Merge pull request #87 from trias-project/return-data-slots

Return data slots
trias-project · Jun 10, 2022 · 5d52674 · 5d52674
2 parents 6c81b63 + 5976058
commit 5d52674
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -26,50 +26,48 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+          ## uncomment when updated terra binaries are ready
+          # - {os: macOS-latest,   r: 'release'}
+          # - {os: windows-latest, r: 'release'}
           - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
           - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
           - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      _R_CHECK_SYSTEM_CLOCK_: false
       RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GH_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        id: install-r
+      - uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@master
 
-      - name: Install pak and query dependencies
+      - name: Query dependencies
         run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
       - name: Install system dependencies
         if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
 
       - name: Install dependencies
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
       - name: Session info
@@ -82,9 +80,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
@@ -94,7 +90,8 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@master
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+          retention-days: 5
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: trias
 Title: Process Data for the Project Tracking Invasive Alien Species
     (TrIAS)
-Version: 1.6.0
+Version: 2.0.0
 Authors@R: 
     c(person(given = "Damiano",
              family = "Oldoni",
@@ -70,4 +70,4 @@ Encoding: UTF-8
 LazyData: true
 LazyDataCompression: bzip2
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -36,8 +36,6 @@ importFrom(dplyr,case_when)
 importFrom(dplyr,count)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
-importFrom(dplyr,distinct_)
-importFrom(dplyr,do)
 importFrom(dplyr,enquo)
 importFrom(dplyr,filter)
 importFrom(dplyr,filter_at)
@@ -47,7 +45,6 @@ importFrom(dplyr,if_else)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
-importFrom(dplyr,mutate_all)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
 importFrom(dplyr,n_distinct)
@@ -60,28 +57,24 @@ importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarize)
 importFrom(dplyr,sym)
-importFrom(dplyr,syms)
 importFrom(dplyr,tally)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(egg,ggarrange)
 importFrom(forcats,fct_rev)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_ribbon)
-importFrom(ggplot2,geom_smooth)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggsave)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,scale_colour_manual)
-importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,xlab)
@@ -104,13 +97,10 @@ importFrom(mgcv,nb)
 importFrom(mgcv,summary.gam)
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
-importFrom(purrr,cross_df)
 importFrom(purrr,list_along)
-importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map2_chr)
 importFrom(purrr,map_chr)
-importFrom(purrr,map_df)
 importFrom(purrr,map_dfr)
 importFrom(purrr,pmap_dfr)
 importFrom(purrr,reduce)
@@ -155,8 +145,6 @@ importFrom(stringr,str_to_lower)
 importFrom(svDialogs,dlgInput)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
-importFrom(tidyr,gather)
-importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,ends_with)
 importFrom(tidyselect,one_of)

diff --git a/R/gbif_has_distribution.R b/R/gbif_has_distribution.R
@@ -11,10 +11,7 @@
 #' occurrenceStatus) and establishmentMeans.
 #' @return a logical, TRUE or FALSE.
 #' @export
-#' @importFrom assertthat assert_that
-#' @importFrom rgbif name_usage
-#' @importFrom dplyr select %>% distinct_ mutate_all
-#' @importFrom purrr map cross_df
+#' @importFrom dplyr %>%
 #' @examples
 #' # numeric taxonKey, atomic parameters
 #' gbif_has_distribution(145953242,
@@ -38,7 +35,7 @@
 #'
 #' # Case insensitive
 #' gbif_has_distribution("145953242",
-#'   countryCode = "be",
+#'   country = "be",
 #'   status = "PRESENT",
 #'   establishmentMeans = "InTrOdUcEd"
 #' )
@@ -115,15 +112,15 @@ gbif_has_distribution <- function(taxon_key, ...) {
         return(FALSE)
       } else {
         # Avoid mismatch due to any upper/lowercase difference
-        user_properties <- map(user_properties, ~ toupper(.))
-        # Check whether at least
+        user_properties <- purrr::map(user_properties, ~ toupper(.))
+        # Check whether at least one property defined by user is present
         has_distr <- dplyr::intersect(
           user_properties %>%
-            cross_df(),
+            purrr::cross_df(),
           distr_properties %>%
-            select(names(user_properties)) %>%
-            distinct_(.dots = names(user_properties)) %>%
-            mutate_all(toupper)
+            dplyr::select(names(user_properties)) %>%
+            dplyr::distinct() %>%
+            dplyr::mutate(dplyr::across(.cols = everything(), toupper))
         ) %>%
           nrow() > 0
         return(has_distr)

diff --git a/R/gbif_verify_keys.R b/R/gbif_verify_keys.R
@@ -31,13 +31,8 @@
 #'   \code{NA} for other two columns. If a key didn't pass the second check
 #'   (\code{is_from_gbif_backbone = FALSE}) then \code{is_synonym} = \code{NA}.
 #' @export
-#' @importFrom assertthat assert_that
-#' @importFrom dplyr pull mutate filter left_join full_join select .data enquo
-#' @importFrom purrr reduce map_df
-#' @importFrom rgbif name_usage
+#' @importFrom dplyr .data %>%
 #' @importFrom rlang !!
-#' @importFrom tidyr gather
-#' @importFrom tidyselect vars_pull
 #' @examples
 #' # input is a vector
 #' keys1 <- c(
@@ -70,36 +65,36 @@
 #' gbif_verify_keys(keys3)
 #' gbif_verify_keys(keys4)
 gbif_verify_keys <- function(keys, col_keys = "key") {
-  assert_that(is.data.frame(keys) | is.vector(keys),
+  assertthat::assert_that(is.data.frame(keys) | is.vector(keys),
     msg = "keys should be a vector, a named list or a data.frame."
   )
   if (is.data.frame(keys)) {
-    assert_that(col_keys %in% names(keys),
+    assertthat::assert_that(col_keys %in% names(keys),
       msg = paste(
         "Column with keys not found.",
         "Did you forget maybe to pass",
         "the right column name to col_keys?"
       )
     )
-    name_col <- vars_pull(names(keys), !!enquo(col_keys))
+    name_col <- tidyselect::vars_pull(names(keys), !!dplyr::enquo(col_keys))
     # extract vector of keys from df
     keys <-
       keys %>%
-      pull(name_col)
+      dplyr::pull(name_col)
   }
   keys <- keys[!is.na(keys)]
   if (length(keys) == 0 | isTRUE(all(keys == ""))) {
     return(NULL)
   } else {
-    assert_that(all(keys != "") == TRUE,
+    assertthat::assert_that(all(keys != "") == TRUE,
       msg = paste(
         "Invalid keys:",
         paste(rep("\"\"\"\"", length(keys[which(keys == "")])),
           collapse = ","
         ), "."
       )
     )
-    assert_that(all(!grepl("\\D", keys)) == TRUE,
+    assertthat::assert_that(all(!grepl("\\D", keys)) == TRUE,
       msg = paste(
         "Invalid keys:",
         paste(keys[which(!grepl("\\D", keys) == FALSE)],
@@ -116,58 +111,58 @@ gbif_verify_keys <- function(keys, col_keys = "key") {
   names(keys) <- as.character(keys)
   gbif_info <-
     keys %>%
-    map(~ tryCatch(name_usage(.)$data[1, ],
+    purrr::map(~ tryCatch(rgbif::name_usage(.)$data[1, ],
       error = function(e) {
         print(paste("Key", ., "is an invalid GBIF taxon key."))
       }
     ))
   check_keys <-
-    map_df(gbif_info, ~ is.character(.) == FALSE)
+    purrr::map_df(gbif_info, ~ is.character(.) == FALSE)
   check_keys <-
     check_keys %>%
-    gather(key = "key", value = "is_taxonKey") %>%
-    mutate(key = as.numeric(.data$key))
+    tidyr::gather(key = "key", value = "is_taxonKey") %>%
+    dplyr::mutate(key = as.numeric(.data$key))
   valid_keys_df <-
     check_keys %>%
-    filter(.data$is_taxonKey == TRUE)
+    dplyr::filter(.data$is_taxonKey == TRUE)
   valid_keys <- gbif_info[which(names(gbif_info) %in% valid_keys_df$key)]
   if (length(valid_keys) > 0) {
     valid_keys_df <-
       valid_keys %>%
-      reduce(bind_rows) %>%
-      mutate(is_from_gbif_backbone = ifelse(.data$datasetKey == uuid_backbone,
+      purrr::reduce(bind_rows) %>%
+      dplyr::mutate(is_from_gbif_backbone = ifelse(.data$datasetKey == uuid_backbone,
         TRUE, FALSE
       ))
     check_keys <-
       check_keys %>%
-      left_join(valid_keys_df %>%
-        select(.data$key, .data$is_from_gbif_backbone),
+      dplyr::left_join(valid_keys_df %>%
+        dplyr::select(.data$key, .data$is_from_gbif_backbone),
       by = "key"
       )
     valid_keys_df <-
       valid_keys_df %>%
-      filter(.data$is_from_gbif_backbone == TRUE) %>%
-      mutate(is_synonym = ifelse(!.data$taxonomicStatus %in% c("ACCEPTED", "DOUBTFUL"),
+      dplyr::filter(.data$is_from_gbif_backbone == TRUE) %>%
+      dplyr::mutate(is_synonym = ifelse(!.data$taxonomicStatus %in% c("ACCEPTED", "DOUBTFUL"),
         TRUE, FALSE
       ))
     check_keys <-
       check_keys %>%
-      left_join(valid_keys_df %>%
-        select(.data$key, .data$is_synonym),
+      dplyr::left_join(valid_keys_df %>%
+        dplyr::select(.data$key, .data$is_synonym),
       by = "key"
       )
   } else {
     check_keys <-
       check_keys %>%
-      mutate(
+      dplyr::mutate(
         is_from_gbif_backbone = NA,
         is_synonym = NA
       )
   }
 
   # recreate possible duplicates by joining input_keys_df with check_keys
   input_keys_df %>%
-    left_join(check_keys,
+    dplyr::left_join(check_keys,
               by = "key")
 }