Merged in recent master release, bumped version number

.Rbuildignore

@@ -18,3 +18,5 @@
 ^CRAN-SUBMISSION$
 ^revdep
 ^.DS_Store
+^help
+

.gitignore

@@ -12,3 +12,5 @@ docs/
 /doc/
 /Meta/
 revdep/
+inst/cheatsheet/APCalign-cheatsheet.pptx
+inst/cheatsheet/establishment-means.pdf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: APCalign
 Title: Resolving Plant Taxon Names Using the Australian Plant Census
-Version: 1.1.0
+Version: 1.1.2.9000
 Authors@R: c(
   person(given = "Daniel", family = "Falster", role = c("aut", "cre", "cph"), email = "[email protected]", comment = c(ORCID = "0000-0002-9814-092X")),
   person(given = "Elizabeth", family = "Wenk", role = c("aut", "ctb"), email = "[email protected]", comment = c(ORCID = "0000-0001-5640-5910")),
@@ -38,7 +38,7 @@ Suggests:
     here,
     testthat (>= 3.0.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 URL: https://traitecoevo.github.io/APCalign/, https://github.com/traitecoevo/APCalign

NAMESPACE

@@ -5,6 +5,7 @@ export(create_species_state_origin_matrix)
 export(create_taxonomic_update_lookup)
 export(default_version)
 export(get_apc_genus_family_lookup)
+export(get_versions)
 export(load_taxonomic_resources)
 export(native_anywhere_in_australia)
 export(standardise_names)

NEWS.md

@@ -1,4 +1,6 @@
-# APCalign 1.1.0
+# APCalign 1.1.2
+
+- Added `get_versions()`
 
 - Create a genus->family lookup from the specified APC release 
 

R/APCalign-package.R

@@ -99,7 +99,8 @@ utils::globalVariables(
     "accepted_name_2",
     "alternative_accepted_name_tmp",
     "pro_parte",
-    "suggested_collapsed_name"
+    "suggested_collapsed_name",
+    "versions"
   )
 )
 

R/create_taxonomic_update_lookup.R

@@ -73,7 +73,7 @@
 #'  makes erroneous matches.
 #' @param identifier A dataset, location or other identifier,
 #'  which defaults to NA.
-#' @param quiet Logical to indicate whether to display messages while
+#' @param quiet Logical to indicate whether to display messages while loading data and 
 #'  aligning taxa.
 #' @param output file path to save the output. If this file already exists,
 #'  this function will check if it's a subset of the species passed in and try
@@ -167,7 +167,7 @@ create_taxonomic_update_lookup <- function(taxa,
                                            APNI_matches = TRUE, 
                                            imprecise_fuzzy_matches = FALSE, 
                                            identifier = NA_character_,
-                                           resources = load_taxonomic_resources(),
+                                           resources = load_taxonomic_resources(quiet = quiet),
                                            quiet = FALSE,
                                            output = NULL) {
 

R/load_taxonomic_resources.R

@@ -27,7 +27,7 @@
 #' @examples
 #' \donttest{
 #' load_taxonomic_resources(stable_or_current_data="stable", 
-#' version="0.0.2.9000")}
+#' version="2024-10-11")}
 #'
 
 load_taxonomic_resources <-
@@ -302,7 +302,7 @@ load_taxonomic_resources <-
 ##'
 ##'
 ##' # Load the a stable version of the dataset
-##' dataset_access_function(version="0.0.2.9000",type = "stable")
+##' dataset_access_function(version="2024-10-11",type = "stable")
 ##'
 ##' @noRd
 dataset_access_function <-
@@ -487,3 +487,45 @@ dataset_get <- function(version = default_version(),
 
   }
 }
+
+
+#' Which versions of taxonomic resources are available?
+#'
+#' @return tibble of dates when APC/APNI resources were downloaded as a Github Release
+#' @export
+#'
+#' @examples
+#' get_versions()
+get_versions <- function() {
+  # Check if there is internet connection
+  ## Dummy variable to allow testing of network
+  network <- as.logical(Sys.getenv("NETWORK_UP", unset = TRUE)) 
+
+  if (!curl::has_internet() | !network) { # Simulate if network is down
+    message("No internet connection, please retry with stable connection (default_version)")
+    return(invisible(NULL))
+  } else {
+
+    # Get all the releases
+    url <-
+      paste0(
+        "https://api.github.com/repos/",
+        "traitecoevo",
+        "/",
+        "APCalign",
+        "/releases"
+      )
+
+    response <- httr::GET(url)
+
+    if(httr::http_error(response) | !network){
+      message("API currently down, try again later")
+      return(invisible(NULL))
+    } else
+      release_data <- httr::content(response, "text") |> jsonlite::fromJSON()
+
+    # Create table
+    dplyr::tibble(versions = unique(release_data$tag_name) |> sort(decreasing = TRUE)) |> 
+      dplyr::filter(!versions == "2020-05-14") #Excluding first ever release because it is not in parquet format
+  }
+}

README.Rmd

@@ -29,31 +29,28 @@ library(APCalign)
 `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 
+## Installation 🛠️
 
 From CRAN:
 
-
 ```{r install, eval= FALSE}
  install.packages("APCalign")
+
+library(APCalign)
 ```
 
- OR for the github version:
+OR for the GitHub version:
 
 ```{r install2, eval= FALSE}
-
- install.packages("remotes")
- remotes::install_github("traitecoevo/APCalign")
+install.packages("remotes")
+remotes::install_github("traitecoevo/APCalign")
 ```
 
 ## A quick demo
 
 Generating a look-up table can be done with just one function:
 
 ```{r,message=FALSE}
-
-library(APCalign)
-
 create_taxonomic_update_lookup( 
   taxa = c(
     "Banksia integrifolia",
@@ -63,10 +60,9 @@ 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:
+If you're going to use `APCalign` more than once, it will save you time to load the taxonomic resources into memory first:
 
 ```{r,message=FALSE}
-
 tax_resources <- load_taxonomic_resources()
 
 create_taxonomic_update_lookup( 
@@ -83,36 +79,43 @@ create_taxonomic_update_lookup(
 Checking for a list of species to see if they are classified as Australian natives:
 
 ```{r, message=FALSE}
-
 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
+## 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
 
-## Learn more
+## Cheatsheet
+
+<a href="https://github.com/traitecoevo/APCalign/tree/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
+
+## 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).
 
+## Show us support 💛
+
+Please consider citing our work, we are really proud of it!
+
+```{r}
+citation("APCalign")
+```
 
-## Found a bug? 
+## 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.