spelling fixes and removing special Mac install instructions (#229)

* spelling fixes and removing special Mac install instructions * adding mac back into CI
traitecoevo · May 29, 2024 · 6acbeac · 6acbeac
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -18,6 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}

diff --git a/NEWS.md b/NEWS.md
@@ -12,7 +12,7 @@ streamlined the package.
 * Write a replacement function for `stringr::word` that is much faster.
 * Additional speed up and accuracy of fuzzy_match function by
   - Restricting reference list to names with the same first letter as input string.
-  - Switch from using `utils::adist` to `stringdist:stringdist(method = "dl")`
+  - Switch from using `utils::adist` to `stringdist::stringdist(method = "dl")`
 * Rework `standardise_names` to remove punctuation from the start of the string
 * Rework `strip_names_extra` (previously `strip_names_2`) to just perform 
 additional functions to `strip_names`, rather than repeating those performed by `strip_names`.

diff --git a/R/align_taxa.R b/R/align_taxa.R
@@ -22,7 +22,7 @@
 #'  synonyms, orthographic variants) over fuzzy matches.
 #' - It prioritises matches to taxa in the APC over names in the APNI.
 #' - It identifies string patterns in input names that suggest a name can only
-#'  be aligned to a genus (hybrids that are not in the APC/ANI; graded species;
+#'  be aligned to a genus (hybrids that are not in the APC/APNI; graded species;
 #'  taxa not identified to species), and indicates these names only have a
 #'  genus-rank match.
 #' 

diff --git a/R/update_taxonomy.R b/R/update_taxonomy.R
@@ -18,7 +18,7 @@
 #' Notes:
 #' - As the input for this function is a table with 5 columns (output by 
 #' align_taxa), this function will only be used when you explicitly want to 
-#' separate the aligment and updating components of APCalign. This function is 
+#' separate the alignment and updating components of APCalign. This function is 
 #' the second half of create_taxonomic_update_lookup.
 #'
 #' @family taxonomic alignment functions

diff --git a/README.Rmd b/README.Rmd
@@ -25,35 +25,23 @@ library(APCalign)
 
 # APCalign <img src="man/figures/APCalign_hex_2.svg" align="right" width="120"/>
 
-'APCalign' uses the [Australian Plant Census (APC)](https://biodiversity.org.au/nsl/services/search/taxonomy) and [Australian Plant Name Index](https://biodiversity.org.au/nsl/services/search/names) to align and update Australian plant taxon name strings. 'APCalign' also supplies information about
-the established status (native/introduced) of plant taxa across different states/territories.
+`APCalign` uses the [Australian Plant Census (APC)](https://biodiversity.org.au/nsl/services/search/taxonomy) and [Australian Plant Name Index](https://biodiversity.org.au/nsl/services/search/names) to align and update Australian plant taxon name strings. 'APCalign' also supplies information about
+the established status (native/introduced) of plant taxa across different states/territories. It's useful for updating species list and intersecting them with the APC consensus understanding of established status (native/introduced).
 
 ## Installation
 
-For Windows and Linux:
-
 ```{r install, eval= FALSE}
 
-# install.packages("remotes")
-# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")
-
-```
-
-for MacOS there is currently an extra line needed to install a working binary of the `arrow` dependency from r-universe instead of CRAN:
-
-```{r install_mac, eval= FALSE}
-
-# install.packages("arrow", repos = c('https://apache.r-universe.dev', 'https://cloud.r-project.org'))
-# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")
-
+ install.packages("remotes")
+ remotes::install_github("traitecoevo/APCalign")
+ 
 ```
 
-
 ## A quick demo
 
 Generating a look-up table can be done with just one function:
 
-```{r}
+```{r,message=FALSE}
 
 library(APCalign)
 
@@ -68,7 +56,7 @@ create_taxonomic_update_lookup(
 
 if you're going to use APCalign more than once, it will save you time to load the taxonomic resources into memory first:
 
-```{r}
+```{r,message=FALSE}
 
 tax_resources <- load_taxonomic_resources()
 
@@ -83,7 +71,7 @@ create_taxonomic_update_lookup(
 )
 ```
 
-Checking for Australian natives:
+Checking for a list of species to see if they are classified as Australian natives:
 
 ```{r, message=FALSE}
 
@@ -96,12 +84,12 @@ We also developed a shiny application for non-R users to update and align their
 
 ## Learn more
 
-Highly recommend looking at our [Getting Started](https://traitecoevo.github.io/APCalign/articles/APCalign.html) vignette to learn about how to use 'APCalign'. You can also learn more about our [taxa matching  algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html).
+Highly recommend looking at our [Getting Started](https://traitecoevo.github.io/APCalign/articles/APCalign.html) vignette to learn about how to use `APCalign`. You can also learn more about our [taxa matching  algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html).
 
 
 ## Found a bug? 
 
-Did you come across an unexpected taxon name change? Elusive error you can't debug - [submit an issue](https://github.com/traitecoevo/APCalign/issues) and we will try our best to help
+Did you come across an unexpected taxon name change? Elusive error you can't debug - [submit an issue](https://github.com/traitecoevo/APCalign/issues) and we will try our best to help.
 
 ## Comments and contributions
 

diff --git a/README.md b/README.md
@@ -10,31 +10,23 @@ coverage](https://codecov.io/gh/traitecoevo/APCalign/branch/master/graph/badge.s
 
 # APCalign <img src="man/figures/APCalign_hex_2.svg" align="right" width="120"/>
 
-‘APCalign’ uses the [Australian Plant Census
+`APCalign` uses the [Australian Plant Census
 (APC)](https://biodiversity.org.au/nsl/services/search/taxonomy) and
 [Australian Plant Name
 Index](https://biodiversity.org.au/nsl/services/search/names) to align
 and update Australian plant taxon name strings. ‘APCalign’ also supplies
 information about the established status (native/introduced) of plant
-taxa across different states/territories.
+taxa across different states/territories. It’s useful for updating
+species list and intersecting them with the APC consensus understanding
+of established status (native/introduced).
 
 ## Installation
 
-For Windows and Linux:
-
 ``` r
 
-# install.packages("remotes")
-# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")
-```
-
-for MacOS there is currently an extra line needed to install a working
-binary of the `arrow` dependency from r-universe instead of CRAN:
-
-``` r
-
-# install.packages("arrow", repos = c('https://apache.r-universe.dev', 'https://cloud.r-project.org'))
-# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")
+ install.packages("remotes")
+ remotes::install_github("traitecoevo/APCalign")
+
 ```
 
 ## A quick demo
@@ -52,58 +44,49 @@ create_taxonomic_update_lookup(
     "Commersonia rosea"
     )
 )
-#> Checking alignments of 3 taxa
+#> ================================================================================================================================================================
+#> # A tibble: 3 × 12
+#>   original_name       aligned_name accepted_name suggested_name genus taxon_rank
+#>   <chr>               <chr>        <chr>         <chr>          <chr> <chr>     
+#> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species   
+#> 2 Acacia longifolia   Acacia long… Acacia longi… Acacia longif… Acac… species   
+#> 3 Commersonia rosea   Commersonia… Androcalva r… Androcalva ro… Andr… species   
+#> # ℹ 6 more variables: taxonomic_dataset <chr>, taxonomic_status <chr>,
+#> #   scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
+#> #   number_of_collapsed_taxa <dbl>
 ```
 
-    #> Loading resources into memory...
-    #> ================================================================================================================================================================
-    #> ...done
-    #>   -> of these 2 names have a perfect match to a scientific name in the APC. Alignments being sought for remaining names.
-    #> # A tibble: 3 × 12
-    #>   original_name       aligned_name accepted_name suggested_name genus taxon_rank
-    #>   <chr>               <chr>        <chr>         <chr>          <chr> <chr>     
-    #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species   
-    #> 2 Acacia longifolia   Acacia long… Acacia longi… Acacia longif… Acac… species   
-    #> 3 Commersonia rosea   Commersonia… Androcalva r… Androcalva ro… Andr… species   
-    #> # ℹ 6 more variables: taxonomic_dataset <chr>, taxonomic_status <chr>,
-    #> #   scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
-    #> #   number_of_collapsed_taxa <dbl>
-
 if you’re going to use APCalign more than once, it will save you time to
 load the taxonomic resources into memory first:
 
 ``` r
 
 tax_resources <- load_taxonomic_resources()
+#> ================================================================================================================================================================
+
+create_taxonomic_update_lookup( 
+  taxa = c(
+    "Banksia integrifolia",
+    "Acacia longifolia",
+    "Commersonia rosea",
+    "not a species"
+    ),
+  resources = tax_resources
+)
+#> # A tibble: 4 × 12
+#>   original_name       aligned_name accepted_name suggested_name genus taxon_rank
+#>   <chr>               <chr>        <chr>         <chr>          <chr> <chr>     
+#> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species   
+#> 2 Acacia longifolia   Acacia long… Acacia longi… Acacia longif… Acac… species   
+#> 3 Commersonia rosea   Commersonia… Androcalva r… Androcalva ro… Andr… species   
+#> 4 not a species       <NA>         <NA>          <NA>           <NA>  <NA>      
+#> # ℹ 6 more variables: taxonomic_dataset <chr>, taxonomic_status <chr>,
+#> #   scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
+#> #   number_of_collapsed_taxa <dbl>
 ```
 
-    #> Loading resources into memory...
-    #> ================================================================================================================================================================
-    #> ...done
-
-    create_taxonomic_update_lookup( 
-      taxa = c(
-        "Banksia integrifolia",
-        "Acacia longifolia",
-        "Commersonia rosea",
-        "not a species"
-        ),
-      resources = tax_resources
-    )
-    #> Checking alignments of 4 taxa
-    #>   -> of these 2 names have a perfect match to a scientific name in the APC. Alignments being sought for remaining names.
-    #> # A tibble: 4 × 12
-    #>   original_name       aligned_name accepted_name suggested_name genus taxon_rank
-    #>   <chr>               <chr>        <chr>         <chr>          <chr> <chr>     
-    #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species   
-    #> 2 Acacia longifolia   Acacia long… Acacia longi… Acacia longif… Acac… species   
-    #> 3 Commersonia rosea   Commersonia… Androcalva r… Androcalva ro… Andr… species   
-    #> 4 not a species       <NA>         <NA>          <NA>           <NA>  <NA>      
-    #> # ℹ 6 more variables: taxonomic_dataset <chr>, taxonomic_status <chr>,
-    #> #   scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
-    #> #   number_of_collapsed_taxa <dbl>
-
-Checking for Australian natives:
+Checking for a list of species to see if they are classified as
+Australian natives:
 
 ``` r
 
@@ -125,7 +108,7 @@ align their taxonomic names. You can find the application here:
 
 Highly recommend looking at our [Getting
 Started](https://traitecoevo.github.io/APCalign/articles/APCalign.html)
-vignette to learn about how to use ‘APCalign’. You can also learn more
+vignette to learn about how to use `APCalign`. You can also learn more
 about our [taxa matching
 algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html).
 
@@ -134,7 +117,7 @@ algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.
 Did you come across an unexpected taxon name change? Elusive error you
 can’t debug - [submit an
 issue](https://github.com/traitecoevo/APCalign/issues) and we will try
-our best to help
+our best to help.
 
 ## Comments and contributions
 

diff --git a/man/align_taxa.Rd b/man/align_taxa.Rd
diff --git a/man/update_taxonomy.Rd b/man/update_taxonomy.Rd
diff --git a/vignettes/APCalign.Rmd b/vignettes/APCalign.Rmd
@@ -9,26 +9,21 @@ vignette: >
 
 
 
-When working with biodiversity data, it is important to verify  taxonomic names with an authoritative list and correct any out-of-date names. The 'APCalign' package simplifies this process by:
+When working with biodiversity data, it is important to verify  taxonomic names with an authoritative list and correct any out-of-date names. The `APCalign` package simplifies this process by:
 
 -   Accessing up-to-date taxonomic information from the [Australian Plant Census](https://biodiversity.org.au/nsl/services/search/taxonomy) and the [Australia Plant Name Index](https://biodiversity.org.au/nsl/services/search/names).
 -   Aligning authoritative names to your taxonomic names using our [fuzzy matching algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html)
 -   Updating your taxonomic names in a transparent, reproducible manner
 
 ## Installation
 
-'APCalign' is currently not on CRAN. You can install its current developmental version using
-
-
-
 ```r
-# install.packages("remotes")
+install.packages("remotes")
 remotes::install_github("traitecoevo/APCalign")
-
 library(APCalign)
 ```
 
-To demonstrate how to use 'APCalign', we will use an example dataset `gbif_lite` which is documented in `?gbif_lite`
+To demonstrate how to use `APCalign`, we will use an example dataset `gbif_lite` which is documented in `?gbif_lite`
 
 
 
@@ -52,14 +47,14 @@ gbif_lite |> print(n = 6)
 
 ## Retrieve taxonomic resources
 
-The first step is to retrieve the entire APC and APNI name databases and store them locally as taxonomic resources. We achieve this using `load_taxonomic_resources()`.
+The first step is to retrieve the entire APC and APNI name databases and store them locally as taxonomic resources. We achieve this using `load_taxonomic_resources()`.  The resources are compressed as parquet files to speed download and local loading. 
 
 There are two versions of the databases that you can retrieve with the `stable_or_current_data` argument. Calling:
 
 -   `stable` will retrieve the most recent, archived version of the databases from our [GitHub releases](https://github.com/traitecoevo/APCalign/releases). This is set as the default option.
 -   `current` will retrieve the up-to-date databases directly from the APC and APNI website.
 
-Note that the databases are quite large so the initial retrieval of `stable` versions will take a few minutes. Once the taxonomic resources have been stored locally, subsequent retrievals will take less time. Retrieving `current` resources will always take longer since it is accessing the latest information from the website. Check out our [Resource Caching](https://traitecoevo.github.io/APCalign/articles/caching.html) article to learn more about how the APC and APNIC databases are accessed, stored and retrieved.
+Note that the databases are reasonably large so the initial retrieval of the core data will take a few minutes. Once the taxonomic resources have been stored locally, subsequent retrievals will take less time. Retrieving `current` resources will always take longer since it is accessing the latest information from the website in an uncompressed format. 
 
 
 ```r

diff --git a/vignettes/articles/reproducibility.Rmd b/vignettes/articles/reproducibility.Rmd
@@ -61,7 +61,7 @@ default_version()
 
 Then copying and pasting the output into `load_taxonomic_resources()` directly. This way makes the version of taxonomic resources more explicit in your code. 
 
-To ensure the specific version of taxonomic resources is availabe for subsequent functions make sure to assign them to an object: 
+To ensure the specific version of taxonomic resources is available for subsequent functions make sure to assign them to an object: 
 
 ```{r}
 resources_0.0.4.9000 <- load_taxonomic_resources(