CRAN prep and minor fixes to documentation (#173)

* simplfying data download and adding a trycatch (#169)  removing contentid for the short term and simplifying data download.

* Graceful testing for load_taxonomic_resources (#164)

* Add GitHub links to DESCRIPTION

* Updated hex #81

* NEWS updates and CRAN comments, Reverse dependency comments

* Updated documentation for create_taxonomic_update_lookup #168

* Minor updates to documentation for resources argument

* Minor documentation changes

---------

Co-authored-by: Will Cornwell <wcornwell@gmail.com>
Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com>
Co-authored-by: Fonti Kar <f.kar@unsw.edu.au>

.Rbuildignore

@@ -16,3 +16,5 @@
 ^Meta$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^revdep
+

DESCRIPTION

@@ -42,4 +42,5 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-URL: https://traitecoevo.github.io/APCalign/
+URL: https://traitecoevo.github.io/APCalign/, https://github.com/traitecoevo/APCalign
+BugReports: https://github.com/traitecoevo/APCalign/issues

NEWS.md

@@ -1,3 +1,11 @@
 # APCalign 0.1.3
 
-* Refined testing for functions that rely on online resources and network connection
+
+* Better handling of errors when API/network connection is down for `load_taxonomic_resources` 
+
+* Refined testing for `load_taxonomic_resources` 
+
+* Revised hex - now is .svg!
+
+* Minor update to documentation for 'create_taxonomic_update_lookup'
+

R/align_taxa.R

@@ -1,6 +1,10 @@
 #' Find taxonomic alignments for a list of names to a version of the Australian Plant Census (APC) through standardizing formatting and checking for spelling issues
 #'
-#' This function uses Australian Plant Census (APC) & the Australian Plant Name Index (APNI) to find taxonomic alignments for a list of names.
+#' This function uses Australian Plant Census (APC) & the Australian Plant Name Index (APNI) to find taxonomic alignments for a list of names. 
+#' It uses the internal function `match_taxa` to attempt to match input strings to taxon names in the APC/APNI. 
+#' It sequentially searches for matches against more than 20 different string patterns, prioritising exact matches (to accepted names as well as  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; taxa not identified to species), and indicates these names only have a genus-rank match.
 #'
 #' @param original_name A list of names to query for taxonomic alignments.
 #' @param output (optional) The name of the file to save the results to.
@@ -14,9 +18,7 @@
 #' @param APNI_matches Name matches to the APNI (Australian Plant Names Index) are turned off as a default.
 #' @param identifier A dataset, location or other identifier, which defaults to NA.
 #'
-#' @return A tibble with columns that include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. See Details
-#' 
-#' @details 
+#' @return A tibble with columns that include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. 
 #' - original_name: the original plant name input.
 #' - aligned_name: the original plant name after the function standardise_names has standardised the syntax of infraspecific taxon designations.
 #' - taxonomic_dataset: the source of the aligned names (APC or APNI).

R/create_species_state_origin_matrix.R

@@ -6,7 +6,7 @@
 #' @family diversity methods
 #' @param resources the taxonomic resources required to make the summary statistics.  Loading this can be slow, so call load_taxonomic_resources separately to greatly speed this function up and pass the resources in.
 #'
-#' @return A data frame with columns representing each state and rows representing each species. The values in each cell represent the origin of the species in that state.
+#' @return A tibble with columns representing each state and rows representing each species. The values in each cell represent the origin of the species in that state.
 #'
 #' @import dplyr
 #' @import stringr

R/create_taxonomic_update_lookup.R

@@ -8,15 +8,13 @@
 #' @param stable_or_current_data either "stable" for a consistent version, or "current" for the leading edge version.
 #' @param version The version number of the dataset to use.
 #' @param taxonomic_splits How to handle one_to_many taxonomic matches.  Default is "return_all".  The other options are "collapse_to_higher_taxon" and "most_likely_species". most_likely_species defaults to the original_name if that name is accepted by the APC; this will be right for certain species subsets, but make errors in other cases, use with caution.
-#' @param full logical for whether the full lookup table is returned or just the two key columns
+#' @param full logical for whether the full lookup table is returned or just key columns
 #' @param resources These are the taxonomic resources used for cleaning, this will default to loading them from a local place on your computer.  If this is to be called repeatedly, it's much faster to load the resources using \code{\link{load_taxonomic_resources}} separately and pass the data in.
 #' @param APNI_matches Name matches to the APNI (Australian Plant Names Index) are turned off as a default. 
 #' @param imprecise_fuzzy_matches Imprecise fuzzy matches are turned off as a default.
 #' @param identifier A dataset, location or other identifier, which defaults to NA.
 #' @param output file path to save the intermediate output to
-#' @return A lookup table containing the accepted and suggested names for each original name input, and additional taxonomic information such as taxon rank, taxonomic status, taxon IDs and genera. See Details.
-#' 
-#' @details
+#' @return A lookup table containing the accepted and suggested names for each original name input, and additional taxonomic information such as taxon rank, taxonomic status, taxon IDs and genera. 
 #' - original_name: the original plant name.
 #' - aligned_name: the input plant name that has been aligned to a taxon name in the APC or APNI by the align_taxa function.
 #' - accepted_name: the APC-accepted plant name, when available.
@@ -57,9 +55,7 @@ create_taxonomic_update_lookup <- function(taxa,
                                            APNI_matches = TRUE, 
                                            imprecise_fuzzy_matches = FALSE, 
                                            identifier = NA_character_,
-                                           resources = load_taxonomic_resources(stable_or_current_data =
-                                                                                  stable_or_current_data,
-                                                                                version = version),
+                                           resources = load_taxonomic_resources(),
                                            output = NULL) {
 
   validate_taxonomic_splits_input(taxonomic_splits)

R/data.R

@@ -4,7 +4,7 @@
 #' 
 #'
 #' @format `gbif_lite`
-#' A data frame with 129 rows and 7 columns:
+#' A tibble with 129 rows and 7 columns:
 #' \describe{
 #'   \item{species}{The name of the first or species of scientificname}
 #'   \item{infraspecificepithet}{	The name of the lowest or terminal infraspecific epithet of the scientificname}

R/load_taxonomic_resources.R

@@ -1,6 +1,6 @@
 #' Load taxonomic resources from either stable or current versions of APC and APNI
 #'
-#' Loads taxonomic resources into the global environment. This function accesses taxonomic data from a dataset using the provided version number or the default version. The loaded data contains two lists: APC and APNI, which contain taxonomic information about plant species in Australia. The function creates several data frames by filtering and selecting data from the loaded lists.
+#' Loads taxonomic resources into the global environment. This function accesses taxonomic data from a dataset using the provided version number or the default version. The loaded data contains two lists: APC and APNI, which contain taxonomic information about plant species in Australia. The function creates several tibbles by filtering and selecting data from the loaded lists.
 #'
 #' @param stable_or_current_data Type of dataset to access. The default is "stable", which loads the
 #'   dataset from a github archived file. If set to "current", the dataset will be loaded from

R/state_diversity_counts.R

@@ -16,7 +16,7 @@
 #' @examples
 #'  \donttest{state_diversity_counts(state = "NSW")}
 state_diversity_counts <- function(state,
-                                   resources = load_taxonomic_resources(version = default_version())) {
+                                   resources = load_taxonomic_resources()) {
   valid_inputs <- c(
     "NSW",
     "NT",

R/update_taxonomy.R

@@ -24,31 +24,6 @@
 #'
 #'
 #' @return A tibble with updated taxonomy for the specified plant names. The tibble contains the following columns:
-#' \itemize{
-#'   \item \code{original_name}: the original plant name.
-#'   \item \code{aligned_name}: the input plant name.
-#'   \item \code{accepted_name}: the APC-accepted plant name, when available.
-#'   \item \code{suggested_name}: the suggested plant name to use. Identical to the accepted_name, when an accepted_name exists.
-#'   \item \code{taxonomic_dataset}: the source of the updated taxonomic information (APC or APNI).
-#'   \item \code{accepted_name_usage_ID}: the unique identifier for the accepted name of the input name.
-#'   \item \code{canonical_name}: the accepted (or known) scientific name for the input name.
-#'   \item \code{scientific_name}: the full scientific name, with authorship.
-#'   \item \code{taxon_rank}: the taxonomic rank of the accepted (or known) name.
-#'   \item \code{taxonomic_status}: the taxonomic status of the accepted (or known) name.
-#'   \item \code{taxonomic_status_aligned}: for taxa where there is ambiguity due to a taxon split, the taxonomic status of each possible match.
-#'   \item \code{aligned_reason}: the explanation of a specific taxon name alignment (from an original name to an aligned name).
-#'   \item \code{update_reason}: the explanation of a specific taxon name update (from an aligned name to an accepted name).
-#'   \item \code{genus}: the genus of the accepted (or known) name.
-#'   \item \code{family}: the family of the accepted (or known) name.
-#'   \item \code{subclass}: the subclass of the accepted name.
-#'   \item \code{taxon_distribution}: the distribution of the accepted name.
-#'   \item \code{taxon_ID}: an identifier for a specific taxon concept.
-#'   \item \code{taxon_ID_genus}: an identifier for the genus.
-#'   \item \code{scientific_name_ID}: an identifier for the nomenclatural (not taxonomic) details of a scientific name.
-#'   \item \code{row_number}: the row number of a specific original_name in the input.
-#' }
-#' 
-#' @details
 #' - original_name: the original plant name.
 #' - aligned_name: the input plant name that has been aligned to a taxon name in the APC or APNI by the align_taxa function.
 #' - accepted_name: the APC-accepted plant name, when available.

README.Rmd

@@ -23,7 +23,7 @@ library(APCalign)
 [![R-CMD-check](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-# APCalign <img src="man/figures/APCalign_hex.png" align="right" width="120"/>
+# 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.

README.md

@@ -8,7 +8,7 @@ coverage](https://codecov.io/gh/traitecoevo/APCalign/branch/master/graph/badge.s
 [![R-CMD-check](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-# APCalign <img src="man/figures/APCalign_hex.png" align="right" width="120"/>
+# 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
@@ -54,8 +54,8 @@ create_taxonomic_update_lookup(
 #> 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_authorship <chr>, aligned_reason <chr>,
-#> #   update_reason <chr>, number_of_collapsed_taxa <dbl>
+#> #   scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
+#> #   number_of_collapsed_taxa <dbl>
 ```
 
 ## Learn more
@@ -64,7 +64,7 @@ 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)
+algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html)
 and how [APC/APNI data is
 cached](https://traitecoevo.github.io/APCalign/articles/caching.html)
 behind-the-scenes.

cran-comments.md

@@ -1,5 +1,18 @@
+## Resubmission
+This is a resubmission. This version we have: 
+
+* Added measures to gracefully fail should API/internet resources/network is down.
+
+* Minor update to documentation for one function
+
 ## R CMD check results
 
 0 errors | 0 warnings | 0 note
 
-* This is a new release.
+
+## Rev Deps
+
+* There are no reverse dependencies that needed to be checked
+
+
+

inst/figures/hex.R

@@ -1,12 +1,16 @@
 library(hexSticker)
 
-imgurl <- file.path("inst/figures/wattle2.png")
-sticker(imgurl, package="APCalign", 
-        p_size = 30,
-        p_x = 1, p_y = 0.70,
-        s_x=1.5, s_y=1, 
-        s_width=0.9, s_height = 0.9,
-        p_color = "goldenrod4",
-        h_color = "goldenrod1",
-        h_fill = "white",
-        filename="man/figures/APCalign_hex.png")
+imgurl <- file.path("inst/figures/APCalign_v2.png")
+sticker(
+  imgurl, 
+  package=" ", 
+  # p_size = 30,
+  # p_x = 1, p_y = 0.70,
+  s_x=1, s_y=1.1, 
+  s_width=0.85, s_height = 0.85,
+  # p_color = "goldenrod4",
+  h_color = "#B38E21",
+  h_fill = "#FBF8C7",
+  filename="man/figures/APCalign_hex_2.png"
+  )
+