update pages

index.html

@@ -82,6 +82,12 @@
 background-size: cover;
       }
 </style>
+<link href="site_libs/htmltools-fill-0.5.6.1/fill.css" rel="stylesheet">
+<link href="site_libs/bslib-grid-styles-0.5.1/grid.css" rel="stylesheet">
+<script src="site_libs/bslib-tag-require-0.5.1/tag-require.js"></script>
+<link href="site_libs/bslib-value_box-styles-0.5.1/value_box.css" rel="stylesheet">
+<script src="site_libs/bslib-card-js-0.5.1/card.min.js"></script>
+<link href="site_libs/bslib-card-styles-0.5.1/card.css" rel="stylesheet">
 
 
 <link rel="stylesheet" href="styles.css">
@@ -178,6 +184,92 @@ <h2 id="toc-title">On this page</h2>
 <h2 class="anchored" data-anchor-id="why-a-forecasting-challenge">Why a forecasting challenge?</h2>
 <p>We are using forecasts to compare the predictability of different ecosystem variables, in different ecosystem conditions to identify the fundamental predictability of freshwater ecosystems.</p>
 <p><br> <br></p>
+<div class="cell">
+<div class="cell-output-display">
+<div class="bslib-grid bslib-mb-spacing html-fill-item" data-require-bs-caller="layout_column_wrap()" data-require-bs-version="5" style="grid-template-columns:repeat(auto-fit, minmax(250px, 1fr));grid-auto-rows:1fr;--bslib-grid-height:auto;--bslib-grid-height-mobile:auto;">
+<div class="bslib-gap-spacing html-fill-container">
+<div class="card bslib-card bslib-mb-spacing html-fill-item html-fill-container bslib-value-box border-0 bg-success" data-bslib-card-init="" data-require-bs-caller="card() value_box()" data-require-bs-version="5 5">
+<div class="card-body bslib-gap-spacing html-fill-item html-fill-container" style="margin-top:auto;margin-bottom:auto;flex:1 1 auto; padding:0;">
+<div class="bslib-grid bslib-mb-spacing html-fill-item value-box-grid" data-require-bs-caller="layout_column_wrap()" data-require-bs-version="5" style="--bslib-grid-height:auto;--bslib-grid-height-mobile:auto;gap:0px; --bslib-value-box-widths:30% 70%;--bslib-value-box-widths-full-screen:1fr auto;">
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-showcase overflow-hidden html-fill-item html-fill-container" style="--bslib-value-box-max-height:100px;--bslib-value-box-max-height-full-screen:67%;"><svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 16 16" class="bi bi-graph-up " style="height:1em;width:1em;fill:currentColor;vertical-align:-0.125em;" aria-hidden="true" role="img"><path fill-rule="evenodd" d="M0 0h1v15h15v1H0V0Zm14.817 3.113a.5.5 0 0 1 .07.704l-4.5 5.5a.5.5 0 0 1-.74.037L7.06 6.767l-3.656 5.027a.5.5 0 0 1-.808-.588l4-5.5a.5.5 0 0 1 .758-.06l2.609 2.61 4.15-5.073a.5.5 0 0 1 .704-.07Z"></path></svg></div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-area html-fill-item html-fill-container border-start">
+<p>Total forecasts submitted to the NEON Challenge</p>
+<p>323</p>
+</div>
+</div>
+</div>
+</div>
+<script data-bslib-card-init="">bslib.Card.initializeAllCards();</script>
+</div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="card bslib-card bslib-mb-spacing html-fill-item html-fill-container bslib-value-box border-0 bg-primary" data-bslib-card-init="" data-require-bs-caller="card() value_box()" data-require-bs-version="5 5">
+<div class="card-body bslib-gap-spacing html-fill-item html-fill-container" style="margin-top:auto;margin-bottom:auto;flex:1 1 auto; padding:0;">
+<div class="bslib-grid bslib-mb-spacing html-fill-item value-box-grid" data-require-bs-caller="layout_column_wrap()" data-require-bs-version="5" style="--bslib-grid-height:auto;--bslib-grid-height-mobile:auto;gap:0px; --bslib-value-box-widths:30% 70%;--bslib-value-box-widths-full-screen:1fr auto;">
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-showcase overflow-hidden html-fill-item html-fill-container" style="--bslib-value-box-max-height:100px;--bslib-value-box-max-height-full-screen:67%;"><svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 16 16" class="bi bi-bullseye " style="height:1em;width:1em;fill:currentColor;vertical-align:-0.125em;" aria-hidden="true" role="img"><path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"></path>
+<path d="M8 13A5 5 0 1 1 8 3a5 5 0 0 1 0 10zm0 1A6 6 0 1 0 8 2a6 6 0 0 0 0 12z"></path>
+<path d="M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6zm0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8z"></path>
+<path d="M9.5 8a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"></path></svg></div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-area html-fill-item html-fill-container border-start">
+<p>Most recent data for model training</p>
+2023-11-04
+</div>
+</div>
+</div>
+</div>
+<script data-bslib-card-init="">bslib.Card.initializeAllCards();</script>
+</div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="card bslib-card bslib-mb-spacing html-fill-item html-fill-container bslib-value-box border-0 bg-primary" data-bslib-card-init="" data-require-bs-caller="card() value_box()" data-require-bs-version="5 5">
+<div class="card-body bslib-gap-spacing html-fill-item html-fill-container" style="margin-top:auto;margin-bottom:auto;flex:1 1 auto; padding:0;">
+<div class="bslib-grid bslib-mb-spacing html-fill-item value-box-grid" data-require-bs-caller="layout_column_wrap()" data-require-bs-version="5" style="--bslib-grid-height:auto;--bslib-grid-height-mobile:auto;gap:0px; --bslib-value-box-widths:30% 70%;--bslib-value-box-widths-full-screen:1fr auto;">
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-showcase overflow-hidden html-fill-item html-fill-container" style="--bslib-value-box-max-height:100px;--bslib-value-box-max-height-full-screen:67%;"><svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 16 16" class="bi bi-bullseye " style="height:1em;width:1em;fill:currentColor;vertical-align:-0.125em;" aria-hidden="true" role="img"><path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"></path>
+<path d="M8 13A5 5 0 1 1 8 3a5 5 0 0 1 0 10zm0 1A6 6 0 1 0 8 2a6 6 0 0 0 0 12z"></path>
+<path d="M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6zm0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8z"></path>
+<path d="M9.5 8a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"></path></svg></div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-area html-fill-item html-fill-container border-start">
+<p>Number of years of data for model training</p>
+<p>10.35</p>
+</div>
+</div>
+</div>
+</div>
+<script data-bslib-card-init="">bslib.Card.initializeAllCards();</script>
+</div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="card bslib-card bslib-mb-spacing html-fill-item html-fill-container bslib-value-box border-0 bg-success" data-bslib-card-init="" data-require-bs-caller="card() value_box()" data-require-bs-version="5 5">
+<div class="card-body bslib-gap-spacing html-fill-item html-fill-container" style="margin-top:auto;margin-bottom:auto;flex:1 1 auto; padding:0;">
+<div class="bslib-grid bslib-mb-spacing html-fill-item value-box-grid" data-require-bs-caller="layout_column_wrap()" data-require-bs-version="5" style="--bslib-grid-height:auto;--bslib-grid-height-mobile:auto;gap:0px; --bslib-value-box-widths:30% 70%;--bslib-value-box-widths-full-screen:1fr auto;">
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-showcase overflow-hidden html-fill-item html-fill-container" style="--bslib-value-box-max-height:100px;--bslib-value-box-max-height-full-screen:67%;"><svg xmlns="http://www.w3.org/2000/svg" viewbox="0 0 16 16" class="bi bi-clipboard-data " style="height:1em;width:1em;fill:currentColor;vertical-align:-0.125em;" aria-hidden="true" role="img"><path d="M4 11a1 1 0 1 1 2 0v1a1 1 0 1 1-2 0v-1zm6-4a1 1 0 1 1 2 0v5a1 1 0 1 1-2 0V7zM7 9a1 1 0 0 1 2 0v3a1 1 0 1 1-2 0V9z"></path>
+<path d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z"></path>
+<path d="M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z"></path></svg></div>
+</div>
+<div class="bslib-gap-spacing html-fill-container">
+<div class="value-box-area html-fill-item html-fill-container border-start">
+<p>Number of variables being forecasted</p>
+<p>10</p>
+</div>
+</div>
+</div>
+</div>
+<script data-bslib-card-init="">bslib.Card.initializeAllCards();</script>
+</div>
+</div>
+</div>
+</div>
+</div>
 <p><br> <br></p>
 </section>
 <section id="what-sites-are-being-forecasted" class="level2">

instructions.html

@@ -210,7 +210,10 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#supported-distributions" id="toc-supported-distributions" class="nav-link" data-scroll-target="#supported-distributions"><span class="header-section-number">4.1</span> Supported distributions</a></li>
   <li><a href="#example-forecasts" id="toc-example-forecasts" class="nav-link" data-scroll-target="#example-forecasts"><span class="header-section-number">4.2</span> Example forecasts</a></li>
   </ul></li>
-  <li><a href="#submission-process" id="toc-submission-process" class="nav-link" data-scroll-target="#submission-process"><span class="header-section-number">5</span> Submission process</a></li>
+  <li><a href="#submission-process" id="toc-submission-process" class="nav-link" data-scroll-target="#submission-process"><span class="header-section-number">5</span> Submission process</a>
+  <ul class="collapse">
+  <li><a href="#timing" id="toc-timing" class="nav-link" data-scroll-target="#timing"><span class="header-section-number">5.1</span> Timing</a></li>
+  </ul></li>
   <li><a href="#post-submission" id="toc-post-submission" class="nav-link" data-scroll-target="#post-submission"><span class="header-section-number">6</span> Post submission</a>
   <ul class="collapse">
   <li><a href="#processing" id="toc-processing" class="nav-link" data-scroll-target="#processing"><span class="header-section-number">6.1</span> Processing</a></li>
@@ -271,7 +274,7 @@ <h2 data-number="3" class="anchored" data-anchor-id="forecast-file-format"><span
 <li><p><code>datetime</code>: forecast timestamp. Format <code>%Y-%m-%d %H:%M:%S</code> with UTC as the time zone. Forecasts submitted with a <code>%Y-%m-%d</code> format will be converted to a full datetime assuming UTC mid-night.</p></li>
 <li><p><code>reference_datetime</code>: The start of the forecast; this should be 0 times steps in the future. There should only be one value of <code>reference_datetime</code> in the file. Format is <code>%Y-%m-%d %H:%M:%S</code> with UTC as the time zone. Forecasts submitted with a <code>%Y-%m-%d</code> format will be converted to a full datetime assuming UTC mid-night.</p></li>
 <li><p><code>duration</code>: the time-step of the forecast. Use the value of <code>P1D</code> for a daily forecast, <code>P1W</code> for a weekly forecast, and <code>PT30M</code> for 30 minute forecast. This value should match the duration of the target variable that you are forecasting. Formatted as <a href="https://en.wikipedia.org/wiki/ISO_8601#Durations">ISO 8601 duration</a></p></li>
-<li><p><code>site_id</code>: code for site (<code>bvre</code>, <code>fcre</code>, or <code>tubr</code>)</p></li>
+<li><p><code>site_id</code>: code for NEON site.</p></li>
 <li><p><code>family</code> name of the probability distribution that is described by the parameter values in the parameter column (see list below for accepted distribution). An ensemble forecast as a family of <code>ensemble</code>. See note below about family</p></li>
 <li><p><code>parameter</code> the parameters for the distribution (see note below about parameter column) or the number of the ensemble member. For example the parameters for normal are <code>mu</code> and <code>sigma</code>.</p></li>
 <li><p><code>variable</code>: standardized variable name</p></li>
@@ -323,50 +326,46 @@ <h3 data-number="4.1" class="anchored" data-anchor-id="supported-distributions">
 <h3 data-number="4.2" class="anchored" data-anchor-id="example-forecasts"><span class="header-section-number">4.2</span> Example forecasts</h3>
 <p>Here is an example of a forecast that uses a normal distribution:</p>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://renc.osn.xsede.org/bio230121-bucket01/vera4cast/forecasts/raw/T20231001231345_daily-2023-10-01-climatology.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
+<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/T20231102190926_aquatics-2023-10-19-climatology.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>dplyr<span class="sc">::</span><span class="fu">glimpse</span>(df)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Rows: 288
-Columns: 11
+<pre><code>Rows: 4,456
+Columns: 8
 $ model_id           &lt;chr&gt; "climatology", "climatology", "climatology", "clima…
-$ datetime           &lt;date&gt; 2023-10-02, 2023-10-02, 2023-10-02, 2023-10-02, 20…
-$ reference_datetime &lt;date&gt; 2023-10-01, 2023-10-01, 2023-10-01, 2023-10-01, 20…
-$ site_id            &lt;chr&gt; "bvre", "bvre", "bvre", "bvre", "bvre", "bvre", "bv…
-$ variable           &lt;chr&gt; "Chla_ugL_mean", "Chla_ugL_mean", "Temp_C_mean", "T…
+$ datetime           &lt;date&gt; 2023-10-20, 2023-10-20, 2023-10-20, 2023-10-20, 20…
+$ reference_datetime &lt;date&gt; 2023-10-19, 2023-10-19, 2023-10-19, 2023-10-19, 20…
+$ site_id            &lt;chr&gt; "ARIK", "ARIK", "ARIK", "ARIK", "ARIK", "ARIK", "AR…
 $ family             &lt;chr&gt; "normal", "normal", "normal", "normal", "normal", "…
 $ parameter          &lt;chr&gt; "mu", "sigma", "mu", "sigma", "mu", "sigma", "mu", …
-$ prediction         &lt;dbl&gt; 10.041987, 2.587292, 18.331126, 2.531732, 9.541139,…
-$ depth_m            &lt;dbl&gt; 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1…
-$ project_id         &lt;chr&gt; "vera4cast", "vera4cast", "vera4cast", "vera4cast",…
-$ duration           &lt;chr&gt; "P1D", "P1D", "P1D", "P1D", "P1D", "P1D", "P1D", "P…</code></pre>
+$ variable           &lt;chr&gt; "oxygen", "oxygen", "temperature", "temperature", "…
+$ prediction         &lt;dbl&gt; 4.542862, 1.448393, 8.070854, 1.330059, 4.194895, 1…</code></pre>
 </div>
 </div>
 <p>For an ensemble (or sample) forecast, the <code>family</code> column uses the word <code>ensemble</code> to designate that it is a ensemble forecast and the parameter column is the ensemble member number (<code>1</code>, <code>2</code>, <code>3</code> …)</p>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://renc.osn.xsede.org/bio230121-bucket01/vera4cast/forecasts/raw/T20231001231348_daily-2023-10-01-persistenceRW.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
+<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(<span class="st">"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/forecasts/raw/T20231102190926_aquatics-2023-10-19-persistenceRW.csv.gz"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>dplyr<span class="sc">::</span><span class="fu">glimpse</span>(df)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Rows: 28,800
-Columns: 11
+<pre><code>Rows: 530,400
+Columns: 8
 $ model_id           &lt;chr&gt; "persistenceRW", "persistenceRW", "persistenceRW", …
-$ datetime           &lt;dttm&gt; 2023-10-02, 2023-10-03, 2023-10-04, 2023-10-05, 20…
-$ reference_datetime &lt;dttm&gt; 2023-10-01, 2023-10-01, 2023-10-01, 2023-10-01, 20…
-$ site_id            &lt;chr&gt; "bvre", "bvre", "bvre", "bvre", "bvre", "bvre", "bv…
+$ datetime           &lt;date&gt; 2023-10-20, 2023-10-21, 2023-10-22, 2023-10-23, 20…
+$ reference_datetime &lt;date&gt; 2023-10-19, 2023-10-19, 2023-10-19, 2023-10-19, 20…
+$ site_id            &lt;chr&gt; "BARC", "BARC", "BARC", "BARC", "BARC", "BARC", "BA…
 $ family             &lt;chr&gt; "ensemble", "ensemble", "ensemble", "ensemble", "en…
 $ parameter          &lt;dbl&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
-$ variable           &lt;chr&gt; "Chla_ugL_mean", "Chla_ugL_mean", "Chla_ugL_mean", …
-$ prediction         &lt;dbl&gt; 10.59539, 13.04463, 13.86989, 13.81281, 14.09787, 1…
-$ depth_m            &lt;dbl&gt; 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1…
-$ project_id         &lt;chr&gt; "vera4cast", "vera4cast", "vera4cast", "vera4cast",…
-$ duration           &lt;chr&gt; "P1D", "P1D", "P1D", "P1D", "P1D", "P1D", "P1D", "P…</code></pre>
+$ variable           &lt;chr&gt; "chla", "chla", "chla", "chla", "chla", "chla", "ch…
+$ prediction         &lt;dbl&gt; 3.7956520, 4.1800958, 3.2470058, 3.4550993, 3.48348…</code></pre>
 </div>
 </div>
 </section>
 </section>
 <section id="submission-process" class="level2" data-number="5">
 <h2 data-number="5" class="anchored" data-anchor-id="submission-process"><span class="header-section-number">5</span> Submission process</h2>
+<section id="timing" class="level3" data-number="5.1">
+<h3 data-number="5.1" class="anchored" data-anchor-id="timing"><span class="header-section-number">5.1</span> Timing</h3>
 <p>Individual forecast files can be uploaded any time.</p>
-<p>Teams will submit their forecast csv files through an R function.</p>
+<p>Teams will submit their forecast csv files through an R function. The csv file can only contain one unique <code>model_id</code> and one unique <code>project_id</code>.</p>
 <p>The function is available using the following code</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"eco4cast/neon4cast"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -382,6 +381,7 @@ <h2 data-number="5" class="anchored" data-anchor-id="submission-process"><span c
 <span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>                         <span class="at">first_submission =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section>
+</section>
 <section id="post-submission" class="level2" data-number="6">
 <h2 data-number="6" class="anchored" data-anchor-id="post-submission"><span class="header-section-number">6</span> Post submission</h2>
 <section id="processing" class="level3" data-number="6.1">