Check compatibility

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: austraits
 Title: Helpful functions to access, summarise and wrangle austraits data
-Version: 2.2.3
+Version: 3.0.0.9000
 Authors@R:
     c(person(given = "Daniel",
              family = "Falster",
@@ -22,7 +22,7 @@ Encoding: UTF-8
 Language: en
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: 
     R (>= 4.0.0),
     RefManageR

NAMESPACE

@@ -25,6 +25,7 @@ export(summarise_austraits)
 export(summarise_trait_means)
 export(trait_pivot_longer)
 export(trait_pivot_wider)
+export(util_list_to_df2)
 import(RefManageR)
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)

R/check_compatibility.R

@@ -0,0 +1,43 @@
+#' @title Check compatibility
+#' @description Function to check whether the data object has been compiled by the traits.build workflow and 
+#' therefore has a data structure that is appropriate for use with austraits functions.
+#' @param austraits dataframe generated by traits build
+#'
+#' @return logical (T/F) output and messaging for uncompatible versions
+#'
+#' @examples
+#' \dontrun{
+#' check_compatibility(austraits)
+#' }
+#' @author Elizabeth Wenk - e.wenk@unsw.edu.au
+
+check_compatibility <- function(austraits) {
+
+  if (is.null(austraits$metadata)) {
+
+    compatible <- FALSE
+
+    writeLines(sprintf("You are working with AusTraits version 3.0 or earlier. This database structure is unsupported by the current version of this package."))
+    writeLines(sprintf("Please see https://github.com/traitecoevo/austraits for details on installing old versions."))
+
+  } else {
+
+    compiled_by_traits.build <-
+      austraits$metadata$related_identifiers %>% 
+      util_list_to_df2() %>%
+      filter(relation_type == "isCompiledBy", stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
+
+    if(is.null(compiled_by_traits.build) | nrow(compiled_by_traits.build) > 0) {
+      compatible <- TRUE
+    } else{
+      compatible <- FALSE
+
+      writeLines(sprintf("You are working with AusTraits version 4, which is unsupported by the current version of this package."))
+      writeLines(sprintf("Please see https://github.com/traitecoevo/austraits for details on installing old versions."))
+    }
+
+  }
+
+  invisible(compatible)
+
+}

R/utils.R

@@ -0,0 +1,20 @@
+#' Convert a list of lists to dataframe
+#'
+#' Convert a list of lists to dataframe; requires that every list have same named elements.
+#'
+#' @param my_list A list of lists to dataframe
+#' @param as_character A logical value, indicating whether the values are read as character
+#' @param on_empty Value to return if my_list is NULL, NA or is length == 0, default = NA
+#'
+#' @export
+#' @examples util_list_to_df2(util_df_to_list(dplyr::starwars))
+util_list_to_df2 <- function(my_list, as_character = TRUE, on_empty = NA) {
+
+  if (is.null(my_list) || any(is.na(my_list)) || length(my_list) == 0)
+    return(on_empty)
+
+  if (as_character)
+    my_list <- lapply(my_list, lapply, as.character)
+
+  dplyr::bind_rows(lapply(my_list, tibble::as_tibble))
+}

README.Rmd

@@ -55,6 +55,23 @@ Otherwise, for a lightweight installation where dependencies for plotting and th
 remotes::install_github("traitecoevo/austraits", upgrade = "ask")
 ```
 
+In September 2024 austraits functions were revamped to support all [traits.build](https://github.com/traitecoevo/traits.build) compiled databases, rather than being linked to [austraits.build](https://github.com/traitecoevo/austraits.build).
+
+Versions of austraits.build (the AusTraits plant trait database) < 5.0 are no longer supported by the current functions. If you are working with an older version of AusTraits, please install an older version of austraits:
+
+For austraits.build versions 4.2 and older: 
+```{r setup, results = 'hide', eval = FALSE}
+#install.packages("remotes")
+remotes::install_github("traitecoevo/austraits@53b637c", dependencies = TRUE, upgrade = "ask")
+
+library(austraits)
+```
+
+Note, if you are unsure what version of AusTraits you are working with, run:
+```{r setup, results = 'hide', eval = FALSE}
+austraits$build_info$version
+```
+
 
 ### Take a good look at our vignettes! `r emo::ji("eyes")`
 

tests/testthat/test-check_compatibiity.R

@@ -0,0 +1,11 @@
+austraits <- list(austraits_3.0.2_lite, 
+                  austraits_5.0.0_lite)
+
+test_check_compatibility <- function(austraits){
+  test_that("check_compatibiity successfully detects if the dataframe is compatible with austraits 3.0", {
+    expect_silent(check_compatibility(austraits_5.0.0_lite))
+    expect_true(check_compatibility(austraits_5.0.0_lite))
+    expect_output(check_compatibility(austraits_3.0.2_lite))
+    expect_false(check_compatibility(austraits_3.0.2_lite))
+  })
+}