New function and bumping to version 1.1.0 (#240)

* Bump version number (1.0.0.9000) [skip ci] * spelling fixes and removing special Mac install instructions (#229) * spelling fixes and removing special Mac install instructions * adding mac back into CI * Cran preparations (#230) * Added example for default_version, updated LICENSE year, added R CMD CHECK results * Comment about Tidy and Mac and HTML validation * Updated CITATION file * Updated version numbers * cleaning up (#231) * Added example for default_version, updated LICENSE year, added R CMD CHECK results * Comment about Tidy and Mac and HTML validation * Updated CITATION file * Updated version numbers * Removed auto package version in citation * Updated CRAN comments * Fixed typo in CITATION * Resubmitted --------- Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> * fixing badges * Tweaks (#234) * fix example * fix vignette paths * testing for issue #235 * still working on #235 * one more try to find the edge case * another edge case? * reformat code in release file * another edge case * reverting previous commit to documentation * adding check on resources to all functions that need resources * bumping version number and updating readme * missed two checking spots * 238 genus family lookup (#239) * dealing with cran and CI issues (#236) * Bump version number (1.0.0.9000) [skip ci] * spelling fixes and removing special Mac install instructions (#229) * spelling fixes and removing special Mac install instructions * adding mac back into CI * Cran preparations (#230) * Added example for default_version, updated LICENSE year, added R CMD CHECK results * Comment about Tidy and Mac and HTML validation * Updated CITATION file * Updated version numbers * cleaning up (#231) * Added example for default_version, updated LICENSE year, added R CMD CHECK results * Comment about Tidy and Mac and HTML validation * Updated CITATION file * Updated version numbers * Removed auto package version in citation * Updated CRAN comments * Fixed typo in CITATION * Resubmitted --------- Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> * fixing badges * Tweaks (#234) * fix example * fix vignette paths * testing for issue #235 * still working on #235 * one more try to find the edge case * another edge case? * reformat code in release file * another edge case * reverting previous commit to documentation * adding check on resources to all functions that need resources * bumping version number and updating readme * missed two checking spots --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> Co-authored-by: Dave Slager <slager@users.noreply.github.com> * Update new * fixing bug in hidden function and re-naming a bit * adding new genus in family function * testing? * namespaces * testing testing * forgot how namespaces work * so many details *sigh* --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> Co-authored-by: Dave Slager <slager@users.noreply.github.com> * bumping version number and updating news * update readme * no empty lines in description --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> Co-authored-by: Dave Slager <slager@users.noreply.github.com>
traitecoevo · Aug 13, 2024 · 005e3d3 · 005e3d3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: APCalign
 Title: Resolving Plant Taxon Names Using the Australian Plant Census
-Version: 1.0.2
+Version: 1.1.0
 Authors@R: c(
   person(given = "Daniel", family = "Falster", role = c("aut", "cre", "cph"), email = "daniel.falster@unsw.edu.au", comment = c(ORCID = "0000-0002-9814-092X")),
   person(given = "Elizabeth", family = "Wenk", role = c("aut", "ctb"), email = "e.wenk@unsw.edu.au", comment = c(ORCID = "0000-0001-5640-5910")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ export(align_taxa)
 export(create_species_state_origin_matrix)
 export(create_taxonomic_update_lookup)
 export(default_version)
+export(get_apc_genus_family_lookup)
 export(load_taxonomic_resources)
 export(native_anywhere_in_australia)
 export(standardise_names)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,9 @@
-# APCalign 1.0.2
 
-Minor update to fix 
+# APCalign 1.1.0
+
+Minor updates and adding one function: 
+
+- Create a genus->family lookup from the specified APC release 
 
 - Deal with the vignette issues that emerged on CRAN 
 - Improve "graceful failing", based on issues that have come up on github CI

diff --git a/R/state_diversity_counts.R b/R/state_diversity_counts.R
@@ -1,8 +1,8 @@
 #' @title State- and territory-level diversity
-#' 
+#'
 #' @description
-#' For Australian states and territories, use geographic distribution data from 
-#' the APC to calculate state-level diversity for native, introduced, 
+#' For Australian states and territories, use geographic distribution data from
+#' the APC to calculate state-level diversity for native, introduced,
 #' and more complicated species origins
 #'
 #' @family diversity methods
@@ -26,6 +26,7 @@
 #'
 #' @examples
 #'  \donttest{state_diversity_counts(state = "NSW")}
+
 state_diversity_counts <- function(state,
                                    resources = load_taxonomic_resources()) {
 
@@ -77,14 +78,45 @@ state_diversity_counts <- function(state,
 
 
 #' @noRd
-get_apc_genus_family_lookup <-
-  function(resources = load_taxonomic_resources()) {
-    apc_s <- dplyr::filter(resources$APC,
-                    taxon_rank == "species")
-    dplyr::tibble(genus = word(apc_s$scientific_name, 1, 1),
-           family = apc_s$family) %>%
+create_apc_genus_family_lookup <-
+  function(resources) {
+    apc_s <- dplyr::filter(resources$APC, taxon_rank == "species")
+    dplyr::tibble(genus = word(apc_s$accepted_name_usage, 1, 1),
+                  family = apc_s$family) |>
       dplyr::distinct() -> lu
     return(lu)
   }
 
-
+#' @title Lookup Family by Genus from APC
+#'
+#' @description
+#' Retrieve the family name for a given genus using taxonomic data from the
+#' Australian Plant Census (APC).
+#'
+#' @param genus A character vector of genus names for which to retrieve the
+#'  corresponding family names.
+#' @param resources The taxonomic resources required to make the lookup. 
+#'  Loading this can be slow, so call \code{\link{load_taxonomic_resources}} 
+#'  separately to speed up this function and pass the resources in.
+#'
+#' @return A data frame with two columns: "genus", indicating the genus name, 
+#'  and "family", indicating the corresponding family name from the APC.
+#'
+#' @seealso \code{\link{load_taxonomic_resources}}
+#'
+#' @export
+#'
+#' @examples
+#'  \donttest{get_apc_genus_family_lookup(genus = c("Acacia", "Eucalyptus"))}
+get_apc_genus_family_lookup <-
+  function(genus, resources = load_taxonomic_resources()) {
+    if (is.null(resources)) {
+      message("Not finding taxonomic resources; check internet connection?")
+      return(NULL)
+    }
+    fam_lu <- create_apc_genus_family_lookup(resources = resources)
+    lu <- dplyr::tibble(genus = genus) %>%
+      dplyr::left_join(fam_lu, by = "genus")
+    if (any(is.na(lu$family))) warning("some non-matches with the APC accepted genus list, check the formatting of your genus vector.")
+    return(lu)
+  }
diff --git a/README.Rmd b/README.Rmd
@@ -31,15 +31,19 @@ the established status (native/introduced) of plant taxa across different states
 
 ## Installation 
 
-```{r install, eval= FALSE}
+From CRAN:
 
- install.packages("APCalign")
 
- # OR for the github version
+```{r install, eval= FALSE}
+ install.packages("APCalign")
+```
+
+ OR for the github version:
+
+```{r install2, eval= FALSE}
 
  install.packages("remotes")
  remotes::install_github("traitecoevo/APCalign")
- 
 ```
 
 ## A quick demo
@@ -83,6 +87,22 @@ Checking for a list of species to see if they are classified as Australian nativ
 native_anywhere_in_australia(c("Eucalyptus globulus","Pinus radiata"), resources = tax_resources)
 
 ```
+
+Getting a family lookup table for genera from the specified taxonomy:
+
+```{r, message=FALSE}
+
+get_apc_genus_family_lookup(c("Eucalyptus",
+                              "Pinus",
+                              "Actinotus",
+                              "Banksia",
+                              "Acacia",
+                              "Triodia"), 
+                            resources = tax_resources)
+
+```
+
+
 ## Shiny application
 
 We also developed a shiny application for non-R users to update and align their taxonomic names. You can find the application here: https://unsw.shinyapps.io/APCalign-app

diff --git a/README.md b/README.md
@@ -23,15 +23,18 @@ of established status (native/introduced).
 
 ## Installation
 
-``` r
+From CRAN:
 
+``` r
  install.packages("APCalign")
+```
 
- # OR for the github version
+OR for the github version:
 
+
+``` r
  install.packages("remotes")
  remotes::install_github("traitecoevo/APCalign")
-
 ```
 
 ## A quick demo
@@ -106,6 +109,28 @@ native_anywhere_in_australia(c("Eucalyptus globulus","Pinus radiata"), resources
 #> 2 Pinus radiata       introduced
 ```
 
+Getting a family lookup table for genera from the specified taxonomy:
+
+``` r
+
+get_apc_genus_family_lookup(c("Eucalyptus",
+                              "Pinus",
+                              "Actinotus",
+                              "Banksia",
+                              "Acacia",
+                              "Triodia"), 
+                            resources = tax_resources)
+#> # A tibble: 6 × 2
+#>   genus      family    
+#>   <chr>      <chr>     
+#> 1 Eucalyptus Myrtaceae 
+#> 2 Pinus      Pinaceae  
+#> 3 Actinotus  Apiaceae  
+#> 4 Banksia    Proteaceae
+#> 5 Acacia     Fabaceae  
+#> 6 Triodia    Poaceae
+```
+
 ## Shiny application
 
 We also developed a shiny application for non-R users to update and

diff --git a/cran-comments.md b/cran-comments.md
@@ -6,4 +6,6 @@
 * This is a resubmission
 * More gracefully handling edge cases involving parts of the internet being down
 * Better handling an error in the vignette specific to certain MacOS versions
+* Adding one user function for genus->family lookup
+
 
diff --git a/man/get_apc_genus_family_lookup.Rd b/man/get_apc_genus_family_lookup.Rd
diff --git a/tests/testthat/benchmarks/family_check.csv b/tests/testthat/benchmarks/family_check.csv
@@ -0,0 +1,5 @@
+genus,family
+Eucalyptus,Myrtaceae
+Pinus,Pinaceae
+Brassica,Brassicaceae
+not a species,NA
diff --git a/tests/testthat/test-state_diversity.R b/tests/testthat/test-state_diversity.R
@@ -33,3 +33,22 @@ test_that("native_anywhere_in_australia() works", {
   expect_equal(native_check, previous_check)
   expect_warning(native_anywhere_in_australia(species = "NOTASPECIES", resources = resources))
 })
+
+
+test_that("get_apc_genus_family_lookup() works", {
+  expect_warning(family_check <-
+                   get_apc_genus_family_lookup(
+                     c(
+                       "Eucalyptus",
+                       "Pinus",
+                       "Brassica",
+                       "not a species"
+                     ),
+                     resources = resources
+                   ))
+  # readr::write_csv(family_check,"tests/testthat/benchmarks/family_check.csv")
+  previous_check <- readr::read_csv("benchmarks/family_check.csv", show_col_types = FALSE)
+  expect_equal(family_check, previous_check)
+})
+
+