Merge pull request #147 from trias-project/Fix-86

Fix 86

.gitignore

@@ -41,3 +41,6 @@ rsconnect/
 
 # Mac OS X
 .DS_Store
+
+# pdfs created by testing plots
+/tests/testthat/*.pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: trias
 Title: Process Data for the Project Tracking Invasive Alien Species
     (TrIAS)
-Version: 3.0.0
+Version: 3.0.1
 Authors@R: c(
     person("Damiano", "Oldoni", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3445-7562")),

NAMESPACE

@@ -6,7 +6,6 @@ export(climate_match)
 export(gbif_get_taxa)
 export(gbif_has_distribution)
 export(gbif_verify_keys)
-export(get_cred)
 export(get_table_pathways)
 export(indicator_introduction_year)
 export(indicator_native_range_year)
@@ -20,12 +19,7 @@ export(visualize_pathways_year_level1)
 export(visualize_pathways_year_level2)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
-importFrom(readr,read_tsv)
-importFrom(readr,write_tsv)
-importFrom(rgbif,occ_download_meta)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,sym)
-importFrom(stringr,str_c)
-importFrom(svDialogs,dlgInput)

NEWS.md

@@ -1,3 +1,7 @@
+# trias 3.0.1
+
+- Function `get_cred()` is not exported anymore (#146). Internally used only.
+
 # trias 3.0.0
 
 - Allow to specify x-scale stepsize for `indicator_native_range_year()` (#143)

R/climate_match.R

@@ -196,7 +196,7 @@ climate_match <- function(region,
                                     "countryCode"
                      )) %>% 
       dplyr::filter(.data$acceptedTaxonKey %in% taxon_key)
-  }else{
+  } else {
     gbif_user <- get_cred("gbif_user")
     gbif_pwd <- get_cred("gbif_pwd")
     gbif_email <- get_cred("gbif_email")

R/get_cred.R

@@ -1,15 +1,16 @@
 #' Interactively get & store credentials in the system environment
 #'
-#' @param x a character with the name of the system environment variable to get
-#'   and store
-#' @return a character vector containing the value of the system variable
-#' @export
-#' @importFrom svDialogs dlgInput
+#' @param x character. Name of the system environment variable to get
+#'   and store.
+#'   
+#' @return character. Vector containing the value(s) of the system variable.
+#' 
+#' @noRd
 get_cred <- function(x) {
   cred <- Sys.getenv(x)
 
   if (cred == "") {
-    input <- dlgInput(paste0("What is your ", x, "?"))
+    input <- svDialogs::dlgInput(paste0("What is your ", x, "?"))
     cred <- input$res
     do.call(Sys.setenv, as.list(purrr::set_names(cred, x)))
   }

R/update_download_list.R

@@ -28,24 +28,21 @@
 #' @return message with the performed updates
 #'
 #' @export
-#' @importFrom rgbif occ_download_meta
-#' @importFrom readr read_tsv write_tsv
-#' @importFrom stringr str_c
 update_download_list <- function(file, download_to_add, input_checklist,
                                  url_doi_base = "https://doi.org/") {
-  downloads <- read_tsv(file,
+  downloads <- readr::read_tsv(file,
     trim_ws = TRUE,
     na = "",
     lazy = FALSE
   )
   # downloadKey not present
   if (is.element(download_to_add, downloads$gbif_download_key) == FALSE) {
-    metadata <- occ_download_meta(key = download_to_add)
+    metadata <- rgbif::occ_download_meta(key = download_to_add)
     gbif_download_status <- metadata$status
-    gbif_download_doi <- str_c(url_doi_base, metadata$doi)
+    gbif_download_doi <- stringr::str_c(url_doi_base, metadata$doi)
     print(gbif_download_doi)
     gbif_download_created <- metadata$created
-    write_tsv(
+    readr::write_tsv(
       x = as.data.frame(list(
         gbif_download_key = toString(download_to_add),
         input_checklist = input_checklist,
@@ -64,15 +61,15 @@ update_download_list <- function(file, download_to_add, input_checklist,
       "added to", file, "; download status =", gbif_download_status
     ))
     # reload file
-    downloads <- read_tsv(file, na = "", lazy = FALSE)
+    downloads <- readr::read_tsv(file, na = "", lazy = FALSE)
   } else {
     print(paste("gbif_download_Key", download_to_add, "already present in", file))
   }
   # check all downloads with status "PREPARING" or "RUNNING".
   changes <- FALSE
   for (i in 1:nrow(downloads)) {
     if (downloads$gbif_download_status[i] %in% c("RUNNING", "PREPARING")) {
-      metadata <- occ_download_meta(key = downloads$gbif_download_key[i])
+      metadata <- rgbif::occ_download_meta(key = downloads$gbif_download_key[i])
       gbif_download_status <- metadata$status
       # status is SUCCEEDED or FAILED
       if (gbif_download_status %in% c("SUCCEEDED", "FAILED")) {
@@ -93,7 +90,7 @@ update_download_list <- function(file, download_to_add, input_checklist,
   if (!changes) {
     print("No changes in download status detected")
   } else {
-    write_tsv(
+    readr::write_tsv(
       x = downloads,
       file = file,
       na = "",

tests/testthat/test-output_gbif_get_taxa.R

@@ -1,4 +1,3 @@
-#' @importFrom readr read_tsv
 context("output_gbif_get_taxa")