ℹ 1,273 more rows show_all(fields) ## # A tibble: 127 × 3 ##    id                   description        type   ##    <chr>                <chr>              <chr>  ##  1 all_image_url        <NA>               fields ##  2 assertion_user_id    Assertions by user fields ##  3 assertions           Record issues      fields ##  4 assertions_missing   <NA>               fields ##  5 assertions_passed    <NA>               fields ##  6 assertions_unchecked <NA>               fields ##  7 basis_of_record      Record type        fields ##  8 catalogue_number     Catalogue Number   fields ##  9 cl10011              <NA>               fields ## 10 class                Class              fields ## # ℹ 117 more rows search_all(fields, \"year\") ## # A tibble: 2 × 3 ##   id              description      type   ##   <chr>           <chr>            <chr>  ## 1 year            Year             fields ## 2 occurrence_year Date (by decade) fields search_taxa(\"lagomorpha\") ## # A tibble: 1 × 8 ##   search_term scientific_name taxon_concept_id rank  kingdom  phylum   class    order      ##   <chr>       <chr>           <chr>            <chr> <chr>    <chr>    <chr>    <chr>      ## 1 lagomorpha  Lagomorpha      785              order Animalia Chordata Mammalia Lagomorpha"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"download-data","dir":"Articles","previous_headings":"","what":"Download data","title":"Choosing an atlas","text":"can build queries normally galah. taxonomic queries, use search_taxa() make sure searches returning correct taxonomic data. Download species occurrence records atlases atlas_occurrences()","code":"galah_config(atlas = \"United Kingdom\") ## Atlas selected: National Biodiversity Network (NBN) [United Kingdom] search_taxa(\"vlps\")   # Returns no data due to misspelling ## # A tibble: 0 × 0 search_taxa(\"vulpes\") # Returns data ## # A tibble: 1 × 12 ##   search_term scientific_name scientific_name_authorship taxon_concept_id rank  kingdom  phylum   class    order family genus superclass ##   <chr>       <chr>           <chr>                      <chr>            <chr> <chr>    <chr>    <chr>    <chr> <chr>  <chr> <chr>      ## 1 vulpes      Vulpes          Frisch, 1775               NBNSYS0000138878 genus Animalia Chordata Mammalia Carn… Canid… Vulp… Tetrapoda galah_call() |>   galah_identify(\"vulpes\") |>   galah_filter(year > 2010) |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 124167 galah_config(atlas = \"Guatemala\") ## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala] galah_call() |>   galah_identify(\"Lagomorpha\") |>   galah_filter(year <= 1980) |>   galah_select(taxon_name, year) |>   atlas_occurrences() ## # A tibble: 4 × 2 ##   taxon_name                       year ##   <chr>                           <dbl> ## 1 Erinnyis ello subsp. ello        1973 ## 2 Manduca rustica Fabricius, 1775  1930 ## 3 Manduca rustica Fabricius, 1775  1930 ## 4 Aellopos titan Burmeister, 1856  1971"},{"path":"https://galah.ala.org.au/R/articles/choosing_an_atlas.html","id":"complex-queries-with-multiple-atlases","dir":"Articles","previous_headings":"","what":"Complex queries with multiple Atlases","title":"Choosing an atlas","text":"also possible create complex queries return data multiple Living Atlases. example, setting atlases within loop galah_config() purrr::map() allows us return total number species records Living Atlas one table.","code":"library(purrr) library(tibble) library(dplyr) library(gt)  atlases <- show_all(atlases)  counts <- map(atlases$region,    function(x){     galah_config(atlas = x)     atlas_counts() })  atlases |>     select(region, institution) |>     bind_cols(bind_rows(counts)) |>     arrange(desc(count)) |>     gt() |>     fmt_number(column = count)"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"record-counts","dir":"Articles","previous_headings":"","what":"Record counts","title":"Download data","text":"atlas_counts() provides summary counts records specified atlas, without needing download records. addition filter arguments, optional group_by argument, provides counts binned requested field.","code":"galah_config(atlas = \"Australia\") # Total number of records in the ALA atlas_counts() ## # A tibble: 1 × 1 ##       count ##       <int> ## 1 132342396 galah_call() |>   galah_group_by(kingdom) |>   atlas_counts() ## # A tibble: 11 × 2 ##    kingdom       count ##    <chr>         <int> ##  1 Animalia  101442503 ##  2 Plantae    26136825 ##  3 Fungi       2293753 ##  4 Chromista   1021828 ##  5 Protista     352983 ##  6 Bacteria     113118 ##  7 Eukaryota      8826 ##  8 Protozoa       4765 ##  9 Archaea        4119 ## 10 Virus          2307 ## 11 Viroid          103"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"species-lists","dir":"Articles","previous_headings":"","what":"Species lists","title":"Download data","text":"common use case atlas data identify species occur specified region, time period, taxonomic group. atlas_species() similar search_taxa, returns taxonomic information unique identifiers tibble. differs able return information taxonomic levels species; also flexible supporting filtering:","code":"species <- galah_call() |>   galah_identify(\"Rodentia\") |>   galah_filter(stateProvince == \"Northern Territory\") |>   atlas_species()    species |> head() ## # A tibble: 6 × 10 ##   kingdom  phylum   class    order    family  genus        species                     author            species_guid    vernacular_name ##   <chr>    <chr>    <chr>    <chr>    <chr>   <chr>        <chr>                       <chr>             <chr>           <chr>           ## 1 Animalia Chordata Mammalia Rodentia Muridae Pseudomys    Pseudomys delicatulus       (Gould, 1842)     https://biodiv… Delicate Mouse  ## 2 Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Mesembriomys gouldii        (J.E. Gray, 1843) https://biodiv… Black-footed T… ## 3 Animalia Chordata Mammalia Rodentia Muridae Zyzomys      Zyzomys argurus             (Thomas, 1889)    https://biodiv… Common Rock-rat ## 4 Animalia Chordata Mammalia Rodentia Muridae Pseudomys    Pseudomys hermannsburgensis (Waite, 1896)     https://biodiv… Sandy Inland M… ## 5 Animalia Chordata Mammalia Rodentia Muridae Melomys      Melomys burtoni             (Ramsay, 1887)    https://biodiv… Grassland Melo… ## 6 Animalia Chordata Mammalia Rodentia Muridae Notomys      Notomys alexis              Thomas, 1922      https://biodiv… Spinifex Hoppi…"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"occurrence-data","dir":"Articles","previous_headings":"","what":"Occurrence data","title":"Download data","text":"download occurrence data need specify email galah_config(). email must associated active ALA account. See information config section Download occurrence records Eolophus roseicapilla","code":"galah_config(email = \"your_email@email.com\", atlas = \"Australia\") occ <- galah_call() |>   galah_identify(\"Eolophus roseicapilla\") |>   galah_filter(     stateProvince == \"Australian Capital Territory\",     year >= 2010,     profile = \"ALA\"   ) |>   galah_select(institutionID, group = \"basic\") |>   atlas_occurrences() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. ## Retrying in 8 seconds. occ |> head() ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 0000a928-d756-42… Eolophus rose… https://biodi…           -35.6             149. 2017-04-19 09:11:00 PRESENT          eBird Australia  ## 2 0001bc78-d2e9-48… Eolophus rose… https://biodi…           -35.2             149. 2019-08-13 15:13:00 PRESENT          eBird Australia  ## 3 0002064f-08ea-42… Eolophus rose… https://biodi…           -35.3             149. 2014-03-16 06:48:00 PRESENT          eBird Australia  ## 4 00022dd2-9f85-48… Eolophus rose… https://biodi…           -35.3             149. 2022-05-08 08:20:00 PRESENT          eBird Australia  ## 5 0002cc35-8d5a-4d… Eolophus rose… https://biodi…           -35.3             149. 2015-11-01 08:00:00 PRESENT          eBird Australia  ## 6 00030a8c-082f-44… Eolophus rose… https://biodi…           -35.3             149. 2022-01-06 11:47:00 PRESENT          eBird Australia  ## # ℹ 1 more variable: institutionID <lgl>"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"media-metadata","dir":"Articles","previous_headings":"","what":"Media metadata","title":"Download data","text":"addition text data describing individual occurrences attributes, ALA stores images, sounds videos associated given record. Metadata records can downloaded R using atlas_media() set filters data download functions. actually download media files computer, use [collect_media()].","code":"media_data <- galah_call() |>   galah_identify(\"Eolophus roseicapilla\") |>   galah_filter(     year == 2020,     cl22 == \"Australian Capital Territory\") |>   atlas_media() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. media_data |> head() ## # A tibble: 6 × 19 ##   media_id recordID scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>    <chr>    <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 ff8322d… 003a192… Eolophus rose… https://biodi…           -35.3             149. 2020-09-12 06:11:00 PRESENT          iNaturalist Aus… ## 2 c66fc81… 015ee7c… Eolophus rose… https://biodi…           -35.4             149. 2020-08-09 05:11:00 PRESENT          iNaturalist Aus… ## 3 fe6d7b9… 05e86b7… Eolophus rose… https://biodi…           -35.4             149. 2020-11-13 22:29:00 PRESENT          NatureMapr       ## 4 2f4d32c… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## 5 7340741… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## 6 89171c4… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 01:50:00 PRESENT          iNaturalist Aus… ## # ℹ 10 more variables: multimedia <chr>, images <chr>, videos <lgl>, sounds <lgl>, creator <chr>, license <chr>, mimetype <chr>, ## #   width <int>, height <int>, image_url <chr>"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"taxonomic-trees","dir":"Articles","previous_headings":"","what":"Taxonomic trees","title":"Download data","text":"atlas_taxonomy provides way build taxonomic trees one clade another using service’s internal taxonomy. Specify taxonomic level tree go galah_filter() using rank argument.","code":"galah_call() |>   galah_identify(\"chordata\") |>   galah_filter(rank == class) |>   atlas_taxonomy() ## # A tibble: 19 × 4 ##    name            rank      parent_taxon_concept_id                                                   taxon_concept_id                  ##    <chr>           <chr>     <chr>                                                                     <chr>                             ##  1 Chordata        phylum    <NA>                                                                      https://biodiversity.org.au/afd/… ##  2 Cephalochordata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  3 Tunicata        subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  4 Appendicularia  class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  5 Ascidiacea      class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  6 Thaliacea       class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/… ##  7 Vertebrata      subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/… ##  8 Agnatha         informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/… ##  9 Myxini          informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/… ## 10 Petromyzontida  informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/… ## 11 Gnathostomata   informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/… ## 12 Amphibia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 13 Aves            class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 14 Mammalia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 15 Pisces          informal  https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/… ## 16 Actinopterygii  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 17 Chondrichthyes  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 18 Sarcopterygii   class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/… ## 19 Reptilia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"configuring-galah","dir":"Articles","previous_headings":"","what":"Configuring galah","title":"Download data","text":"Various aspects galah package can customized.","code":""},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"email","dir":"Articles","previous_headings":"Configuring galah","what":"Email","title":"Download data","text":"download occurrence records, need provide email address registered service want use (e.g. ALA can create account ). email registered, stored config:","code":"galah_config(email = \"myemail@gmail.com\")"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"setting-your-directory","dir":"Articles","previous_headings":"Configuring galah","what":"Setting your directory","title":"Download data","text":"default, galah stores downloads temporary folder, meaning local files automatically deleted R session ended. behaviour can altered downloaded files preserved setting directory non-temporary location.","code":"galah_config(directory = \"example/dir\")"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"setting-the-download-reason","dir":"Articles","previous_headings":"Configuring galah","what":"Setting the download reason","title":"Download data","text":"ALA requires provide reason downloading occurrence data (via galah atlas_occurrences() function). reason set “scientific research” default, can change using galah_config(). See show_all_reasons() valid download reasons.","code":"galah_config(download_reason_id = your_reason_id)"},{"path":"https://galah.ala.org.au/R/articles/download_data.html","id":"debugging","dir":"Articles","previous_headings":"Configuring galah","what":"Debugging","title":"Download data","text":"things aren’t working expected, detail (particularly web requests caching behaviour) can obtained setting verbose configuration option:","code":"galah_config(verbose = TRUE)"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_all-search_all","dir":"Articles","previous_headings":"","what":"show_all() & search_all()","title":"Look up information","text":"galah 1.5.0, two simplified functions look information: show_all() search_all(). individual functions able return types information one place, rather using specific sub-functions look information. example, show available Living Atlases supported: search specific available Living Atlas: show fields: search specific field: list information types can used show_all() search_all():","code":"show_all(atlases) ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk search_all(atlases, \"Spain\") ## # A tibble: 1 × 4 ##   region institution acronym url                 ##   <chr>  <chr>       <chr>   <chr>               ## 1 Spain  GBIF Spain  GBIF.es https://www.gbif.es show_all(fields) ## # A tibble: 646 × 3 ##    id                  description               type   ##    <chr>               <chr>                     <chr>  ##  1 _nest_parent_       <NA>                      fields ##  2 _nest_path_         <NA>                      fields ##  3 _root_              <NA>                      fields ##  4 abcdTypeStatus      <NA>                      fields ##  5 acceptedNameUsage   Accepted name             fields ##  6 acceptedNameUsageID Accepted name             fields ##  7 accessRights        Access rights             fields ##  8 annotationsDoi      <NA>                      fields ##  9 annotationsUid      Referenced by publication fields ## 10 assertionUserId     Assertions by user        fields ## # ℹ 636 more rows search_all(fields, \"australian states\") ## # A tibble: 2 × 3 ##   id     description                            type   ##   <chr>  <chr>                                  <chr>  ## 1 cl2013 ASGS Australian States and Territories fields ## 2 cl22   Australian States and Territories      fields"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_all_-subfunctions","dir":"Articles","previous_headings":"","what":"show_all_ subfunctions","title":"Look up information","text":"show_all useful variety cases, can still call underlying subfunctions prefer. functions - prefix show_all_ - return tibble exactly ; showing possible values category specified. functions include: show_all_fields show_all_atlases show_all_ranks show_all_profiles show_all_reasons show_all_ functions require arguments. Simply call function return accepted values tibble:","code":"show_all_atlases() ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk show_all_reasons() ## # A tibble: 13 × 2 ##       id name                             ##    <int> <chr>                            ##  1     1 biosecurity management/planning  ##  2    11 citizen science                  ##  3     5 collection management            ##  4     0 conservation management/planning ##  5     7 ecological research              ##  6     3 education                        ##  7     2 environmental assessment         ##  8    12 restoration/remediation          ##  9     4 scientific research              ## 10     8 systematic research/taxonomy     ## 11    13 species modelling                ## 12     6 other                            ## 13    10 testing"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"search_-subfunctions","dir":"Articles","previous_headings":"","what":"search_ subfunctions","title":"Look up information","text":"second subset lookup subfunctions use search_ prefix, differ show_all_ require query work. used search detailed information can’t summarised across whole atlas, include: search_taxa search_identifiers search_fields show_values Search single taxon multiple taxa name search_taxa. Alternatively, search_identifiers partner function search_taxa. already know taxonomic identifier, can search taxa identifier belongs search_identifiers: Sifting output show_all_fields find specific field can inefficient. Instead, might wish use search_fields look specific fields match search. search_taxa, search_fields requires query work.","code":"search_taxa(\"reptilia\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_taxa(\"reptilia\", \"aves\", \"mammalia\", \"pisces\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_identifiers(\"urn:lsid:biodiversity.org.au:afd.taxon:682e1228-5b3c-45ff-833b-550efd40c399\") ## # A tibble: 1 × 15 ##   search_term    success scientific_name taxon_concept_id rank  rank_id   lft   rgt match_type kingdom kingdom_id phylum phylum_id class ##   <chr>          <lgl>   <chr>           <chr>            <chr>   <int> <int> <int> <chr>      <chr>   <chr>      <chr>  <chr>     <chr> ## 1 urn:lsid:biod… TRUE    REPTILIA        https://biodive… class    3000 46718 49924 taxonIdMa… Animal… https://b… Chord… https://… Rept… ## # ℹ 1 more variable: class_id <chr> search_fields(\"date\") |> head() ## # A tibble: 6 × 3 ##   id             description     type   ##   <chr>          <chr>           <chr>  ## 1 eventDate      Event Date      fields ## 2 lastLoadDate   lastLoadDate    fields ## 3 datePrecision  Date precision  fields ## 4 eventDateEnd   <NA>            fields ## 5 dateIdentified Date Identified fields ## 6 raw_eventDate  <NA>            fields"},{"path":"https://galah.ala.org.au/R/articles/look_up_information.html","id":"show_values-search_values","dir":"Articles","previous_headings":"","what":"show_values() & search_values()","title":"Look up information","text":"desired field found, can use show_values understand information contained within field, e.g. provides information need pass meaningful queries galah_filter. works types query, data profiles:","code":"search_all(fields, \"basis\") |> show_values() ## ! Search returned 2 matched fields. ## • Showing values for 'basisOfRecord'. ## # A tibble: 9 × 1 ##   basisOfRecord       ##   <chr>               ## 1 Human observation   ## 2 Preserved specimen  ## 3 Observation         ## 4 Occurrence          ## 5 Machine observation ## 6 Material Sample     ## 7 Living specimen     ## 8 Material Citation   ## 9 Fossil specimen galah_call() |>    galah_filter(basisOfRecord == \"LIVING_SPECIMEN\") |>    atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 126135 search_all(profiles, \"ALA\") |>    show_values() |>    head() ## • Showing values for 'ALA'. ## # A tibble: 6 × 5 ##      id enabled description                                                                                          filter displayOrder ##   <int> <lgl>   <chr>                                                                                                <chr>         <int> ## 1    94 TRUE    \"Exclude all records where spatial validity is \\\"false\\\"\"                                            \"-spa…            1 ## 2    96 TRUE    \"Exclude all records with an assertion that the scientific name provided does not match any of the … \"-ass…            1 ## 3    97 TRUE    \"Exclude all records with an assertion that the scientific name provided is not structured as a val… \"-ass…            2 ## 4    98 TRUE    \"Exclude all records with an assertion that the name and classification supplied can't be used to c… \"-ass…            3 ## 5    99 TRUE    \"Exclude all records with an assertion that kingdom provided doesn't match a known kingdom e.g. Ani… \"-ass…            4 ## 6   100 TRUE    \"Exclude all records with an assertion that the scientific name provided in the record does not mat… \"-ass…            5"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_identify-search_taxa","dir":"Articles","previous_headings":"","what":"galah_identify & search_taxa","title":"Narrow your results","text":"Perhaps unsurprisingly, search_taxa searches taxonomic information. uses fuzzy matching work lot like search bar Atlas Living Australia website, can use search taxa scientific name. Finding desired taxon search_taxa important step using taxonomic information download data galah. example, search reptiles, first need identify whether correct query: want specific providing additional taxonomic information search_taxa, can provide tibble (data.frame) containing levels taxonomic hierarchy: know search matches correct taxon taxa, can use galah_identify narrow results queries: ’re using international atlas, search_taxa automatically switch using local name-matching service. example, Portugal uses GBIF taxonomic backbone, integrates seamlessly standard workflow. Conversely, UK’s National Biodiversity Network (NBN), ’ taxonomic backbone, supported using function call.","code":"search_taxa(\"Reptilia\") ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 Reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… search_taxa(tibble(genus = \"Eolophus\", kingdom = \"Aves\")) ## # A tibble: 1 × 13 ##   search_term   scientific_name scientific_name_autho…¹ taxon_concept_id rank  match_type kingdom phylum class order family genus issues ##   <chr>         <chr>           <chr>                   <chr>            <chr> <chr>      <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  ## 1 Eolophus_Aves Eolophus        Bonaparte, 1854         https://biodive… genus exactMatch Animal… Chord… Aves  Psit… Cacat… Eolo… noIss… ## # ℹ abbreviated name: ¹​scientific_name_authorship galah_call() |>   galah_identify(\"Reptilia\") |>   atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 1682010 taxa <- search_taxa(tibble(genus = \"Eolophus\", kingdom = \"Aves\"))  galah_call() |>  galah_identify(taxa) |>  atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 1093469 galah_config(atlas = \"Portugal\") ## Atlas selected: GBIF Portugal (GBIF.pt) [Portugal] galah_call() |>    galah_identify(\"Lepus\") |>    galah_group_by(species) |>    atlas_counts() ## # A tibble: 5 × 2 ##   species           count ##   <chr>             <int> ## 1 Lepus granatensis  1378 ## 2 Lepus microtis       64 ## 3 Lepus europaeus      10 ## 4 Lepus saxatilis       2 ## 5 Lepus capensis        1 galah_config(atlas = \"United Kingdom\") ## Atlas selected: National Biodiversity Network (NBN) [United Kingdom] galah_call() |>    galah_filter(genus == \"Bufo\") |>    galah_group_by(species) |>    atlas_counts() ## # A tibble: 3 × 2 ##   species       count ##   <chr>         <int> ## 1 Bufo bufo     94517 ## 2 Bufo spinosus    88 ## 3 Bufo marinus      1"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_filter","dir":"Articles","previous_headings":"","what":"galah_filter","title":"Narrow your results","text":"Perhaps important function galah galah_filter, used filter rows queries: find available fields corresponding valid values, use field lookup functions show_all(fields), search_all(fields) & show_values(). Finally, special case galah_filter make complex taxonomic queries possible using search_taxa. using taxonConceptID field, possible build queries exclude certain taxa, example. can useful paraphyletic concepts invertebrates:","code":"galah_config(atlas = \"Australia\") ## Atlas selected: Atlas of Living Australia (ALA) [Australia] # Get total record count since 2000 galah_call() |>   galah_filter(year > 2000) |>   atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 90875204 # Get total record count for iNaturalist in 2021 galah_call() |>   galah_filter(     year > 2000,     dataResourceName == \"iNaturalist Australia\") |>   atlas_counts() ## # A tibble: 1 × 1 ##     count ##     <int> ## 1 5850806 galah_call() |>   galah_filter(      taxonConceptID == search_taxa(\"Animalia\")$taxon_concept_id,      taxonConceptID != search_taxa(\"Chordata\")$taxon_concept_id   ) |>   galah_group_by(class) |>   atlas_counts() ## # A tibble: 30 × 2 ##    class          count ##    <chr>          <int> ##  1 Insecta      5887288 ##  2 Gastropoda    940371 ##  3 Maxillopoda   793499 ##  4 Arachnida     701320 ##  5 Malacostraca  657455 ##  6 Polychaeta    276460 ##  7 Bivalvia      225965 ##  8 Anthozoa      218244 ##  9 Cephalopoda   145902 ## 10 Demospongiae  118515 ## # ℹ 20 more rows"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_apply_profile","dir":"Articles","previous_headings":"","what":"galah_apply_profile","title":"Narrow your results","text":"working ALA, notable feature ability specify profile remove records suspect way. see full list data quality profiles, use show_all(profiles).","code":"galah_call() |>   galah_filter(year > 2000) |>   galah_apply_profile(ALA) |>   atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 80883916"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_group_by","dir":"Articles","previous_headings":"","what":"galah_group_by","title":"Narrow your results","text":"Use galah_group_by group record counts summarise counts specified fields:","code":"# Get record counts since 2010, grouped by year and basis of record galah_call() |>   galah_filter(year > 2015 & year <= 2020) |>   galah_group_by(year, basisOfRecord) |>   atlas_counts() ## # A tibble: 36 × 3 ##    year  basisOfRecord         count ##    <chr> <chr>                 <int> ##  1 2020  Human observation   6553463 ##  2 2020  Occurrence           419842 ##  3 2020  Preserved specimen    84298 ##  4 2020  Machine observation   39643 ##  5 2020  Observation           24887 ##  6 2020  Material Sample        1677 ##  7 2020  Living specimen          62 ##  8 2019  Human observation   5735637 ##  9 2019  Occurrence           290610 ## 10 2019  Preserved specimen   165505 ## # ℹ 26 more rows"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_select","dir":"Articles","previous_headings":"","what":"galah_select","title":"Narrow your results","text":"Use galah_select choose columns returned downloading records: can also use dplyr functions work dplyr::select() galah_select()","code":"# Get *Reptilia* records from 1930, but only 'eventDate' and 'kingdom' columns occurrences <- galah_call() |>   galah_identify(\"reptilia\") |>   galah_filter(year == 1930) |>   galah_select(kingdom, species, eventDate) |>   atlas_occurrences()  occurrences |> head() ## # A tibble: 6 × 3 ##   kingdom  species                 eventDate           ##   <chr>    <chr>                   <dttm>              ## 1 Animalia Gehyra variegata        1930-11-30 00:00:00 ## 2 Animalia Intellagama lesueurii   1930-01-01 00:00:00 ## 3 Animalia Lampropholis guichenoti 1930-10-02 00:00:00 ## 4 Animalia Acanthophis antarcticus 1930-01-01 00:00:00 ## 5 Animalia <NA>                    1930-04-23 00:00:00 ## 6 Animalia Pseudechis porphyriacus 1930-01-01 00:00:00 occurrences <- galah_call() |>   galah_identify(\"reptilia\") |>   galah_filter(year == 1930) |>   galah_select(starts_with(\"accepted\") | ends_with(\"record\")) |>   atlas_occurrences()  occurrences |> head() ## # A tibble: 6 × 6 ##   acceptedNameUsage acceptedNameUsageID basisOfRecord      raw_basisOfRecord OCCURRENCE_STATUS_INFERRED_FROM_BASIS…¹ userDuplicateRecord ##   <chr>             <lgl>               <chr>              <chr>             <lgl>                                   <lgl>               ## 1 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 2 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 3 <NA>              NA                  PRESERVED_SPECIMEN Museum specimen   FALSE                                   FALSE               ## 4 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## 5 <NA>              NA                  PRESERVED_SPECIMEN PreservedSpecimen FALSE                                   FALSE               ## 6 <NA>              NA                  HUMAN_OBSERVATION  HumanObservation  FALSE                                   FALSE               ## # ℹ abbreviated name: ¹​OCCURRENCE_STATUS_INFERRED_FROM_BASIS_OF_RECORD"},{"path":"https://galah.ala.org.au/R/articles/narrow_your_results.html","id":"galah_geolocate","dir":"Articles","previous_headings":"","what":"galah_geolocate","title":"Narrow your results","text":"Use galah_geolocate specify geographic area region limit search:","code":"# Get list of perameles species only in area specified: # (Note: This can also be specified by a shapefile) wkt <- \"POLYGON((131.36328125 -22.506468769126,135.23046875 -23.396716654542,134.17578125 -27.287832521411,127.40820312499 -26.661206402316,128.111328125 -21.037340349154,131.36328125 -22.506468769126))\"  galah_call() |>   galah_identify(\"perameles\") |>   galah_geolocate(wkt) |>   atlas_species() ## # A tibble: 1 × 10 ##   kingdom  phylum   class    order           family      genus     species            author        species_guid         vernacular_name ##   <chr>    <chr>    <chr>    <chr>           <chr>       <chr>     <chr>              <chr>         <chr>                <chr>           ## 1 Animalia Chordata Mammalia Peramelemorphia Peramelidae Perameles Perameles eremiana Spencer, 1897 https://biodiversit… Desert Bandico…"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"masked-functions","dir":"Articles","previous_headings":"","what":"Masked functions","title":"Object-Oriented Programming in galah","text":"default method building queries galah first use galah_call() create query object called data_request. object class specific galah. object class data_request, galah can trigger functions use specific methods object class, even function name used another package. example, users can use filter() group_by() functions dplyr instead galah_filter() galah_group_by() construct query. Consequently, following queries synonymous: Thanks object-oriented programming, galah “masks” filter() group_by() functions use methods defined data_request objects instead. full list masked functions : arrange() (dplyr) count() (dplyr) identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() Note functions evaluated lazily; amend underlying object, amend nature data call evaluated. actually build run query, ’ll need use one different set dplyr verbs: collapse(), compute() collect().","code":"galah_call() |>   galah_filter(genus == \"Crinia\") |>   class() ## [1] \"data_request\" galah_call() |>   galah_filter(genus == \"Crinia\", year == 2020) |>   galah_group_by(species) |>   atlas_counts() galah_call() |>    filter(genus == \"Crinia\", year == 2020) |>   group_by(species) |>   atlas_counts() ## # A tibble: 16 × 2 ##    species                 count ##    <chr>                   <int> ##  1 Crinia signifera        58579 ##  2 Crinia parinsignifera   12782 ##  3 Crinia glauerti          3090 ##  4 Crinia georgiana         1490 ##  5 Crinia remota             784 ##  6 Crinia sloanei            644 ##  7 Crinia insignifera        536 ##  8 Crinia tinnula            417 ##  9 Crinia deserticola        278 ## 10 Crinia pseudinsignifera   236 ## 11 Crinia tasmaniensis       189 ## 12 Crinia bilingua            75 ## 13 Crinia subinsignifera      45 ## 14 Crinia riparia             10 ## 15 Crinia flindersensis        3 ## 16 Crinia nimba                1"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"advanced-query-building","dir":"Articles","previous_headings":"","what":"Advanced query building","title":"Object-Oriented Programming in galah","text":"usual way begin query request data galah using galah_call(). version 2.0, make galah flexible modular, underlying architecture galah_call() divided several types request_ functions. can begin pipe one dedicated request_ functions (rather galah_call()) depending type data want collect. example, want download occurrences, use request_data(): ’ll notice query differs slightly typical query structure users galah familiar . desired data type, \"occurrences\", specified beginning query within request_data() rather end using atlas_occurrences(). Specifying data type start allows users make use advanced query building using three newly implemented stages query building: collapse(), compute() collect(). stages mirror existing functions dplyr querying databases, act following way: collapse() converts object query. allows users inspect API calls sent. Depending request, function may also call ‘supplementary’ APIs collect required information, Taxon Concept Identifiers field names. compute() intended send query question requested API processing. particularly important occurrences, can useful submit query retrieve later time. compute() stage required, however, compute() simply converts query new class (computed_query). collect() retrieves requested data workspace, returning tibble. can use sequence, just leap ahead stage want: benefit using collapse(), compute() collect() queries modular. particularly useful large data requests galah. Users can send query using compute(), download data query finished — downloading collect() later — rather waiting request finish within R. Additionally, functions modular generally easier interrogate debug. Previously functions several different things, making difficult know APIs called, , purpose. Partitioning queries three distinct stages much transparent, allows users check query construction prior sending request. example, query constructed following information, returned collapse(). collapse() stage includes additional argument (.expand) , set TRUE, shows APIs called construct user-requested query. especially useful debugging.","code":"x <- request_data(\"occurrences\") |> # note that \"occurrences\" is the default `type`   filter(species == \"Crinia tinnula\",           year == 2010) |>   collect() x <- request_data() |>   filter(genus == \"Crinia\", year == 2020) |>   group_by(species) |>   arrange(species) |>   count()  collapse(x) ## Object of class query with type data/occurrences-count-groupby  ## url: https://biocache-ws.ala.org.au/ws/occurrences/facets?fq=%28genus%3A%22...  ## arrange: species (ascending) compute(x) ## Object of class computed_query with type data/occurrences-count-groupby  ## url: https://biocache-ws.ala.org.au/ws/occurrences/facets?fq=%28genus%3A%22...  ## arrange: species (ascending) collect(x) |> head() ## # A tibble: 6 × 2 ##   species              count ##   <chr>                <int> ## 1 Crinia bilingua         75 ## 2 Crinia deserticola     278 ## 3 Crinia flindersensis     3 ## 4 Crinia georgiana      1490 ## 5 Crinia glauerti       3090 ## 6 Crinia insignifera     536 # Create and send query to be calculated server-side request <- request_data() |>   identify(\"perameles\") |>   filter(year > 1900) |>   compute()    # Download data request |>   collect() request_data() |>   identify(\"perameles\") |>   filter(year > 1900) |>   collapse() ## Object of class query with type data/occurrences  ## url: https://biocache-ws.ala.org.au/ws/occurrences/offline/download?fq=%28l..."},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"new-object-classes","dir":"Articles","previous_headings":"","what":"New object classes","title":"Object-Oriented Programming in galah","text":"hood, different query-building verbs amend object new class: collapse() returns class query, list containing type slot one urls compute() returns single object class computed_query collect() doesn’t add new data class (returns class tibble) can called directly, via method type arguments galah_call(), specify dedicated request_ function data type return. demonstrate mean, take following calls, despite using different syntax, return number records available year 2020: Another example list available fields selected atlas: show values states territories: Although little reason use request_metadata() rather show_all() time, cases larger databases like GBIF return huge data.frames metadata. galah allows users use collapse(), compute() collect() types requests, meaning users able download large metadata queries using process detailed “Advanced query building” get around issue.","code":"# new syntax request_data() |>   filter(year == 2020) |>   count() |>   collect()  # similar, but using `galah_call()` galah_call(method = \"data\",            type = \"occurrences-count\") |>   filter(year == 2020) |>   collect()  # original syntax galah_call() |>   galah_filter(year == 2020) |>   atlas_counts() request_metadata(type = \"fields\") |>   collect()  galah_call(method = \"metadata\",             type = \"fields\") |>   collect()  show_all(fields) request_metadata() |>   filter(field == \"cl22\") |>   unnest() |>   collect()  galah_call(method = \"metadata\",             type = \"fields-unnest\") |>   galah_filter(id == \"cl22\") |>   collect()  search_all(fields, \"cl22\") |>   show_values()"},{"path":"https://galah.ala.org.au/R/articles/object_oriented_programming.html","id":"do-i-need-to-use-advanced-query-building","dir":"Articles","previous_headings":"","what":"Do I need to use advanced query building?","title":"Object-Oriented Programming in galah","text":"Despite benefits, plans require new syntax; functions prefixed galah_ atlas_ going away. Indeed, perfect redundancy old new syntax cases, others serve different purposes. atlas_media() example, several calls made joined way reduces number steps required user. hood, however, atlas_ functions now entirely built using syntax.","code":""},{"path":"https://galah.ala.org.au/R/articles/piping.html","id":"piping-with-galah_call","dir":"Articles","previous_headings":"","what":"Piping with galah_call()","title":"Piping in galah","text":"may noticed examples dplyr pipes begin data, galah pipes begin galah_call() (sure add parentheses!). function tells galah using pipes construct query. Follow preferred pipe (|> base %>% magrittr). can narrow query line--line using galah_ functions. Finally, end atlas_ function identify type data want query. example using counts bandicoot records: second example, download occurrence records bandicoots 2021, also include information records zero coordinates: Note order galah_ functions added doesn’t matter, long galah_call() goes first, atlas_ function comes last.","code":"galah_call() |>   galah_identify(\"perameles\") |>   galah_filter(year >= 2020) |>   galah_group_by(species, year) |>   atlas_counts() ## # A tibble: 15 × 3 ##    species                year  count ##    <chr>                  <chr> <int> ##  1 Perameles nasuta       2021   3475 ##  2 Perameles nasuta       2022   1701 ##  3 Perameles nasuta       2020   1576 ##  4 Perameles nasuta       2023    714 ##  5 Perameles gunnii       2023    122 ##  6 Perameles gunnii       2021     71 ##  7 Perameles gunnii       2022     64 ##  8 Perameles gunnii       2020     49 ##  9 Perameles bougainville 2021     84 ## 10 Perameles bougainville 2022     72 ## 11 Perameles bougainville 2020      1 ## 12 Perameles pallescens   2022     30 ## 13 Perameles pallescens   2023     26 ## 14 Perameles pallescens   2021     25 ## 15 Perameles pallescens   2020     11 galah_call() |>   galah_identify(\"perameles\") |>   galah_filter(year == 2021) |>   galah_select(group = \"basic\", ZERO_COORDINATE) |>   atlas_occurrences() |>   head() ## Retrying in 1 seconds. ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 00108221-afc6-42… Perameles nas… https://biodi…           -28.8             153. 2021-09-29 00:00:00 PRESENT          NSW BioNet Atlas ## 2 001e914d-0281-41… Perameles nas… https://biodi…           -33.8             151. 2021-04-19 00:00:00 PRESENT          NSW BioNet Atlas ## 3 00233c1e-66df-4d… Perameles nas… https://biodi…           -33.8             151. 2021-02-27 00:00:00 PRESENT          NSW BioNet Atlas ## 4 003064b3-490a-49… Perameles nas… https://biodi…           -27.5             152. 2021-11-05 12:06:00 PRESENT          iNaturalist Aus… ## 5 004fd28b-a899-4a… Perameles nas… https://biodi…           -33.8             151. 2021-07-24 00:00:00 PRESENT          NSW BioNet Atlas ## 6 0068547b-b091-4a… Perameles nas… https://biodi…           -33.8             151. 2021-01-28 00:00:00 PRESENT          NSW BioNet Atlas ## # ℹ 1 more variable: ZERO_COORDINATE <lgl>"},{"path":"https://galah.ala.org.au/R/articles/piping.html","id":"using-dplyr-functions-in-galah","dir":"Articles","previous_headings":"","what":"Using dplyr functions in galah","title":"Piping in galah","text":"version 1.5.1, possible call dplyr functions natively within galah amend queries processed, .e.: full list masked functions : identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() count() (dplyr) synonym atlas_counts()","code":"# galah syntax galah_call() |>   galah_filter(year >= 2020) |>   galah_group_by(year) |>   atlas_counts() ## # A tibble: 4 × 2 ##   year    count ##   <chr>   <int> ## 1 2022  8409790 ## 2 2021  8254306 ## 3 2020  7124140 ## 4 2023  3446001 # dplyr syntax galah_call() |>   filter(year >= 2020) |>   group_by(year) |>   count() ## Object of type `data_request` containing: ## • type occurrences-count ## • filter year >= 2020 ## • group_by year"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"about","dir":"Articles","previous_headings":"","what":"About","title":"Quick start guide","text":"galah R interface biodiversity data hosted ‘living atlases’; set organisations share common codebase, act nodes Global Biodiversity Information Facility (GBIF). organisations collate store observations individual life forms, using ‘Darwin Core’ data standard. galah enables users locate download species observations, taxonomic information, record counts, associated media images sounds. Users can restrict queries particular taxa locations specifying columns rows returned query, restricting results observations meet particular quality-control criteria. functions return tibble standard format.","code":""},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Quick start guide","text":"install CRAN: install development version GitHub: Load package","code":"install.packages(\"galah\") install.packages(\"remotes\") remotes::install_github(\"AtlasOfLivingAustralia/galah\") library(galah)"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"choosing-an-atlas","dir":"Articles","previous_headings":"","what":"Choosing an atlas","title":"Quick start guide","text":"default, galah downloads information Atlas Living Australia (ALA). show full list Atlases currently supported galah, use show_all(atlases). Use galah_config() set Atlas use. automatically populate server configuration selected Atlas. default, atlas Australia.","code":"show_all(atlases) ## # A tibble: 11 × 4 ##    region         institution                                                             acronym url                          ##    <chr>          <chr>                                                                   <chr>   <chr>                        ##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au       ##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at ##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br         ##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee         ##  5 France         Portail français d'accès aux données d'observation sur les espèces      OpenObs https://openobs.mnhn.fr      ##  6 Global         Global Biodiversity Information Facility                                GBIF    https://gbif.org             ##  7 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt    ##  8 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt          ##  9 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es          ## 10 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se  ## 11 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk galah_config(atlas = \"United Kingdom\")"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"building-queries","dir":"Articles","previous_headings":"","what":"Building queries","title":"Quick start guide","text":"Functions return data chosen atlas prefix atlas_; e.g. find total number records atlas, use: pass complex queries, start galah_call() function pipe additional arguments modify query. modifying functions galah_ prefix support non-standard evaluation (NSE). Alternatively, can use subset dplyr verbs pipe queries, assuming start galah_call(). narrow search particular taxonomic group, use galah_identify() identify. Note function accepts scientific names case sensitive. ’s good practice first use search_taxa() check taxa provide returns correct taxonomic results.","code":"galah_config(atlas = \"ALA\") atlas_counts() ## # A tibble: 1 × 1 ##       count ##       <int> ## 1 132342396 galah_call() |>    galah_filter(year >= 2020) |>    atlas_counts() ## # A tibble: 1 × 1 ##      count ##      <int> ## 1 27234237 galah_call() |>   filter(year >= 2020) |>    group_by(year) |>   count() |>   collect() ## # A tibble: 4 × 2 ##   year    count ##   <chr>   <int> ## 1 2022  8409790 ## 2 2021  8254306 ## 3 2020  7124140 ## 4 2023  3446001 search_taxa(\"reptilia\") # Check whether taxonomic info is correct ## # A tibble: 1 × 9 ##   search_term scientific_name taxon_concept_id                                              rank  match_type kingdom phylum class issues ##   <chr>       <chr>           <chr>                                                         <chr> <chr>      <chr>   <chr>  <chr> <chr>  ## 1 reptilia    REPTILIA        https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactMatch Animal… Chord… Rept… noIss… galah_call() |>   galah_filter(year >= 2020) |>    galah_identify(\"reptilia\") |>    atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 226794"},{"path":"https://galah.ala.org.au/R/articles/quick_start_guide.html","id":"downloading-records","dir":"Articles","previous_headings":"","what":"Downloading records","title":"Quick start guide","text":"common use case galah download ‘occurrence’ records; observations plants animals made contributors atlas. download, first register relevant atlas, provide registration email. GBIF queries, need provide email, username, password registered GBIF. Search fields field IDs filter query. can customise records require query atlas question. Check vignettes detail use functions.","code":"galah_config(email = \"email@email.com\") search_all(fields, \"australian states\") ## # A tibble: 2 × 3 ##   id     description                            type   ##   <chr>  <chr>                                  <chr>  ## 1 cl2013 ASGS Australian States and Territories fields ## 2 cl22   Australian States and Territories      fields result <- galah_call() |>   galah_identify(\"Litoria\") |>   galah_filter(year >= 2020, cl22 == \"Tasmania\") |>   galah_select(basisOfRecord, group = \"basic\") |>   atlas_occurrences() ## Retrying in 1 seconds. ## Retrying in 2 seconds. ## Retrying in 4 seconds. result |> head() ## # A tibble: 6 × 9 ##   recordID          scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus dataResourceName ##   <chr>             <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>            <chr>            ## 1 00250163-ec50-4e… Litoria        https://biodi…           -41.2             147. 2023-08-23 01:49:28 PRESENT          iNaturalist Aus… ## 2 003e0f63-9f95-4a… Litoria ewing… https://biodi…           -42.9             148. 2022-12-23 19:27:00 PRESENT          iNaturalist Aus… ## 3 00410554-5289-41… Litoria ewing… https://biodi…           -41.7             147. 2021-05-06 00:00:00 PRESENT          FrogID           ## 4 0081e7ef-459b-42… Litoria ewing… https://biodi…           -43.2             147. 2020-08-02 00:00:00 PRESENT          FrogID           ## 5 0086def1-8415-4b… Litoria ewing… https://biodi…           -41.2             147. 2020-12-31 00:00:00 PRESENT          FrogID           ## 6 00b40ee7-074b-4d… Litoria ewing… https://biodi…           -41.5             147. 2020-11-01 00:00:00 PRESENT          FrogID           ## # ℹ 1 more variable: basisOfRecord <chr>"},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"contextual-and-spatial-layers","dir":"Articles","previous_headings":"","what":"Contextual and spatial layers","title":"Spatial filtering","text":"Often want filter results commonly defined spatial regions, states, LGAs IBRA/IMCRA regions. ALA contains large range (>100) contextual spatial layers, -built searchable queriable fields. denoted names beginning \"cl\", followed identifying number may 6 digits long. fields based shapefiles, contain names regions layers record lies . strongly recommend using search_fields() check whether contextual layer already exists ALA matches require proceeding methods spatial filtering. fields able queried galah_filter()generally easier use. Suppose interested querying records Red-Necked Avocet (Recurvirostra novaehollandiae) particular protected wetlands, Coorong wetlands South Australia. can search ALA fields wetlands. search identifies layer cl901 seems match looking . can either view possible values field show_values(), search particular field. can filter occurrences exact matches value, \"Lake Eyre\". galah query can built follows:","code":"library(galah) library(tidyverse) library(gt) library(sf) galah_config(email = \"your_email_here\", verbose = FALSE) search_fields(\"wetlands\") ## # A tibble: 1 × 3 ##   id    description                     type   ##   <chr> <chr>                           <chr>  ## 1 cl901 Directory of Important Wetlands fields search_fields(\"cl901\") |> search_values(\"coorong\") ## • Showing values for 'cl901'. ## # A tibble: 1 × 1 ##   cl901                                       ##   <chr>                                       ## 1 The Coorong, Lake Alexandrina & Lake Albert galah_call() |>   galah_identify(\"Recurvirostra novaehollandiae\") |>   galah_filter(cl901 == \"The Coorong, Lake Alexandrina & Lake Albert\") |>   atlas_occurrences() |>   head(5) |>   gt::gt() ## Retrying in 1 seconds."},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"galah_geolocate","dir":"Articles","previous_headings":"","what":"galah_geolocate()","title":"Spatial filtering","text":"server-side spatial information useful, likely cases shapefile region wish query pre-loaded contextual layer ALA. case, shapefiles can introduced filtering process using {sf} package galah_geolocate() function. Shapefiles can provided sf object, whether importing sf::st_read() taking POLYGON MULTIPOLYGON character string transforming sf::st_as_sfc(). instance, might interested species occurrences King George Square, Brisbane. can take MULTIPOLYGON object square (sourced Brisbane City Council) transform sfc sf objects. can provide MULTIPOLYGON filter argument galah_geolocate() assess species recorded King George Square. second argument galah_geolocate() called type, defaults value \"polygon\". setting type argument \"bbox\", provided POLYGON MULTIPOLYGON converted smallest bounding box (rectangle) contains POLYGON. case, records included may exactly lie inside provided shape.","code":"king_george_sq <- \"MULTIPOLYGON(((153.0243 -27.46886, 153.0242 -27.46896, 153.0236 -27.46837, 153.0239 -27.46814, 153.0239 -27.46813, 153.0242 -27.46789, 153.0244 -27.46805, 153.0245 -27.46821, 153.0246 -27.46828, 153.0247 -27.46835, 153.0248 -27.46848, 153.0246 -27.4686, 153.0246 -27.46862, 153.0245 -27.46871, 153.0243 -27.46886)))\" |>   sf::st_as_sfc() |>    sf::st_as_sf() galah_call() |>   galah_filter() |>   galah_geolocate(king_george_sq) |>   galah_select(decimalLatitude, decimalLongitude, eventDate, scientificName, vernacularName) |>   atlas_occurrences() |>    head(10) |>   gt::gt() galah_call() |>   galah_filter() |>   galah_geolocate(king_george_sq, type = \"bbox\") |>   galah_select(decimalLatitude, decimalLongitude, eventDate, scientificName, vernacularName) |>   atlas_occurrences() |>   head(10) |>   gt::gt() ## Data returned for bounding box: ## xmin = 153.0236 xmax = 153.0248 ymin = -27.46896 ymax = -27.46789"},{"path":"https://galah.ala.org.au/R/articles/spatial_filtering.html","id":"large-shapefiles","dir":"Articles","previous_headings":"galah_geolocate()","what":"Large shapefiles","title":"Spatial filtering","text":"type argument option \"bbox\" provided sf objects >500 vertices accepted ALA. event large shapefile, using type = \"bbox\" least enable initial reduction data downloaded, finer filtering actual shapefile obtain desired set occurrences. Alternatively, one can also perform \"bbox\" reduction passing shape galah_geolocate() using sf::st_bbox(). common situation occur shapefile multiple shapes provided, interested grouping results shape. mock workflow using subset shapefile 2,184 Brisbane parks. Let’s say interested knowing parks Brisbane postcode 4075 occurrences Scaly-Breasted Lorikeet, Trichoglossus chlorolepidotus, since 2020. can download entire shapefile link, perform filtering summarising follows: shapefiles cover large geographic areas caveat even bounding box doesn’t restrict number records value can downloaded easily. case, recommend nuances detailed methods can performed using looping techniques. One ALA Labs blog posts, Hex maps species occurrence data, written detailing approach larger problems .","code":"brisbane_parks <- sf::st_read(\"path/to/Park___Locations.shp\") |>   sf::st_make_valid() |>   filter(POST_CODE == 4075) # Convert shapefile to a bounding box brisbane_parks_bbox <- brisbane_parks |> sf::st_bbox()  # Find all occurrences of Trichoglossus chlorolepidotus in the bounding box in 2022 lorikeet_brisbane <- galah_call() |>   galah_filter(scientificName == \"Trichoglossus chlorolepidotus\",                 year >= 2020) |>   galah_geolocate(brisbane_parks_bbox, type = \"bbox\") |>   atlas_occurrences() ## Data returned for bounding box: ## xmin = 152.96331 xmax = 152.99668 ymin = -27.57737 ymax = -27.51606 # Filter records down to only those in the shapefile polygons lorikeet_brisbane |>   # Create a point geometry based on the occurrence coordinates   sf::st_as_sf(coords = c(\"decimalLongitude\", \"decimalLatitude\"), crs = sf::st_crs(brisbane_parks), remove = FALSE) |>   # identify which park each occurrence sits in with st_intersects()   mutate(intersection = sf::st_intersects(geometry, brisbane_parks) |> as.integer(),          park = ifelse(is.na(intersection), NA, brisbane_parks$PARK_NAME[intersection])) |>   # Filter out occurrences that did not occur in a park   filter(!is.na(park)) |>   # Drop the geometry column   sf::st_drop_geometry() |>   # Summarise the top 10 parks for lorikeet sightings in 2022   group_by(park) |>   summarise(counts = n()) |>   arrange(desc(counts)) |>   head(10) ## # A tibble: 10 × 2 ##    park                           counts ##    <chr>                           <int> ##  1 SHERWOOD ARBORETUM                276 ##  2 NYUNDARE-BA PARK                  271 ##  3 FAULKNER PARK                      51 ##  4 STRICKLAND TERRACE PARK            33 ##  5 FORT ROAD BUSHLAND                 31 ##  6 GRACEVILLE RIVERSIDE PARKLANDS     31 ##  7 BENARRAWA RESERVE                  19 ##  8 NOSWORTHY PARK                     16 ##  9 HORACE WINDOW RESERVE               9 ## 10 GRACEVILLE AVENUE PARK              6"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"search_taxa","dir":"Articles","previous_headings":"","what":"search_taxa()","title":"Taxonomic filtering","text":"search_taxa() enables users look taxonomic names downloading data, allows disambiguating homonyms checking search term matches taxon name ALA . search_taxa() returns scientific name, authorship, rank, full classification taxon matched provided search term.","code":"search_taxa(\"Petroica boodang\") |> gt::gt() # Muscicapa chrysoptera is a synonym for the Flame Robin, Petroica phoenicea # Guniibuu is the Yuwaalaraay Indigenous name for the Red-Capped Robin, Petroica goodenovii search_taxa(\"Muscicapa chrysoptera\", \"Guniibuu\") |> gt::gt() search_taxa(\"Morganella\") |> gt::gt() ## Warning: Search returned multiple taxa due to a homonym issue. ## ℹ Please provide another rank in your search to clarify taxa. ## ℹ Use a `tibble` to clarify taxa, see `?search_taxa`. ## ✖ Homonym issue with \"Morganella\". search_taxa(tibble(kingdom = \"Fungi\", genus = \"Morganella\")) |> gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_identify","dir":"Articles","previous_headings":"","what":"galah_identify()","title":"Taxonomic filtering","text":"galah_identify() similar search_taxa(), except can used within piped workflow retrieve counts, species, records e.g. recommend using search_taxa() prior calling galah_identify() workflow confirm validity provided search term. Setting search = TRUE passes results search_taxa() galah_identify(), also speeds query.","code":"galah_call() |>   galah_identify(\"Petroica boodang\") |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 118998 galah_call() |>   galah_identify(\"Muscicapa chrysoptera\", \"Guniibuu\") |>   atlas_species() |>    gt::gt() galah_call() |>   galah_identify(tibble(kingdom = \"Fungi\", genus = \"Morganella\")) |>   atlas_occurrences() |>   head() |>    gt::gt() robins <- search_taxa(\"Muscicapa chrysoptera\", \"Guniibuu\")   galah_call() |>   galah_identify(robins$taxon_concept_id, search = FALSE) |>   atlas_counts() ## Error: ## ! The `search` argument of `galah_identify()` was deprecated in galah 2.0.0 and is now defunct. ## ℹ `galah_identify()` now always does a search to verify search terms. To pass identifiers, please use `filter(lsid == ##   'identifier_here') instead."},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_filter","dir":"Articles","previous_headings":"","what":"galah_filter()","title":"Taxonomic filtering","text":"galah_filter() subsets records searching exact matches expression, may also used taxonomic filtering e.g. can useful searching paraphyletic polyphyletic groups, done using galah_identify(). example, get counts non-chordates:","code":"galah_call() |>   galah_filter(species == \"Petroica boodang\") |>   atlas_counts() ## # A tibble: 1 × 1 ##    count ##    <int> ## 1 118998 aus_petroica <- c(\"Petroica boodang\", \"Petroica goodenovii\",                    \"Petroica phoenicea\", \"Petroica rosea\",                   \"Petroica rodinogaster\", \"Petroica multicolor\")  galah_call() |>   galah_filter(species == aus_petroica) |>   galah_group_by(species, vernacularName) |>   atlas_counts() |>    gt::gt() galah_call() |>   galah_filter(kingdom == \"Animalia\", phylum != \"Chordata\") |>   galah_group_by(phylum) |>   atlas_counts() |>   head() |>    gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/taxonomic_filtering.html","id":"galah_filter-galah_identify-and-taxonomic-ranks","dir":"Articles","previous_headings":"","what":"galah_filter(), galah_identify(), and taxonomic ranks","title":"Taxonomic filtering","text":"Deciding using galah_filter() galah_identify() query comes record classified, whether correct unique name classification taxa interest. ALA fields primary taxonomic ranks (kingdom, phylum, class, order, family, genus, species) secondary ranks (e.g. subfamily, subgenus), may used galah_filter() galah_identify(). Additionally, field named scientificName, refers lowest taxonomic rank record identified e.g. , instance, correct species subspecies name, searching matches species subspecies fields, respectively, provide precise results. field scientificName may include subgenera. ’ve used search_taxa() get ALA-matched name taxon want records identified particular level classification, searching matches scientificName recommended. Paraphyletic polyphyletic groups may contain taxa identified different taxonomic levels. case, simpler use search_taxa() galah_identify() rather galah_filter(). example , search_taxa() matches terms one genus, three species, two subspecies. can used piped workflow galah_identify().","code":"galah_call() |>   galah_identify(tibble(genus = \"Pitta\")) |>   galah_group_by(scientificName, taxonRank) |>   atlas_counts() |>   filter(!is.na(scientificName)) |>   gt::gt() tas_endemic <- c(\"Sarcophilus\", # Tasmanian Devil                  \"Bettongia gaimardi\", # Tasmanian Bettong                  \"Melanodryas vittata\", # Dusky Robin                  \"Platycercus caledonicus\",# Green Rosella                  \"Aquila audax fleayi\", # Tasmanian Wedge-Tailed Eagle                  \"Tyto novaehollandiae castanops\") # Tasmanian Masked Owl  search_taxa(tas_endemic) |> gt::gt() galah_call() |>   galah_identify(tas_endemic) |>   galah_group_by(scientificName) |>   atlas_counts() |>   arrange(scientificName) |>   gt::gt()"},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"year-month-and-day","dir":"Articles","previous_headings":"","what":"Year, Month and Day","title":"Temporal filtering","text":"ALA contains -built year, month, day fields every record. queried numeric fields (.e. July = 7) can used quick data exploration filtering. fields useful date limits query can easily defined year, month /day. instance, can get monthly counts amphibians 2021 using year month fields. also important observe outputted month column type character even though values numeric. case year, month day fields. However, can queried either numeric character values within galah_filter(). One limitation using fields queries galah_filter() independence; used query within windows bounded two dates day month filters applied universally. instance, consider native perennial Australian wildflower Chamaescilla corymbosa, whose known growth flowering times August–October. might interested number records species first week spring (.e. September) last 10 years. following query provide results 1/9/2013 7/9/2023. Rather, return results fall within 3 windows .","code":"library(galah) library(tidyverse) library(gt) library(lubridate) galah_config(email = \"your_email_here\", verbose = FALSE) galah_call() |>   galah_filter(class == \"Amphibia\", year == 2021) |>   galah_group_by(month) |>   atlas_counts() ## # A tibble: 12 × 2 ##    month     count ##    <chr>     <int> ##  1 October   52816 ##  2 September 42206 ##  3 January   32825 ##  4 August    26252 ##  5 March     25423 ##  6 February  23473 ##  7 November  23389 ##  8 July      12301 ##  9 April     10005 ## 10 June       9217 ## 11 May        8083 ## 12 December   3998 galah_call() |>   galah_filter(species == \"Chamaescilla corymbosa\",                year >= 2013, year <= 2023, month == 9, day >= 1, day <= 7) |>   galah_group_by(year) |>   atlas_counts() |>   arrange(year) ## # A tibble: 11 × 2 ##    year  count ##    <chr> <int> ##  1 2013      8 ##  2 2014     13 ##  3 2015      8 ##  4 2016      7 ##  5 2017      1 ##  6 2018      9 ##  7 2019      5 ##  8 2020     20 ##  9 2021     36 ## 10 2022     25 ## 11 2023     52"},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"occurrence-dates","dir":"Articles","previous_headings":"","what":"Occurrence dates","title":"Temporal filtering","text":"bespoke way query exact dates records, users can use eventDate field. field contains exact date time information records enables specific time windows queried easily. caveat time/date must provided specific format galah_filter() ALA query work. required format dates eventDate ISO 8601 International Date Standard format. requires dates times form “YYYY-MM-DDTHH:MM:SSZ”. Note T middle actual letter “T” delimit date time components, “Z” officially denotes time queried UTC (Greenwich Meridian) time. Timezones can confusing best times, however easiest remember ALA records recorded local time location, times treated effectively UTC times. upshot specific formatting , instance, time writing paragraph, 4:26pm 2nd August 2023, represented \"2023-08-02T16:26:44Z\" ALA, even though officially timezone \"+0930\". eventDate specifies time seconds, recommended greater less queries used rather exact matches. used galah_filter(), can easily identify many records humpback whale (Megaptera novaeangliae) occurred since species removed Australian threatened species list 26/02/2022. can unintuitive provide dates format. Luckily, simple convert standard R dates {lubridate} dates format already required “YYYY-MM-DD” form. took date (26/02/2022), converted form using base R lubridate follows: sending query, outputted eventDate values returned galah query date class \"POSIXct\".","code":"galah_call() |>   galah_filter(species == \"Megaptera novaeangliae\",                 eventDate >= \"2022-02-26T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1   542 humpback_date <- \"26/02/2022\" # Base R paste0(as.Date(humpback_date, format = \"%d/%m/%Y\"), \"T00:00:00Z\") ## [1] \"2022-02-26T00:00:00Z\" # lubridate paste0(dmy(humpback_date), \"T00:00:00Z\") ## [1] \"2022-02-26T00:00:00Z\""},{"path":"https://galah.ala.org.au/R/articles/temporal_filtering.html","id":"upload-dates","dir":"Articles","previous_headings":"","what":"Upload dates","title":"Temporal filtering","text":"important date field present ALA pertains date record provided ALA. field called firstLoadedDate formatted exactly manner eventDate. Different data providers provide batches records ALA different intervals. iNaturalist Australia provide weekly uploads data, eBird provides yearly uploads. firstLoadedDate can especially useful finding new records ALA provided since last checked. instance, can use see many observations Sulphur-Crested Cockatoos recorded first week 2023 actually loaded ALA following week: Note lower bound required firstLoadedDate eventDate imposes proxy (records can’t uploaded ’ve occurred).","code":"# Total records of Cactua galerita in Jan 1-7 galah_call() |>   galah_filter(species == \"Cacatua galerita\",                eventDate >= \"2023-01-07T00:00:00Z\",                 eventDate < \"2023-01-08T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1   388 # Records of Cactua galerita uploaded in Jan 1-14 galah_call() |>   galah_filter(species == \"Cacatua galerita\",                eventDate >= \"2023-01-07T00:00:00Z\",                 eventDate < \"2023-01-08T00:00:00Z\",                firstLoadedDate < \"2023-01-15T00:00:00Z\") |>   atlas_counts() ## # A tibble: 1 × 1 ##   count ##   <int> ## 1     6"},{"path":"https://galah.ala.org.au/R/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Martin Westgate. Author, maintainer. Matilda Stevenson. Author. Dax Kellie. Author. Peggy Newman. Author.","code":""},{"path":"https://galah.ala.org.au/R/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Westgate M, Stevenson M, Kellie D, Newman P (2024). galah: Biodiversity Data GBIF Node Network. R package version 2.0.1, https://CRAN.R-project.org/package=galah.","code":"@Manual{,   title = {galah: Biodiversity Data from the GBIF Node Network},   author = {Martin Westgate and Matilda Stevenson and Dax Kellie and Peggy Newman},   year = {2024},   note = {R package version 2.0.1},   url = {https://CRAN.R-project.org/package=galah}, }"},{"path":[]},{"path":"https://galah.ala.org.au/R/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Biodiversity Data from the GBIF Node Network","text":"galah R interface biodiversity data hosted Global Biodiversity Information Facility (GBIF) members GBIF node network maintain APIs (.e. ‘living atlases’). organisations collate store observations individual life forms, using ‘Darwin Core’ data standard. galah built maintained Science & Decision Support Team Atlas Living Australia (ALA). galah enables users locate download species occurrence records (observations, specimens, eDNA records, etc.), taxonomic information, associated media images sounds, restrict queries particular taxa locations. Users can specify columns returned query, restrict results occurrences meet particular data-quality criteria. functions return tibble standard format. package named bird name (Eolophus roseicapilla), widely-distributed endemic Australian species. logo designed Ian Brennan. comments, questions suggestions, please contact us.","code":""},{"path":"https://galah.ala.org.au/R/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Biodiversity Data from the GBIF Node Network","text":"quick start guide provides introduction package functions. outline package structure, list available functions, run ?galah view reference page.","code":""},{"path":"https://galah.ala.org.au/R/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Biodiversity Data from the GBIF Node Network","text":"Install CRAN: Install development version GitHub: galah depends sf location-based searches. install galah need make sure system meets sf system requirements, specified .","code":"install.packages(\"galah\") install.packages(\"remotes\") remotes::install_github(\"AtlasOfLivingAustralia/galah-R\")"},{"path":[]},{"path":"https://galah.ala.org.au/R/index.html","id":"citations","dir":"","previous_headings":"","what":"Citations","title":"Biodiversity Data from the GBIF Node Network","text":"generate citation package version using, can run ’re using occurrence data downloaded galah publication, please generate DOI cite . request DOI download occurrence record, set mint_doi = TRUE call atlas_occurrences(). generate citation downloaded occurrence records, pass tibble generated atlas_citation().","code":"citation(package = \"galah\") # Download occurrence records with a DOI  occ <- atlas_occurrences(..., mint_doi = TRUE)  # See DOI attr(occ, \"doi\")  # Generate citation atlas_citation(occ)"},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange rows of a query — arrange.data_request","title":"Arrange rows of a query — arrange.data_request","text":"arrange.data_request() arranges rows query server side, meaning prior sending query, query constructed way information arranged query processed. data returned query rows already pre-arranged. benefit using arrange() within galah_call() faster process arranging rows server side arranging rows locally downloaded data, especially dataset large complex. arrange() can used within galah_call() pipe, queries  type = \"occurrences-count\". galah_call() pipe must include count() finish collect() (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange rows of a query — arrange.data_request","text":"","code":"# S3 method for data_request arrange(.data, ...)  # S3 method for metadata_request arrange(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange rows of a query — arrange.data_request","text":".data object class data_request ... Either count index","code":""},{"path":"https://galah.ala.org.au/R/reference/arrange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange rows of a query — arrange.data_request","text":"","code":"if (FALSE) {  # Arrange grouped counts by ascending year galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(year) |>   count() |>   collect()    # Arrange grouped counts by ascending record count galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(count) |>   count() |>   collect()  # Arrange grouped counts by descending year galah_call() |>   identify(\"Crinia\") |>   filter(year >= 2020) |>   group_by(year) |>   arrange(desc(year)) |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a citation for occurrence data — atlas_citation","title":"Generate a citation for occurrence data — atlas_citation","text":"data.frame generated using atlas_occurrences(), mint_doi argument set TRUE, DOI associated dataset appended resulting data.frame attribute. function simply formats DOI citation can included scientific publication. Please also consider citing package, using information citation(\"galah\").","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a citation for occurrence data — atlas_citation","text":"","code":"atlas_citation(data)"},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a citation for occurrence data — atlas_citation","text":"data data.frame: occurrence data generated atlas_occurrences()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a citation for occurrence data — atlas_citation","text":"string containing citation dataset.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a citation for occurrence data — atlas_citation","text":"","code":"if (FALSE) { atlas_citation(doi) }"},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Return a count of records — atlas_counts","title":"Return a count of records — atlas_counts","text":"Prior downloading data often valuable estimate many records available, deciding query feasible, estimating long take download. Alternatively, kinds reporting, count observations may required, example understanding observations growing shrinking particular locations, particular taxa. end, atlas_counts() takes arguments format atlas_occurrences(), provides either total count records matching criteria, data.frame counts matching criteria supplied group_by argument.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return a count of records — atlas_counts","text":"","code":"atlas_counts(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL,   group_by = NULL,   limit = NULL,   type = c(\"occurrences\", \"species\") )  # S3 method for data_request count(x, ..., wt, sort, name)"},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return a count of records — atlas_counts","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile() group_by data.frame: object class galah_group_by, returned galah_group_by(). Alternatively vector field names (see search_all(fields) show_all(fields). limit numeric: maximum number categories return, defaulting 100. limit NULL, results returned. categories take . type string: one c(\"occurrences-count\", \"species-count\"). Defaults \"occurrences-count\", returns number records match selected criteria; alternatively returns number species. Formerly accepted arguments (\"records\" \"species\") deprecated remain functional. x object class data_request, created using galah_call() ... currently ignored wt currently ignored sort currently ignored name currently ignored","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return a count of records — atlas_counts","text":"object class tbl_df data.frame (aka tibble) returning: single number, group_by specified , summary counts grouped field(s), group_by specified","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return a count of records — atlas_counts","text":"","code":"if (FALSE) { # classic syntax: galah_call() |>   galah_filter(year == 2015) |>   atlas_counts()  # synonymous with: request_data() |>   filter(year == 2015) |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":null,"dir":"Reference","previous_headings":"","what":"Get metadata on images, sounds and videos — atlas_media","title":"Get metadata on images, sounds and videos — atlas_media","text":"addition text data describing individual occurrences attributes, ALA stores images, sounds videos associated given record. atlas_media displays metadata media types.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get metadata on images, sounds and videos — atlas_media","text":"","code":"atlas_media(   request = NULL,   identify = NULL,   filter = NULL,   select = NULL,   geolocate = NULL,   data_profile = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get metadata on images, sounds and videos — atlas_media","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() select list: generated call galah_select() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get metadata on images, sounds and videos — atlas_media","text":"object class tbl_df data.frame (aka tibble) metadata requested media.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get metadata on images, sounds and videos — atlas_media","text":"atlas_media() works first finding occurrence records matching filter contain media, downloading metadata media. actually download files , use collect_media(). may beneficial requesting large number records show progress bar setting verbose = TRUE galah_config().","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/atlas_media.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get metadata on images, sounds and videos — atlas_media","text":"","code":"if (FALSE) { # Download Regent Honeyeater records with multimedia attached galah_call() |>   galah_identify(\"Regent Honeyeater\") |>   galah_filter(year == 2011) |>   atlas_media()  # Download multimedia galah_call() |>   galah_identify(\"Regent Honeyeater\") |>   galah_filter(year == 2011) |>   atlas_media() |>   collect_media(path = \"folder/your-directory\")  # Specify a single media type to download galah_call() |>   galah_identify(\"Eolophus Roseicapilla\") |>   galah_filter(multimedia == \"Sound\") |>   atlas_media()  # It's good to check how many records have media files before downloading galah_call() |>   galah_filter(multimedia == c(\"Image\", \"Sound\", \"Video\")) |>   galah_group_by(multimedia) |>   atlas_counts()       # post version 2.0, it is possible to run all steps in sequence # first, get occurrences, making sure to include media fields: occurrences_df <- request_data() |>   identify(\"Regent Honeyeater\") |>   filter(!is.na(images), year == 2011) |>   select(group = \"media\") |>   collect()   # second, get media metadata media_info <- request_metadata() |>   filter(media == occurrences_df) |>   collect()    # the two steps above + `right_join()` are synonmous with `atlas_media()` # third, get images request_files() |>   filter(media == media_df) |>   collect(thumbnail = TRUE)    # step three is synonymous with `collect_media()` }"},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect a set of occurrences — atlas_occurrences","title":"Collect a set of occurrences — atlas_occurrences","text":"common form data stored living atlases observations individual life forms, known 'occurrences'. function allows user search occurrence records match specific criteria, return tibble analysis. Optionally, user can also request DOI given download facilitate citation re-use specific data resources.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect a set of occurrences — atlas_occurrences","text":"","code":"atlas_occurrences(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL,   select = NULL,   mint_doi = FALSE,   doi = NULL,   file = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect a set of occurrences — atlas_occurrences","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile() select data.frame: generated call galah_select() mint_doi logical: default DOI generated. Set TRUE intend use data publication similar. doi string: (optional) DOI download. provided overrides arguments. available ALA. file string: (Optional) file name. given, set data date time added. file path (directory) always given galah_config()$package$directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect a set of occurrences — atlas_occurrences","text":"object class tbl_df data.frame (aka tibble) occurrences, containing columns specified galah_select().","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Collect a set of occurrences — atlas_occurrences","text":"Note unless care taken, queries can particularly large. cases simply take long time process, number requested records >50 million, call return data. Users can test whether threshold reached first calling atlas_counts() using arguments intend pass atlas_occurrences(). may also beneficial requesting large number records show progress bar setting verbose = TRUE galah_config(), use compute() run call collecting later collect().","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect a set of occurrences — atlas_occurrences","text":"","code":"if (FALSE) { # Download occurrence records for a specific taxon galah_config(email = \"your_email_here\") galah_call() |>   galah_identify(\"Reptilia\") |>   atlas_occurrences()  # Download occurrence records in a year range galah_call() |>   galah_identify(\"Litoria\") |>   galah_filter(year >= 2010 & year <= 2020) |>   atlas_occurrences()    # Or identically with alternative syntax request_data() |>   identify(\"Litoria\") |>   filter(year >= 2010 & year <= 2020) |>   collect()    # Download occurrences records in a WKT-specified area polygon <- \"POLYGON((146.24960 -34.05930,                      146.37045 -34.05930,                      146.37045 -34.152549,                      146.24960 -34.15254,                      146.24960 -34.05930))\" galah_call() |>    galah_identify(\"Reptilia\") |>   galah_filter(year >= 2010, year <= 2020) |>   galah_geolocate(polygon) |>   atlas_occurrences()    }"},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect the set of species observed within the specified filters — atlas_species","title":"Collect the set of species observed within the specified filters — atlas_species","text":"reasons users may need check every record meeting search criteria (.e. using atlas_occurrences()), common use case simply identify species occur specified region, time period, taxonomic group. function returns data.frame one row per species, columns giving associated taxonomic information.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect the set of species observed within the specified filters — atlas_species","text":"","code":"atlas_species(   request = NULL,   identify = NULL,   filter = NULL,   geolocate = NULL,   data_profile = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect the set of species observed within the specified filters — atlas_species","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter() geolocate string: generated call galah_geolocate() data_profile string: generated call galah_apply_profile()","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect the set of species observed within the specified filters — atlas_species","text":"object class tbl_df data.frame (aka tibble), returning matching species data.frame object attributes listing user-supplied arguments data_request (.e., identify, filter, geolocate, columns)","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Collect the set of species observed within the specified filters — atlas_species","text":"primary use case function extract species-level information given set criteria defined search_taxa(), galah_filter() galah_geolocate(). purpose simply get taxonomic information restricted filtering, search_taxa() efficient. Similarly, counts required include filter without returning taxonomic detail, atlas_counts() efficient (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect the set of species observed within the specified filters — atlas_species","text":"","code":"if (FALSE) { # First register a valid email address galah_config(email = \"ala4r@ala.org.au\")  # Get a list of species within genus \"Heleioporus\" # (every row is a species with associated taxonomic data) galah_call() |>   galah_identify(\"Heleioporus\") |>   atlas_species()  # Get a list of species within family \"Peramelidae\" galah_call() |>   galah_identify(\"peramelidae\") |>   atlas_species()    # Or alternatively request_data(type = \"species\") |>   identify(\"peramelidae\") |>   collect()  # It's good idea to find how many species there are before downloading galah_call() |>   galah_identify(\"Heleioporus\") |>   atlas_counts(type = \"species\") # Or alternatively request_data(type = \"species\") |>   identify(\"Heleioporus\") |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Search taxonomic trees — atlas_taxonomy","title":"Search taxonomic trees — atlas_taxonomy","text":"ALA ' internal taxonomy derived authoritative sources. atlas_taxonomy provides means query taxonomy, returning tibble showing child nodes parent derived .","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search taxonomic trees — atlas_taxonomy","text":"","code":"atlas_taxonomy(   request = NULL,   identify = NULL,   filter = NULL,   constrain_ids = NULL )"},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search taxonomic trees — atlas_taxonomy","text":"request optional data_request object: generated call galah_call(). identify data.frame: generated call galah_identify(). filter data.frame: generated call galah_filter(rank == \"chosen_rank\"). identity clade downwards search stop. constrain_ids string: Optional string limit taxon_concept_id's returned. useful restricting taxonomy particular authoritative sources. Default \"biodiversity.org.au\" Australia (can overridded setting constrain_ids = NULL) NULL otherwise. Powered grepl() meaning supports regular expressions.","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search taxonomic trees — atlas_taxonomy","text":"tibble containing taxon names, ranks parent/child IDs","code":""},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search taxonomic trees — atlas_taxonomy","text":"approach used function recursive, meaning becomes slow large queries atlas_taxonomy(search_taxa(\"Plantae\"), down_to = galah_down_to(species)). Although inputs search_taxa down_to case-insensitive, node names always returned title case.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/atlas_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search taxonomic trees — atlas_taxonomy","text":"","code":"if (FALSE) { # Get a taxonomic tree of *Chordata* down to the class level galah_call() |>    galah_identify(\"chordata\") |>   galah_filter(rank == class) |>   atlas_taxonomy() }"},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a query — collapse_galah","title":"Generate a query — collapse_galah","text":"collapse() constructs valid query can inspected sent. typically occurs end pipe, traditionally begun galah_call(), used define query. version 2.0, objects class data_request (created using request_data()), metadata_request (request_metadata()) files_request (request_files()) supported collapse(). objects can created using galah_call() via method argument.","code":""},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a query — collapse_galah","text":"","code":"# S3 method for data_request collapse(x, ..., mint_doi, .expand = FALSE)  # S3 method for metadata_request collapse(x, .expand = FALSE, ...)  # S3 method for files_request collapse(x, thumbnail = FALSE, ...)"},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a query — collapse_galah","text":"x object class data_request, metadata_request files_request ... Arguments passed methods mint_doi Logical: DOI minted download? applies type = \"occurrences\" atlas chosen \"ALA\". .expand Logical: query_set returned? object shows requisite data needed process supplied query. Defaults FALSE; TRUE append query_set extra slot query object. thumbnail Logical: thumbnail-size images returned? Defaults FALSE, indicating full-size images required.","code":""},{"path":"https://galah.ala.org.au/R/reference/collapse_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a query — collapse_galah","text":"object class query, list-like object containing least slots type url.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve a database query — collect_galah","title":"Retrieve a database query — collect_galah","text":"collect() attempts retrieve result query selected API.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve a database query — collect_galah","text":"","code":"# S3 method for data_request collect(x, ..., wait = TRUE, file = NULL)  # S3 method for metadata_request collect(x, ...)  # S3 method for files_request collect(x, ...)  # S3 method for query collect(x, ..., wait = TRUE, file = NULL)  # S3 method for computed_query collect(x, ..., wait = TRUE, file = NULL)"},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve a database query — collect_galah","text":"x object class data_request, metadata_request files_request (galah_call()); oject class query_set query (collapse() compute()) ... Arguments passed methods wait logical; galah wait response? Defaults FALSE. applies type = \"occurrences\" \"species\". file (Optional) file name. given, set data date time added. file path (directory) always given galah_config()$package$directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve a database query — collect_galah","text":"cases, collect() returns tibble containing requested data. requested data yet ready (.e. occurrences wait set FALSE), function returns object class query can used recheck download later time.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect media files — collect_media","title":"Collect media files — collect_media","text":"function downloads full-sized thumbnail images media files using information atlas_media local directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect media files — collect_media","text":"","code":"collect_media(df, thumbnail = FALSE, path)"},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect media files — collect_media","text":"df tibble: returned atlas_media() pipe starting request_data(type = \"media\"). thumbnail logical: TRUE download small thumbnail-sized images, rather full size images (default). path string:  Use galah_config(directory = \"path--directory)\" instead. Supply path local folder/directory downloaded media saved .","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect media files — collect_media","text":"Invisibly returns tibble listing number files downloaded, grouped HTML status codes. Primarily called side effect downloading available image & media files user local directory.","code":""},{"path":"https://galah.ala.org.au/R/reference/collect_media.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect media files — collect_media","text":"","code":"if (FALSE) { # Use `atlas_media()` to return a `tibble` of records that contain media x <- galah_call() |>    galah_identify(\"perameles\") |>   galah_filter(year == 2015) |>   atlas_media()  # To download media files, add `collect_media()` to the end of a query  galah_config(directory = \"media_files\") collect_media(x) }"},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute a query — compute_galah","title":"Compute a query — compute_galah","text":"compute() useful several purposes. original purpose send request data, can processed server retrieved later time (via collect()).","code":""},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute a query — compute_galah","text":"","code":"# S3 method for data_request compute(x, ...)  # S3 method for metadata_request compute(x, ...)  # S3 method for files_request compute(x, ...)  # S3 method for query compute(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute a query — compute_galah","text":"x object class data_request, metadata_request files_request (.e. constructed using pipe) query (.e. constructed collapse()) ... Arguments passed methods","code":""},{"path":"https://galah.ala.org.au/R/reference/compute_galah.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute a query — compute_galah","text":"object class computed_query, identical class query except occurrence data, also contains information status request.","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated functions — galah_down_to","title":"Deprecated functions — galah_down_to","text":"include: galah_down_to() favour galah_filter()","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated functions — galah_down_to","text":"","code":"galah_down_to(...)"},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated functions — galah_down_to","text":"... name single taxonomic rank","code":""},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated functions — galah_down_to","text":"string named rank","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/deprecated-functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deprecated functions — galah_down_to","text":"","code":"if (FALSE) { # Return a taxonomic tree of *Chordata* down to the class level galah_call() |>     galah_identify(\"Vertebrata\") |>     galah_down_to(class) |>     atlas_taxonomy() }"},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":null,"dir":"Reference","previous_headings":"","what":"Biodiversity Data from the GBIF Node Network — galah","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Global Biodiversity Information Facility (GBIF; https://www.gbif.org) provides tools enable users find, access, combine visualise biodiversity data. galah enables R community directly access data resources hosted GBIF several subsidiary organisations, known 'nodes'. basic unit observation stored infrastructures occurrence record, based Darwin Core' data standard (https://dwc.tdwg.org); however galah also enables users locate download taxonomic information, associated media images sounds, restricting queries particular taxa locations. Users can specify columns returned query, restrict results observations meet particular quality-control criteria. outside Australia, 'galah' common name Eolophus roseicapilla, widely-distributed Australian bird species.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Piping functions galah_call() request_() et al.  Start build data query collapse() Generate query compute() Compute query collect() Retrieve database query Lazy data manipulation identify() galah_identify() Search taxonomic identifiers filter() galah_filter()Filter records select() galah_select()Fields report information group_by() galah_group_by() Fields group counts st_crop() galah_geolocate() Specify location apply_profile() galah_apply_profile() Restrict data pass predefined checks (ALA ) slice_head() Choose first n rows download arrange() Arrange rows query server side Download data atlas_occurrences() Download occurrence records atlas_counts() count() Count number records species returned query atlas_species() Download species lists atlas_taxonomy() Return section ALA taxonomic tree atlas_media() View images sounds available download collect_media() Download images sounds Look information search_taxa() Search taxa using text-search search_identifiers() Search taxa using taxonomic identifiers show_all() & search_all() Data generating filter queries show_values() & search_values() Show search values within fields, profiles, lists, collections, datasets providers Configure session galah_config() Package configuration options Cite atlas_citation() Citation dataset","code":""},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"terminology","dir":"Reference","previous_headings":"","what":"Terminology","title":"Biodiversity Data from the GBIF Node Network — galah","text":"get value galah, helpful understand terminology. occurrence record contains taxonomic information, usually information observation , location. addition record-specific information, living atlases append contextual information record, particularly data spatial layers reflecting climate gradients political boundaries. also run number quality checks record, resulting assertions attached record. piece information associated given occurrence record stored field, corresponds column imported R data.frame. See show_all(fields) view valid fields, layers assertions, conduct search using search_all(fields). Data fields important provide means filter occurrence records;  .e. return information need, . Consequently, much architecture galah designed make filtering simple possible. easiest way start pipe galah_call() follow relevant dplyr function; starting filter(), also including select(), group_by() others. Functions without relevant dplyr synonym include galah_identify()/identify() choosing taxon, galah_geolocate()/ st_crop() choosing specific location. combining different filters, possible build complex queries return valuable information given problem. notable extension filtering approach remove records low 'quality'. living atlases perform quality control checks records store. checks used generate new fields, can used filter records unsuitable particular applications. However, many possible data quality checks, always clear appropriate given instance. Therefore, galah supports data quality profiles, can passed galah_apply_profile() quickly remove undesirable records. full list data quality profiles returned show_all(profiles). Note service currently available Australian atlas (ALA).","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Biodiversity Data from the GBIF Node Network — galah","text":"Maintainer: Martin Westgate martin.westgate@csiro.au Authors: Matilda Stevenson Dax Kellie dax.kellie@csiro.au Peggy Newman peggy.newman@csiro.au","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a data quality profile — galah_apply_profile","title":"Apply a data quality profile — galah_apply_profile","text":"'profile' group filters pre-applied ALA. Using data profile allows query filtered quickly relevant quality-assured data fit--purpose. example, \"ALA\" profile designed exclude lower quality records, whereas profiles apply filters specific species distribution modelling (e.g. CDSM).","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a data quality profile — galah_apply_profile","text":"","code":"galah_apply_profile(...)  apply_profile(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a data quality profile — galah_apply_profile","text":"... profile name. string - name abbreviation data quality profile apply query. Valid values can seen using show_all(profiles) .data object class data_request","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply a data quality profile — galah_apply_profile","text":"tibble containing valid data profile value.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Apply a data quality profile — galah_apply_profile","text":"Note one profile can loaded time; multiple profiles given, first valid profile used. bespoke editing filters within profile, use galah_filter()","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_apply_profile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply a data quality profile — galah_apply_profile","text":"","code":"if (FALSE) { # Apply a data quality profile to a query galah_call() |>    galah_identify(\"reptilia\") |>   galah_filter(year == 2021) |>   galah_apply_profile(ALA) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Start building a query — galah_call","title":"Start building a query — galah_call","text":"download data selected atlas, one must construct query. query tells atlas API data download return, well filtered. Using galah_call() allows build piped query download data, way wrangle data dplyr tidyverse. Since version 2.0, galah_call() wrapper group underlying request_ functions. functions can begin piped query end collapse(), compute() collect(). underlying request_ #' functions useful allow galah separate different types requests perform better. example, filter.data_request translates filters R solr, whereas filter.metadata_request searches using search term. details see object-oriented programming vignette: vignette(\"object_oriented_programming\", package = \"galah\")","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start building a query — galah_call","text":"","code":"galah_call(method = c(\"data\", \"metadata\", \"files\"), type, ...)  request_data(   type = c(\"occurrences\", \"occurrences-count\", \"occurrences-doi\", \"species\",     \"species-count\"),   ... )  request_metadata(type)  request_files(type = c(\"media\"))"},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start building a query — galah_call","text":"method string: request function called. one \"data\" (default), \"metadata\" \"files\" type string: form data returned? Acceptable values specified corresponding request function ... Zero arguments alter query. See 'details'.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start building a query — galah_call","text":"sub-function returns different object class: request_data() returns data_request. request_metadata returns metadata_request, request_files() returns files_request.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start building a query — galah_call","text":"atlas several types data can chosen. Currently supported \"occurrences\" (default), \"species\" \"media\" (latter currently ALA). also possible use type = \"occurrences-count\" type = \"species-count\"; practice synonymous galah_call() |> count(), therefore practically useful debugging (via collapse() compute()). named arguments supported via .... practice, functions galah_ prefix S3 methods ported dplyr assign information correct slots internally. Overwriting user-defined alternatives possible, advised. Accepted arguments : filter (accepts galah_filter() filter()) select (accepts galah_select() select) group_by (accepts galah_group_by() group_by()) identify (accepts galah_identify() identify()) geolocate (accepts galah_geolocate(), galah_polygon() galah_bbox() st_crop()) limit (accepts slice_head()) doi (accepts sting listing valid DOI, specific collect() type = \"doi\") Unrecognised names ignored collect() related functions.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Start building a query — galah_call","text":"","code":"if (FALSE) {  # Begin your query with `galah_call()`, then pipe using `%>%` or `|>`  # Get number of records of *Aves* from 2001 to 2004 by year galah_call() |>   galah_identify(\"Aves\") |>   galah_filter(year > 2000 & year < 2005) |>   galah_group_by(year) |>   atlas_counts()    # Get information for all species in *Cacatuidae* family galah_call() |>   galah_identify(\"Cacatuidae\") |>   atlas_species()    # Download records of genus *Eolophus* from 2001 to 2004 galah_config(email = \"your-email@email.com\")  galah_call() |>   galah_identify(\"Eolophus\") |>   galah_filter(year > 2000 & year < 2005) |>   atlas_occurrences()   # ---------- # Since galah 2.0.0, a pipe can start with a `request_` function. # This allows users to use `collapse()`, `compute()` and `collect()`.  # Get number of records of *Aves* from 2001 to 2004 by year request_data(type = \"occurrences-count\") |>   galah_identify(\"Aves\") |>   galah_filter(year > 2000 & year < 2005) |>   galah_group_by(year) |>   collect()  # Get information for all species in *Cacatuidae* family request_data(type = \"species\") |>   galah_identify(\"Cacatuidae\") |>   collect()    # Get metadata information about supported atlases in galah request_metadata(type = \"atlases\") |>   collect()  }"},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Get or set configuration options that control galah behaviour — galah_config","title":"Get or set configuration options that control galah behaviour — galah_config","text":"galah package supports large data downloads, also interfaces ALA requires users services provide registered email address reason downloading data. galah_config function provides way manage issues simply possible.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get or set configuration options that control galah behaviour — galah_config","text":"","code":"galah_config(...)"},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get or set configuration options that control galah behaviour — galah_config","text":"... Options can defined using form name = \"value\". Valid arguments : api-key string: registered API key (currently unused). atlas string: Living Atlas point , Australia default. Can organisation name, acronym, region (see show_all_atlases() admissible values) directory string: directory use cache. default temporary directory, means results cached within R session cleared automatically user exits R. user may wish set non-temporary directory caching across sessions. directory must exist file system. download_reason_id numeric string: \"download reason\" required. ALA services, either numeric ID (currently 0--13) string (see show_all(reasons) list valid ID codes names). default NA. ALA services require valid download_reason_id code, either specified directly associated R function. email string: email address registered chosen atlas. ALA, can register address. password string: registered password (GBIF ) run_checks logical: galah run checks filters columns. making lots requests sequentially, checks can slow process lead HTTP 500 errors, turned . Defaults TRUE. send_email logical: receive email query atlas_occurrences()? Defaults FALSE; can useful instances, example tracking DOIs assigned specific downloads later citation. username string: registered username (GBIF ) verbose logical: galah give verbose progress bars? Defaults FALSE.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get or set configuration options that control galah behaviour — galah_config","text":"galah_config(), list options. galah_config(...) called arguments, nothing returned configuration set.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get or set configuration options that control galah behaviour — galah_config","text":"","code":"if (FALSE) { # To download occurrence records, enter your email in `galah_config()`.  # This email should be registered with the atlas in question.  galah_config(email = \"your-email@email.com\")   # Turn on caching in your session galah_config(caching = TRUE)   # Some ALA services require that you add a reason for downloading data.  # Add your selected reason using the option `download_reason_id` galah_config(download_reason_id = 0)  # To look up all valid reasons to enter, use `show_all(reasons)` show_all(reasons)  # Make debugging in your session easier by setting `verbose = TRUE` galah_config(verbose = TRUE) }"},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query by specifying filters — galah_filter","title":"Narrow a query by specifying filters — galah_filter","text":"\"Filters\" arguments form field logical value used narrow number records returned specific query. example, common users request records particular year (year == 2020), return records except fossils (basisOfRecord != \"FossilSpecimen\"). result galah_filter() can passed filter argument atlas_occurrences(), atlas_species(), atlas_counts() atlas_media().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query by specifying filters — galah_filter","text":"","code":"galah_filter(..., profile = NULL)  # S3 method for data_request filter(.data, ...)  # S3 method for metadata_request filter(.data, ...)  # S3 method for files_request filter(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query by specifying filters — galah_filter","text":"... filters, form field logical value profile Use galah_apply_profile instead. .data object class files_request, created using request_files()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query by specifying filters — galah_filter","text":"tibble containing filter values.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query by specifying filters — galah_filter","text":"galah_filter uses non-standard evaluation (NSE), designed compatible possible dplyr::filter() syntax. statements passed galah_filter() (except profile argument) take form field - logical - value. Permissible examples include: = == (e.g. year = 2020) !=, e.g. year != 2020) > >= (e.g. year >= 2020) < <= (e.g. year <= 2020) statements (e.g. year == 2018 | year == 2020) statements (e.g. year >= 2000 & year <= 2020) cases R fail parse inputs single equals sign (=), particularly statements separated & |. problem can avoided using double-equals (==) instead. Notes behaviour Separating statements comma equivalent statement; Ergo galah_filter(year >= 2010 & year < 2020) galah_filter(year >= 2010, year < 2020). statements must include field name; galah_filter(year == 2010 | year == 2021) works, galah_filter(year == c(2010, 2021)), galah_filter(year == 2010 | 2021) fails. possible use object specify required values, e.g. year_value <- 2010; galah_filter(year > year_value) solr supports range queries text well numbers; valid: galah_filter(cl22 >= \"Tasmania\")","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query by specifying filters — galah_filter","text":"","code":"if (FALSE) { # Filter query results to return records of interest galah_call() |>   galah_filter(year >= 2019,                basisOfRecord == \"HumanObservation\") |>   atlas_counts()  # Alternatively, the same call using `dplyr` functions: request_data() |>   filter(year >= 2019,                basisOfRecord == \"HumanObservation\") |>   count() |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query to within a specified area — galah_bbox","title":"Narrow a query to within a specified area — galah_bbox","text":"Restrict results specified area using galah_geolocate(). Areas can specified either polygons bounding boxes, depending type. Alternatively, users can call underlying functions directly via galah_bbox() galah_polygon(). Finally, possible use sf syntax calling st_crop(), synonymous galah_polygon(). calling galah_geolocate(), default type \"polygon\", narrows queries within area supplied POLYGON. Polygons must specified either sf object, 'well-known text' (WKT) string, shapefile. Shapefiles must simple accepted ALA. Alternatively, set type = \"bbox\" narrow queries within bounding box. Bounding boxes can extracted supplied sf object shapefile. bounding box can also supplied bbox object (via sf::st_bbox()) tibble/data.frame.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query to within a specified area — galah_bbox","text":"","code":"galah_bbox(...)  galah_geolocate(..., type = c(\"polygon\", \"bbox\"))  galah_polygon(...)  # S3 method for data_request st_crop(x, y, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query to within a specified area — galah_bbox","text":"... single sf object, WKT string shapefile. Bounding boxes can supplied tibble/data.frame bbox type string: one c(\"polygon\", \"bbox\"). Defaults \"polygon\". type = \"polygon\", multipolygon built via galah_polygon(). type = \"bbox\", multipolygon built via galah_bbox(). multipolygon used narrow query ALA. x object class data_request, created using galah_call() y valid Well-Known Text string (wkt), POLYGON MULTIPOLYGON","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query to within a specified area — galah_bbox","text":"length-1 string (class character) containing multipolygon WKT string representing area provided.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query to within a specified area — galah_bbox","text":"type = \"polygon\", WKT strings longer 10000 characters sf objects 500 vertices accepted ALA. polygons  may need simplified. type = \"bbox\", sf objects shapefiles converted bounding box query ALA.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_geolocate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query to within a specified area — galah_bbox","text":"","code":"if (FALSE) { # Search for records within a polygon using a shapefile location <- sf::st_read(\"path/to/shapefile.shp\") galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location) |>   atlas_counts()    # Search for records within the bounding box of a shapefile location <- sf::st_read(\"path/to/shapefile.shp\") galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location, type = \"bbox\") |>   atlas_counts()  # Search for records within a polygon using an `sf` object location <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" |>  sf::st_as_sfc() galah_call() |>   galah_identify(\"reptilia\") |>   galah_polygon(location) |>   atlas_counts()    # Alternatively, we can use `st_crop()` as a synonym for `galah_polygon()`.  # Hence the above example can be rewritten as: request_data() |>   identify(\"reptilia\") |>   st_crop(location) |>   count() |>   collect()     # Search for records using a Well-known Text string (WKT) wkt <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(wkt) |>   atlas_counts()  # Search for records within the bounding box extracted from an `sf` object location <- \"POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))\" |>   sf::st_as_sfc() galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(location, type = \"bbox\") |>   atlas_counts()  # Search for records using a bounding box of coordinates b_box <- sf::st_bbox(c(xmin = 143, xmax = 148, ymin = -29, ymax = -28),                       crs = sf::st_crs(\"WGS84\")) galah_call() |>   galah_identify(\"reptilia\") |>   galah_geolocate(b_box, type = \"bbox\") |>   atlas_counts()  # Search for records using a bounding box in a `tibble` or `data.frame` b_box <- tibble::tibble(xmin = 148, ymin = -29, xmax = 143, ymax = -21) galah_call() |>   galah_identify(\"vulpes\") |>   galah_geolocate(b_box, type = \"bbox\") |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify fields to group when downloading record counts — galah_group_by","title":"Specify fields to group when downloading record counts — galah_group_by","text":"count.data_request() atlas_counts() support server-side grouping data. Grouping can used return record counts grouped multiple, valid fields (found search_all(fields)).","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify fields to group when downloading record counts — galah_group_by","text":"","code":"galah_group_by(...)  # S3 method for data_request group_by(.data, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify fields to group when downloading record counts — galah_group_by","text":"... zero individual column names include .data object class data_request","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify fields to group when downloading record counts — galah_group_by","text":"arguments provided, returns data.frame columns name type, per select.data_request().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_group_by.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specify fields to group when downloading record counts — galah_group_by","text":"","code":"if (FALSE) { galah_call() |>    galah_group_by(basisOfRecord) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":null,"dir":"Reference","previous_headings":"","what":"Narrow a query by passing taxonomic identifiers — galah_identify","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"conducting search creating data query, common identify known taxon group taxa narrow records results returned.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"","code":"galah_identify(..., search = NULL)  # S3 method for data_request identify(x, ...)  # S3 method for metadata_request identify(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"... One scientific names. search galah_identify() now always search verify search terms; ergo argument ignored. x object class metadata_request, created using request_metadata()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"tibble containing identified taxa.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"galah_identify() used identify taxa want returned search data query. Users pass scientific names taxonomic identifiers pipes provide data biological group interest. good use search_taxa() search_identifiers() first check taxa provide galah_identify() return correct results.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_identify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Narrow a query by passing taxonomic identifiers — galah_identify","text":"","code":"if (FALSE) { # Specify a taxon. A valid taxon will return an identifier. galah_identify(\"reptilia\")  # Specify more than one taxon at a time. galah_identify(\"reptilia\", \"mammalia\", \"aves\", \"pisces\")  # Use `galah_identify()` to narrow your queries galah_call() |>    galah_identify(\"Eolophus\") |>   atlas_counts()  # Within a pipe, `identify()` and `galah_identify()` are synonymous. # hence the following is identical to the previous example: request_data() |>   identify(\"Eolophus\") |>   count() |>   collect()  # If you know a valid taxon identifier, use `galah_filter()` instead. # (This was formerly supported by `galah_identify()` with `search = FALSE`) id <- \"https://biodiversity.org.au/afd/taxa/009169a9-a916-40ee-866c-669ae0a21c5c\" galah_call() |>    galah_filter(lsid == id) |>   atlas_counts() }"},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify fields for occurrence download — galah_select","title":"Specify fields for occurrence download — galah_select","text":"GBIF partner nodes store content hundreds different fields, users often require thousands millions records time. reduce time taken download data, limit complexity resulting tibble, sensible restrict fields returned atlas_occurrences(). function allows easy selection fields, commonly-requested groups columns, following syntax shared dplyr::select(). full list available fields can viewed show_all(fields). Note select() galah_select() supported atlases allow downloads, exception GBIF, columns returned.","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify fields for occurrence download — galah_select","text":"","code":"galah_select(..., group)  # S3 method for data_request select(.data, ..., group)"},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify fields for occurrence download — galah_select","text":"... zero individual column names include group string: (optional) name one column groups include. Valid options \"basic\", \"event\" \"assertions\" .data object class data_request, created using galah_call()","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify fields for occurrence download — galah_select","text":"tibble specifying name type column include call atlas_counts() atlas_occurrences().","code":""},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Specify fields for occurrence download — galah_select","text":"Calling argument group = \"basic\" returns following columns: decimalLatitude decimalLongitude eventDate scientificName taxonConceptID recordID dataResourceName occurrenceStatus Using group = \"event\" returns following columns: eventRemarks eventTime eventID eventDate samplingEffort samplingProtocol Using group = \"media\" returns following columns: multimedia multimediaLicence images videos sounds Using group = \"assertions\" returns quality assertion-related columns. list assertions shown show_all_assertions().","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/galah_select.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specify fields for occurrence download — galah_select","text":"","code":"if (FALSE) { # Download occurrence records of *Perameles*,  # Only return scientificName and eventDate columns galah_config(email = \"your-email@email.com\") galah_call() |>   galah_identify(\"perameles\")|>   galah_select(scientificName, eventDate) |>   atlas_occurrences()  # Only return the \"basic\" group of columns and the basisOfRecord column galah_call() |>   galah_identify(\"perameles\") |>   galah_select(basisOfRecord, group = \"basic\") |>   atlas_occurrences()    # When used in a pipe, `galah_select()` and `select()` are synonymous. # Hence the previous example can be rewritten as: request_data() |>   identify(\"perameles\") |>   select(basisOfRecord, group = \"basic\") |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"Print galah objects — print_galah_objects","title":"Print galah objects — print_galah_objects","text":"version 2.0, galah supports several bespoke object types. Classes data_request, metadata_request files_request starting pipes download different types information. objects parsed using collapse() query object, contains one URLs necessary return requested information. object passed compute() /collect(). Finally, galah_config() creates object class galah_config (unsurprisingly) stores configuration information.","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print galah objects — print_galah_objects","text":"","code":"# S3 method for data_request print(x, ...)  # S3 method for files_request print(x, ...)  # S3 method for metadata_request print(x, ...)  # S3 method for query print(x, ...)  # S3 method for computed_query print(x, ...)  # S3 method for query_set print(x, ...)  # S3 method for galah_config print(x, ...)"},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print galah objects — print_galah_objects","text":"x object appropriate class ... Arguments passed methods","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print galah objects — print_galah_objects","text":"Print return object; instead prints description object console","code":""},{"path":"https://galah.ala.org.au/R/reference/print_galah_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print galah objects — print_galah_objects","text":"","code":"# The most common way to start a pipe is with `galah_call()` # later functions update the `data_request` object galah_call() |> # same as calling `request_data()`   filter(year >= 2020) |>   group_by(year) |>   count() #> Object of type `data_request` containing: #> • type occurrences-count #> • filter year >= 2020 #> • group_by year  # Metadata requests are formatted in a similar way request_metadata() |>   filter(field == basisOfRecord) |>   unnest() #> Object of type `metadata_request` containing: #> • type fields-unnest #> • filter field == basisOfRecord  # Queries are converted into a `query_set` by `collapse()` x <- galah_call() |> # same as calling `request_data()`   filter(year >= 2020) |>   count() |>   collapse() print(x) #> Object of class query with type data/occurrences-count  #> url: https://biocache-ws.ala.org.au/ws/occurrences/search?fq=%28year%3A%5B2...      # Each `query_set` contains one or more `query` objects x[[3]] #> [1] \"totalRecords\""},{"path":"https://galah.ala.org.au/R/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. dplyr arrange, collapse, collect, compute, count, filter, group_by, select, slice_head graphics identify sf st_crop","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Search for record information — search_all","title":"Search for record information — search_all","text":"living atlases store huge amount information, beyond occurrence records main output. galah, one way users can investigate information searching specific option category type information interested . Functions prefixed search_ , displaying matches search term within valid options information specified suffix. search_all() helper function can searches within multiple types information search_ sub-functions. See Details () accepted values.","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search for record information — search_all","text":"","code":"search_all(type, query)  search_assertions(query)  search_apis(query)  search_atlases(query)  search_collections(query)  search_datasets(query)  search_fields(query)  search_identifiers(...)  search_licences(query)  search_lists(query)  search_profiles(query)  search_providers(query)  search_ranks(query)  search_reasons(query)  search_taxa(...)"},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search for record information — search_all","text":"type string specify type parameters searched. query string specifying search term. Searches case-sensitive. ... set strings tibble queried","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search for record information — search_all","text":"object class tbl_df data.frame (aka tibble) containing data match search query.","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search for record information — search_all","text":"five categories information, specific sub-functions look-type information. available types information search_all() :","code":""},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Search for record information — search_all","text":"Darwin Core terms https://dwc.tdwg.org/terms/","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/search_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search for record information — search_all","text":"","code":"if (FALSE) { # Search for fields that include the word \"date\" search_all(fields, \"date\")  # Search for fields that include the word \"marine\" search_all(fields, \"marine\")  # Search using a single taxonomic term # (see `?search_taxa()` for more information) search_all(taxa, \"Reptilia\") # equivalent  # Look up a unique taxon identifier # (see `?search_identifiers()` for more information) search_all(identifiers,             \"https://id.biodiversity.org.au/node/apni/2914510\")  # Search for species lists that match \"endangered\" search_all(lists, \"endangered\") # equivalent  # Search for a valid taxonomic rank, \"subphylum\" search_all(ranks, \"subphylum\")  # An alternative is to download the data and then `filter` it. This is  # largely synonymous, and allows greater control over which fields are searched. request_metadata(type = \"fields\") |>  collect() |>  dplyr::filter(grepl(\"date\", id)) }"},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Show valid record information — show_all","title":"Show valid record information — show_all","text":"living atlases store huge amount information, beyond occurrence records main output. galah, one way users can investigate information showing available options categories type information interested . Functions prefixed show_all_ , displaying valid options information specified suffix. show_all() helper function can display multiple types information show_all_ sub-functions.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show valid record information — show_all","text":"","code":"show_all(..., limit = NULL)  show_all_apis(limit = NULL)  show_all_assertions(limit = NULL)  show_all_atlases(limit = NULL)  show_all_collections(limit = NULL)  show_all_datasets(limit = NULL)  show_all_fields(limit = NULL)  show_all_licences(limit = NULL)  show_all_lists(limit = NULL)  show_all_profiles(limit = NULL)  show_all_providers(limit = NULL)  show_all_ranks(limit = NULL)  show_all_reasons(limit = NULL)"},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show valid record information — show_all","text":"... String showing type information requested. See Details () accepted values. limit Optional number values return. Defaults NULL, .e. records","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show valid record information — show_all","text":"object class tbl_df data.frame (aka tibble) containing data interest.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show valid record information — show_all","text":"five categories information, specific sub-functions look-type information. available types information show_all_ :","code":""},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Show valid record information — show_all","text":"Darwin Core terms https://dwc.tdwg.org/terms/","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/show_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show valid record information — show_all","text":"","code":"if (FALSE) { # See all supported atlases show_all(atlases)  # Show a list of all available data quality profiles show_all(profiles)  # Show a listing of all accepted reasons for downloading occurrence data show_all(reasons)  # Show a listing of all taxonomic ranks show_all(ranks)  # `show_all()` is synonymous with `request_metadata() |> collect()` request_metadata(type = \"fields\") |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Show or search for values within a specified field — show_values","title":"Show or search for values within a specified field — show_values","text":"Users may wish see specific values within chosen field, profile list narrow queries understand information interest. show_values() provides users values. search_values() allows users search specific values within specified field.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show or search for values within a specified field — show_values","text":"","code":"show_values(df)  search_values(df, query)"},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show or search for values within a specified field — show_values","text":"df search result search_fields(), search_profiles() search_lists(). query string specifying search term. case sensitive.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show or search for values within a specified field — show_values","text":"tibble values specified field, profile list.","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show or search for values within a specified field — show_values","text":"Field contains categorical numeric values. example: field \"year\" contains values 2021, 2020, 2019, etc. field \"stateProvince\" contains values New South Wales, Victoria, Queensland, etc. used narrow queries galah_filter(). Profile consists many individual quality filters. example, \"ALA\" profile consists values: Exclude records spatial validity FALSE Exclude records latitude value zero Exclude records longitude value zero List contains list species, usually taxonomic name. example, Endangered Plant species list contains values: Acacia curranii (Curly-bark Wattle) Brachyscome papillosa (Mossgiel Daisy) Solanum karsense (Menindee Nightshade)","code":""},{"path":"https://galah.ala.org.au/R/reference/show_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show or search for values within a specified field — show_values","text":"","code":"if (FALSE) { # Show values in field 'cl22' search_fields(\"cl22\") |>    show_values()  # This is synonymous with `request_metadata() |> unnest()`. # For example, the previous example can be run using: request_metadata() |>   filter(field == \"cl22\") |>   unnest() |>   collect()   # Search for any values in field 'cl22' that match 'tas' search_fields(\"cl22\") |>    search_values(\"tas\")  # See items within species list \"dr19257\" search_lists(\"dr19257\") |>    show_values() }"},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset first rows of data_request — slice_head.data_request","title":"Subset first rows of data_request — slice_head.data_request","text":"simple function set limit argument atlas_counts() using dplyr syntax. galah 2.0.0, slice_head() supported queries type occurrences-count(), metadata requests. Note also slice_head() lazily evaluated; affects query run compute() (likely) collect().","code":""},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset first rows of data_request — slice_head.data_request","text":"","code":"# S3 method for data_request slice_head(.data, ..., n, prop, by = NULL)  # S3 method for metadata_request slice_head(.data, ..., n, prop, by = NULL)"},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset first rows of data_request — slice_head.data_request","text":".data object class data_request, created using galah_call() ... currently ignored n number rows returned. data grouped (using group_by), operation performed group. prop currently ignored, added later currently ignored","code":""},{"path":"https://galah.ala.org.au/R/reference/slice_head.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset first rows of data_request — slice_head.data_request","text":"","code":"if (FALSE) { # Limit number of rows returned to 3. # In this case, our query returns the top 3 years with most records. galah_call() |>   identify(\"perameles\") |>   filter(year > 2010) |>   group_by(year) |>   count() |>   slice_head(n = 3) |>   collect() }"},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Non-generic tidyverse functions — tidyverse_functions","title":"Non-generic tidyverse functions — tidyverse_functions","text":"Several useful functions tidyverse packages generic, meaning can define class-specific versions functions implement galah; examples include filter(), select() group_by(). However, also functions defined within tidyverse packages generic. cases re-implemented functions galah. consequence supporting consistent syntax tidyverse, cost potentially introducing conflicts. can avoided using :: operator required (see examples).","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Non-generic tidyverse functions — tidyverse_functions","text":"","code":"desc(...)  unnest(.query)"},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Non-generic tidyverse functions — tidyverse_functions","text":"... column order .query object class metadata_request","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Non-generic tidyverse functions — tidyverse_functions","text":"galah::desc() returns tibble used arrange.data_request() arrange rows query. galah::unnest() returns object class metadata_request.","code":""},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Non-generic tidyverse functions — tidyverse_functions","text":"following functions included: desc() (dplyr): Use within arrange() specify arrangement descending unnest() (tidyr): Use 'drill ' nested information fields, lists, profiles, taxa galah versions use lazy evaluation.","code":""},{"path":[]},{"path":"https://galah.ala.org.au/R/reference/tidyverse_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Non-generic tidyverse functions — tidyverse_functions","text":"","code":"if (FALSE) { # Arrange grouped record counts by descending year galah_call() |>   identify(\"perameles\") |>   filter(year > 2019) |>   count() |>   arrange(galah::desc(year)) |>   collect()  # Return values of field `basisOfRecord` request_metadata() |>    galah::unnest() |>    filter(field == basisOfRecord) |>    collect()    # Using `galah::unnest()` in this way is equivalent to: show_all(fields, \"basisOfRecord\") |>    show_values() }"},{"path":[]},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-2-0-1","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 2.0.1","text":"collapse() now returns query object, rather query_set, gains .expand argument optionally append query_set debugging purposes (#217).","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-2-0-1","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 2.0.1","text":"Avoid triggering multiple errors galah_identify() returns matched taxa (#219) Improve clarity quick start guide vignette (#221) show_values() longer truncates rows 30 (#222) Column ID name returned search_all(lists) now matches correct field ID galah_filter() (#225)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-200","dir":"Changelog","previous_headings":"","what":"galah 2.0.0","title":"galah 2.0.0","text":"CRAN release: 2023-11-20","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"object-oriented-programming-2-0-0","dir":"Changelog","previous_headings":"","what":"Object-oriented programming","title":"galah 2.0.0","text":"galah 2.0.0 now built around object-oriented programming principles. architectural change makes query building galah modular transparent. result, galah 2.0.0 allows easier debugging gives users options advanced query building (information, see “Object-oriented programming” vignette galah website) (#183).","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"collapse-compute-collect-2-0-0","dir":"Changelog","previous_headings":"","what":"collapse(), compute(), collect()","title":"galah 2.0.0","text":"New underlying architecture behind every function pings API galah separates query building 3 stages: Convert object query_set lists APIs pinged (collapse()), send queries required APIs (compute()), return data tibble (collect()) (#183). New architecture solves timing-issue downloading large numbers records (#180, #192) galah_filter(), galah_select() related functions now evaluated lazily; API calls made compute() called, meaning earlier programming stages faster easier debug.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"major-improvements-to-galah_filter-2-0-0","dir":"Changelog","previous_headings":"","what":"Major improvements to galah_filter()","title":"galah 2.0.0","text":"galah_filter() upgraded use hierarchical parsing architecture suggested Advanced R. result, galah_filter() faster evaluates expressions consistently (#196, #169) galah_filter() now supports .na, !, c() & %% (#196)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-2-0-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 2.0.0","text":"potions package underlies galah_config() better options management (#193) Addition slice_head() desc() masked functions use galah atlas_counts() query. New vignettes added advanced taxonomic, spatial temporal filtering (#42)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-2-0-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 2.0.0","text":"Fixed parsing | galah_filter() (#169) show_values() errors nicely API (#184) Sporadic atlas$region error loading galah fixed potions package implementation (#178) DOI longer missing attribute atlas_occurrences(mint_doi = TRUE) (#182) Fixed bug order fields group_by() sometimes caused error (#201) Fixed parsing ampersands (&) query results (#203) galah builds correct data_request object wrapped function (#207)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-154","dir":"Changelog","previous_headings":"","what":"galah 1.5.4","title":"galah 1.5.4","text":"CRAN release: 2023-10-14 Patch release fix minor issues devel systems CRAN.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-153","dir":"Changelog","previous_headings":"","what":"galah 1.5.3","title":"galah 1.5.3","text":"CRAN release: 2023-07-01 Minor release address CRAN issues. Last release 2.0.0.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-152","dir":"Changelog","previous_headings":"","what":"galah 1.5.2","title":"galah 1.5.2","text":"CRAN release: 2023-03-10 Minor release resolve issues CRAN, recent bugs.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.5.2","text":"Prevent error providing tibble input search_taxa() (e.g., resolve homonyms, #168) Better error message email address required, given (#179) Add informative message users call galah_select() atlas = GBIF (supported; #181) Ensure DOIs added downloads requested (#182) Improve tests avoid flagging issues CRAN one atlases (#184) Resolve problem queries replaced ... galah_filter() (#186)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-151","dir":"Changelog","previous_headings":"","what":"galah 1.5.1","title":"galah 1.5.1","text":"CRAN release: 2023-01-13","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"mask-function-names-from-other-packages-1-5-1","dir":"Changelog","previous_headings":"","what":"Mask function names from other packages","title":"galah 1.5.1","text":"experimental feature version 1.5.1 ability call functions packages (#161), synonyms galah_ functions. : identify() ({graphics}) synonym galah_identify() select() (dplyr) synonym galah_select() group_by() (dplyr) synonym galah_group_by() slice_head() (dplyr) synonym limit argument atlas_counts() st_crop() (sf) synonym galah_polygon() count() (dplyr) synonym atlas_counts() implemented S3 methods objects class data_request, created galah_call(). Hence new function names work piped galah_call().","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"experimental-support-for-gbif-queries-1-5-1","dir":"Changelog","previous_headings":"","what":"Experimental support for GBIF queries","title":"galah 1.5.1","text":"Global Biodiversity Information Facility (GBIF) umbrella organisation atlases supply data. Hence logical able query GBIF ’s “nodes” (.e. living atlases) via common API. Supported functions : search_taxa galah_identify name matching show_all(fields) show_all(assertions) show_all() calls give ‘collections’ information limited 20 records default, GBIF datasets often huge. search_all() generally reliable show_values() GBIF field galah_filter galah_group_by (therefore filter group_by(), see ), galah_select. atlas_counts() (therefore count(), see ) atlas_occurrences() & atlas_species(); implemented via ‘downloads’ system, meaning queries can larger, may slow current implementation experimental back-end changes expected future. Users require stable implementation use {rgbif} package.","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-5-1","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.5.1","text":"galah_config() gains print function, now uses fuzzy matching atlas field match region, organisation acronym (defined show_all(atlases)). example use case match organisations via acronyms, e.g. galah_config(atlas = \"ALA\"). Improved support data Spain via gbif.es (name-matching, lists, spatial) Swapped provider data France; formerly gbif.fr, now OpenObs, per advice maintainers Reading data disk now uses readr::read_csv place utils::read.csv improved speed show_all (associated sub-functions) gain limit argument, set NULL (.e. limit) default galah longer imports data.table, since function previously used package (rbindlist) duplicated dplyr::bind_rows Help files now built without markdown improved speed (mainly building)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-1","dir":"Changelog","previous_headings":"","what":"Bug fixes:","title":"galah 1.5.1","text":"New function url_paginate() handle cases pagination needed, total data length unknown (e.g. show_all_lists(), #170). galah_select(group = \"assertions\") always enacted properly atlas_occurrences, won’t lead overly long urls (#137). called without field names, recordID added avoid triggering ‘default’ set columns. atlas_species works minor changes API; requires registered email function","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-150","dir":"Changelog","previous_headings":"","what":"galah 1.5.0","title":"galah 1.5.0","text":"CRAN release: 2022-10-27","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"expanded-support-for-querying-other-international-living-atlases-1-5-0","dir":"Changelog","previous_headings":"","what":"Expanded support for querying other International Living Atlases","title":"galah 1.5.0","text":"Support complex queries 10 Living Atlases, including France, Guatemala Sweden. Complex queries can constructed using galah_call(), filtered galah_ functions, downloaded atlas_ functions. Previously, functionality possible queries ALA (#126)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"collect_media-1-5-0","dir":"Changelog","previous_headings":"","what":"collect_media()","title":"galah 1.5.0","text":"Show available media: atlas_media() returns tibble available media files Download media: collect_media() downloads list media atlas_media() local machine Download image thumbnails specifying type = \"thumbnails\" collect_media() (#140)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"updates-to-galah_geolocate-1-5-0","dir":"Changelog","previous_headings":"","what":"Updates to galah_geolocate()","title":"galah 1.5.0","text":"galah_geolocate() now supports filtering queries using polygons bounding boxes. Overall improvements bug fixes galah_geolocate() new internal functions galah_polygon() galah_bbox() (#125)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"show_all-search_all--show_values-search_values-1-5-0","dir":"Changelog","previous_headings":"","what":"show_all(), search_all() & show_values(), search_values()","title":"galah 1.5.0","text":"Experimental functions show_all() search_all() flexible look-functions can search information {galah}, rather separate search_/show_all_ functions (e.g. search_fields(), search_atlases(), show_all_fields(), show_all_reasons(), etc) (#127, #132) Added look-support collections, data providers, data resources, licenses, APIs species lists (e.g. list endangered species) (#126, #127, #132, #151) Checking valid values within fields, profiles species lists improved functions show_values() & search_values() (#131)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-5-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.5.0","text":"Apply data quality profiles pipe galah_apply_profile() function (#130) Improved internal consistency galah_ functions (#133) galah_geolocate() longer depends archived {wellknown} package (#141) Added support queries exclude/include missing values (e.g. galah_filter(species != \"\") galah_filter(species == \"\") (#143) Re-download previously-minted DOI collect_doi() (#140) checks ensure galah fails gracefully API fails (#157)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-5-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.5.0","text":"galah_select() longer adds “basic” group columns automatically (#128) galah_config() doesn’t display incorrect preserve = TRUE message (#136) Fixes error selecting assertion columns galah_select() (#137) atlas_counts() atlas_occurrences() longer return different record numbers field empty (#138) atlas_media() results longer differ results returned galah_filter() & atlas_counts() (#151)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-140","dir":"Changelog","previous_headings":"","what":"galah 1.4.0","title":"galah 1.4.0","text":"CRAN release: 2022-01-24","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"revamped-syntax-1-4-0","dir":"Changelog","previous_headings":"","what":"Revamped syntax","title":"galah 1.4.0","text":"ala_ functions renamed use prefix atlas_. change reflects functionality international atlases (.e., atlas_occurrences, atlas_counts, atlas_species, atlas_media, atlas_taxonomy, atlas_citation) (#103) select_taxa replaced 3 functions: galah_identify, search_taxa search_identifiers. galah_identify used building data queries, whereas search_taxa search_identifiers now exclusively used search taxonomic information. Syntax changes intended reflect usage expected output (#112, #122) select_ functions renamed use prefix galah_. Specifically, galah_filter, galah_select galah_geolocate replace select_filters, select_columns select_locations. syntax changes reflect move towards consistency dplyr naming functionality (#101, #108) find_ functions provide listing possible values renamed show_all_ (.e., show_all_profiles, show_all_ranks, show_all_atlases, show_all_cached_files, show_all_fields, show_all_reasons). find_ functions require input return specific results renamed search_ (.e., search_field_values, search_profile_attributes) (#112, #113)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_group_by-1-4-0","dir":"Changelog","previous_headings":"","what":"galah_group_by","title":"galah 1.4.0","text":"Group fields using galah_group_by(), groups summarises record counts based categorical field values, similar dplyr::group_by() (#90, #95)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_down_to-1-4-0","dir":"Changelog","previous_headings":"","what":"galah_down_to","title":"galah 1.4.0","text":"Select taxonomic level taxonomic tree go galah_down_to() + atlas_taxonomy(), uses tidy evaluation like galah_ functions (#101, #120)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"pipe-queries-using-galah_call-1-4-0","dir":"Changelog","previous_headings":"","what":"Pipe queries using galah_call","title":"galah 1.4.0","text":"Build data queries using piping syntax (.e., |>, %>%) first using galah_call(), narrowing queries galah_ functions finishing queries atlas_ function (#60, #120). S3 methods now implemented functions allow piping (#40)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-4-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.4.0","text":"Improved error messages using {glue} {rlang} (#117) Revamped syntax functions return output tibbles (#110, #118) Pass vectors galah_filter (#91, #92) Cache valid fields faster field look (#73, #116) New vignettes updated syntax (#104, #105), plus improvements previous vignettes. Updated R Markdown-style documentation added warnings deprecated functions (#113, #121)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-4-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.4.0","text":"galah longer returns error ALA system /API fails (#102, #119) search_taxa returns correct IDs search terms parentheses (#96) search_taxa returns best-fit taxonomic result ranks specified data.frame tibble (#115)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-131","dir":"Changelog","previous_headings":"","what":"galah 1.3.1","title":"galah 1.3.1","text":"CRAN release: 2021-08-21","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"search_taxonomy-renamed-to-ala_taxonomy-1-3-1","dir":"Changelog","previous_headings":"","what":"search_taxonomy() renamed to ala_taxonomy()","title":"galah 1.3.1","text":"bug fix: ala_taxonomy longer fails nodes ranked informal unranked (#86) function now returns tree built using data.tree package change function name required greater consistency data-providing functions galah","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"vignettes-1-3-1","dir":"Changelog","previous_headings":"","what":"Vignettes","title":"galah 1.3.1","text":"vignettes now pre-compiled avoid failing CRAN (#85) expanded vignette navigating taxonomic information (#42)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-130","dir":"Changelog","previous_headings":"","what":"galah 1.3.0","title":"galah 1.3.0","text":"CRAN release: 2021-08-06","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah_config-1-3-0","dir":"Changelog","previous_headings":"","what":"galah_config()","title":"galah 1.3.0","text":"ala_config() renamed galah_config() improve internal consistency (#68)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"search_taxonomy-1-3-0","dir":"Changelog","previous_headings":"","what":"search_taxonomy()","title":"galah 1.3.0","text":"search_taxonomy() provides means search taxonomic names check results ‘correct’ proceeding download data via ala_occurrences(), ala_species() ala_counts() (e.g., ambiguous homonymous) (#64 #75) search_taxonomy() returns information author authority taxonomic names (#79) search_taxonomy() consistently orders column names, including correct taxonomic order rank (#81)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"caching-helper-functions-1-3-0","dir":"Changelog","previous_headings":"","what":"Caching helper functions","title":"galah 1.3.0","text":"find_cached_files() lists user cached files stored metadata (#57) clear_cached_files() removes previously cached files stored metadata (#71) ala_counts(), ala_occurrences(), ala_media() ala_species() now refresh_cache argument remove previously cached files replace current query (#71)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-3-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.3.0","text":"Cache files saved RDS format, making query attributes easier find, including data DOI, search url (#55, #32, #28) ala_media() caches media metadata galah_config(caching = TRUE) search_fields() allows user pass qid argument (#59) Users can now optionally skip filter count validation checks spatial biocache web services setting galah_config(run_checks = FALSE). helps users avoid slowing data request download speeds many requests made quick succession via galah_filter() ala_occurrences() (#61, #80) ala_counts(), select_columns() search_fields() now use match.arg approximate strings fuzzy matching (#66) Better handling cache errors improved error messages (#70)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-3-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.3.0","text":"select_columns(group = 'assertions') now sends qa = includeall ALA web service API return assertion columns (#48) ala_occurrences() returns data DOI ala_occurrences(mint_doi = TRUE) re-downloads data called multiple times (#56) ala_occurrences() longer converts field names -CAPS camelCase (#62)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-120","dir":"Changelog","previous_headings":"","what":"galah 1.2.0","title":"galah 1.2.0","text":"CRAN release: 2021-07-02","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"living-atlases-1-2-0","dir":"Changelog","previous_headings":"","what":"Living Atlases","title":"galah 1.2.0","text":"ala_config() allows users specify international Atlas download data (#21)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-2-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.2.0","text":"ala_media() includes file path downloaded media returned metadata (#22) Data returned ala_occurrences() contains search_url used download records; takes user website search page (#32) ala_species() provides helpful error species found (#39) Data quality filters created using specific web service argument, rather constructing filters attributes (#37) select_taxa() optional all_ranks argument return intermediate rank information (#35)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"bug-fixes-1-2-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"galah 1.2.0","text":"R > 4.0.0 now required (#43, #45) select_taxa() behaves expected character strings 32 36 characters provided (#23) Caching functionality ala_occurrences() uses columns expected (#30) galah_filter() negates assertion filters required, fixing issue assertion values ignored (#27) select_taxa() longer throws error queries one term differing number columns return value (#41) ala_counts() returns data.frame consistent column classes group_by parameter called multiple times ala_config(caching = TRUE) (#47) ala_ functions fail gracefully non-id character string passed (#49)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-110","dir":"Changelog","previous_headings":"","what":"galah 1.1.0","title":"galah 1.1.0","text":"CRAN release: 2021-05-05","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"downloading-media-1-1-0","dir":"Changelog","previous_headings":"","what":"Downloading media","title":"galah 1.1.0","text":"ala_media() now takes select_ arguments ala_ functions (#18) Filtering media metadata e.g. licence type possible (#19) search_fields now media type argument option Performance improvement download times (#13) Progress bar displayed downloads verbose == TRUE (#8) media download types supported","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"select_-functions-1-1-0","dir":"Changelog","previous_headings":"","what":"select_ functions","title":"galah 1.1.0","text":"galah_location auto-detects type argument provided takes single argument, query, place sf wkt (#17) select_taxa auto-detects type argument provided takes single argument, query, place term term_type (#16)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"minor-improvements-1-1-0","dir":"Changelog","previous_headings":"","what":"Minor improvements","title":"galah 1.1.0","text":"Provide useful error message empty occurrence download (#7) ala_counts uses group_by field name returned data.frame column name (#6) ala_occurrences sends sourceId parameter ALA (#5) search_fields provides helpful error invalid types (#11)","code":""},{"path":"https://galah.ala.org.au/R/news/index.html","id":"galah-100","dir":"Changelog","previous_headings":"","what":"galah 1.0.0","title":"galah 1.0.0","text":"CRAN release: 2021-04-06 First version galah, built earlier functionality ALA4R package.","code":""}]