Merge pull request #641 from ropensci/cran_release

rgbif 3.7.6 cran release

.github/workflows/R-CMD-check.yaml

@@ -12,9 +12,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - { os: windows-latest, r: 'release'}
-        - { os: macOS-latest, r: 'release'}
-        - { os: ubuntu-20.04, r: 'release'}
+        - { os: windows-latest, r: 'release', rtools: '42'}
+        - { os: macOS-latest, r: 'release', rtools: ''}
+        - { os: ubuntu-20.04, r: 'release', rtools: ''}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -31,6 +31,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          rtools-version: ${{ matrix.config.rtools }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,7 +48,7 @@ jobs:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
-
+          
       - name: Install pak
         run: |
           install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/")
@@ -70,18 +71,14 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           pak::local_install_dev_deps()
-          install.packages("stringi")
-          install.packages("sf")
-          install.packages("protolite")
-          pak::pkg_install(c("rcmdcheck", "maps", "scales", "colorspace", "raster"))
+          pak::pkg_install(c("sf","rcmdcheck", "maps", "scales", "colorspace", "raster", "protolite"))
         shell: Rscript {0}
 
       - name: Install dependencies macOS and Windows
         if: runner.os == 'macOS' || runner.os == 'Windows'
         run: |
-          install.packages('terra', repos='https://rspatial.r-universe.dev') # issue #597
           pak::local_install_dev_deps()
-          pak::pkg_install(c("stringi","rcmdcheck", "sf", "maps", "scales", "colorspace", "raster", "protolite"))
+          pak::pkg_install(c("sf","rcmdcheck", "maps", "scales", "colorspace", "raster", "protolite"))
         shell: Rscript {0}
 
       - name: Session info

.github/workflows/check-cron.yml

@@ -3,6 +3,7 @@ on:
     branches:
       - master
       - actions
+      - cran_release
   schedule:
     - cron: '0 0 */3 * *' # every 3 days
 
@@ -62,10 +63,7 @@ jobs:
       - name: Install dependencies
         run: |
           pak::local_install_dev_deps()
-          install.packages("stringi")
-          install.packages("sf")
-          install.packages("protolite")
-          pak::pkg_install(c("rcmdcheck", "maps", "scales", "colorspace", "raster"))
+          pak::pkg_install(c("rcmdcheck", "maps", "scales", "colorspace", "raster", "protolite"))
         shell: Rscript {0}
 
       - name: Session info

DESCRIPTION

@@ -8,7 +8,7 @@ Description: A programmatic interface to the Web Service methods
     retrieving information on data providers, getting species occurrence
     records, getting counts of occurrence records, and using the GBIF
     tile map service to make rasters summarizing huge amounts of data.
-Version: 3.7.5.5
+Version: 3.7.6
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut", comment = c(ORCID="0000-0003-1444-9135")),

NEWS.md

@@ -1,3 +1,33 @@
+rgbif 3.7.6
+===========
+
+### BREAKING CHANGE
+
+* `occ_count()` parameter `type` is now deprecated and will no longer work correctly. Please see `occ_count_country()`, `occ_count_pub_country()`, `occ_count_year()`, `occ_count_basis_of_record()` for replacements. (#622)
+
+### DEPRECATED
+
+* `occ_count()` parameters `georeferenced`, `type`, `date`, `to`, `from` are no longer supported and not guaranteed to work correctly. (#622)
+* `occ_facet()` and `count_facet()` are now deprecated use `occ_count(facet="x")` instead. 
+
+### NEW FEATURES
+
+* `lit_search()` now supports searching the GBIF literature API. (#591)
+* `occ_count()` now supports almost all `occ_search()` queries. (#622)
+* `occ_count()` now supports the facets interface through `occ_count(facet="x")`. (#622)  
+* `organizations()` (aka publishers) now supports the use of getting lists of publishers by `country`. (#606)
+* `occ_download()` and `occ_search()` now support downloading and getting occurrences a certain distance from known country/area centroids via the parameter `distanceFromCentroidInMeters`. (#594)
+
+### MINOR IMPROVEMENTS
+
+* `occ_search()` now supports more multi-valued parameters. (#617) 
+* Removed dependencies on `randgeo` and `conditionz`. (#624) (#625)
+
+### Documentation 
+
+New article explaining `occ_count()` changes and new features [Getting Occurrence Counts From GBIF](https://docs.ropensci.org/rgbif/articles/occ_counts.html).
+
+
 rgbif 3.7.5
 ===========
 
@@ -49,8 +79,7 @@ rgbif 3.7.3
 ### DEPRECATED
 
 * `networks()` is deprecated and called `network()` instead. (#527)
-* `parsenames()` is deprecated and called `name_parse()` for better alignment
-with other `name_*` functions. (#504)
+* `parsenames()` is deprecated and called `name_parse()` for better alignment with other `name_*` functions. (#504)
 
 ### BUG FIXES
 

R/lit_search.R

@@ -221,9 +221,14 @@ lit_search <- function(
                    "&offset=",offset_seq,
                    "&limit=",limit_seq)
   }
+  # clean urls
+  urls <- sapply(urls,function(x) utils::URLencode(x))
+  urls <- sapply(urls,function(x) gsub("\\[|\\]","",x)) # remove any square brackets
+  # make request 
   ll <- gbif_async_get(urls,parse=TRUE)
   data <- process_lit_async_results(ll,flatten=flatten)
   meta <- rgbif_compact(ll[[length(urls)]])
+  # clean results
   meta$results <- NULL
   meta$offset <- NULL
   meta$limit <- NULL

R/occ_count.r

@@ -100,11 +100,21 @@
 #' 
 #' }
 occ_count <- function(...,occurrenceStatus="PRESENT", curlopts = list()) {
-
   args <- list(...)
   args <- rgbif_compact(c(args,occurrenceStatus=occurrenceStatus))
   arg_names <- names(args)
 
+  # check if arg is acceptable
+  formal_args <- names(formals(occ_search))
+  facet_args <- c("facetLimit","facet","facetMincount","facetMultiselect")
+  legacy_args <- c("georeferenced","date","to","from","type")
+  # acceptable arguments or ignored arguments
+  ign_args <- c("limit","start","fields","return","skip_validate","geom_big","geom_size","geom_n","...")
+  acc_args <- c(formal_args,facet_args,legacy_args)
+
+  bad_args <- (arg_names[(!arg_names %in% acc_args) | (arg_names %in% ign_args)])
+  if(length(bad_args) > 0) warning(paste(bad_args,collapse=",")," not acceptable args for occ_count() and will be ignored.")
+
   # check for multiple values 
   if(any(!sapply(args,length) == 1)) stop("Multiple values of the form c('a','b') are not supported. Use 'a;b' instead.")
 
@@ -214,6 +224,12 @@ occ_count <- function(...,occurrenceStatus="PRESENT", curlopts = list()) {
              facetLimit = args$facetLimit)
 
  if("facet" %in% arg_names) {
+      not_facet_arg <- c("skip_validate","...","curlopts","facetMultiselect",
+                         "facetMincount", "facet","return","fields","start",
+                         "limit","verbatimTaxonId","geometry", "geom_big",
+                         "geom_size","geom_n","search")
+      acc_facet_arg <- formal_args[!formal_args %in% not_facet_arg]
+   if(!args$facet %in% acc_facet_arg) stop("Bad facet arg.")
    count <- stats::setNames(res$facet[[1]],c(args$facet,"count"))
  } else {
    count <- as.numeric(res$meta$count)

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/ropensci/rgbif",
   "issueTracker": "https://github.com/ropensci/rgbif/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "3.7.5",
+  "version": "3.7.6",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -150,18 +150,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=sf"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "randgeo",
-      "name": "randgeo",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=randgeo"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "vcr",
@@ -337,23 +325,11 @@
       "sameAs": "https://CRAN.R-project.org/package=R6"
     },
     "12": {
-      "@type": "SoftwareApplication",
-      "identifier": "conditionz",
-      "name": "conditionz",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=conditionz"
-    },
-    "13": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "14": {
+    "13": {
       "@type": "SoftwareApplication",
       "identifier": "wk",
       "name": "wk",
@@ -370,11 +346,11 @@
   "applicationCategory": "Biodiversity",
   "isPartOf": "https://ropensci.org",
   "keywords": ["GBIF", "specimens", "API", "web-services", "occurrences", "species", "taxonomy", "gbif", "api", "data", "biodiversity", "rstats", "r", "spocc", "r-package", "lifewatch", "oscibio"],
-  "fileSize": "10891.58KB",
+  "fileSize": "12364.127KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
-      "datePublished": "2022",
+      "datePublished": "2023",
       "author": [
         {
           "@type": "Person",
@@ -414,7 +390,7 @@
       ],
       "name": "rgbif: Interface to the Global Biodiversity Information Facility API",
       "url": "https://CRAN.R-project.org/package=rgbif",
-      "description": "R package version 3.7.5"
+      "description": "R package version 3.7.6"
     },
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -1,7 +1,8 @@
 ## Test environments
 
 * local windows, R 4.2.2
-* ubuntu 18.04, R 4.2.2 (GitHub Actions)
+* windows latest R 4.2.2 (GitHub Actions)
+* ubuntu 20.04, R 4.2.2 (GitHub Actions)
 * macOS latest, R 4.2.2 (GitHub Actions)
 
 ## R CMD check results
@@ -10,7 +11,7 @@
 
 ## Reverse dependencies
 
-* I have run R CMD check on the 16 reverse dependencies. Reverse dependency checks at <https://github.com/ropensci/rgbif/actions?query=workflow%3Arevdep>. No problems were found related to this package.
+* I have run R CMD check on the 15 reverse dependencies. Reverse dependency checks at <https://github.com/ropensci/rgbif/actions?query=workflow%3Arevdep>. No problems were found related to this package.
 
 --------
 

tests/fixtures/dataset_metrics.yml

@@ -17,11 +17,11 @@ http_interactions:
       status: HTTP/1.1 200 OK
       content-type: application/json
     body:
-      encoding: UTF-8
+      encoding: ''
       file: no
-      string: '{"key":1284962,"datasetKey":"863e6d6b-f602-4495-ac30-881482b6f799","usagesCount":7,"synonymsCount":0,"distinctNamesCount":7,"nubMatchingCount":7,"colMatchingCount":6,"nubCoveragePct":100,"colCoveragePct":85,"countByConstituent":{},"countByKingdom":{"ANIMALIA":7},"countByRank":{"KINGDOM":1,"PHYLUM":1,"CLASS":1,"ORDER":1,"FAMILY":1,"GENUS":1,"SPECIES":1},"countNamesByLanguage":{},"countExtRecordsByExtension":{"DESCRIPTION":7,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0,"VERNACULAR_NAME":0},"countByOrigin":{"DENORMED_CLASSIFICATION":6,"SOURCE":1},"countByIssue":{"NOMENCLATURAL_STATUS_INVALID":1},"otherCount":{},"downloaded":"2022-07-09T23:51:15.843+00:00"}'
-  recorded_at: 2022-07-12 12:28:01 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: '{"key":1806059,"datasetKey":"863e6d6b-f602-4495-ac30-881482b6f799","usagesCount":7,"synonymsCount":0,"distinctNamesCount":7,"nubMatchingCount":7,"colMatchingCount":6,"nubCoveragePct":100,"colCoveragePct":85,"countByConstituent":{},"countByKingdom":{"ANIMALIA":7},"countByRank":{"KINGDOM":1,"PHYLUM":1,"CLASS":1,"ORDER":1,"FAMILY":1,"GENUS":1,"SPECIES":1},"countNamesByLanguage":{},"countExtRecordsByExtension":{"DESCRIPTION":7,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0,"VERNACULAR_NAME":0},"countByOrigin":{"DENORMED_CLASSIFICATION":6,"SOURCE":1},"countByIssue":{"NOMENCLATURAL_STATUS_INVALID":1},"otherCount":{},"downloaded":"2022-12-09T11:32:03.702+00:00"}'
+  recorded_at: 2023-03-22 11:30:52 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
     uri: https://api.gbif.org/v1/dataset/863e6d6b-f602-4495-ac30-881482b6f799/metrics
@@ -40,11 +40,11 @@ http_interactions:
       status: HTTP/1.1 200 OK
       content-type: application/json
     body:
-      encoding: UTF-8
+      encoding: ''
       file: no
-      string: '{"key":1284962,"datasetKey":"863e6d6b-f602-4495-ac30-881482b6f799","usagesCount":7,"synonymsCount":0,"distinctNamesCount":7,"nubMatchingCount":7,"colMatchingCount":6,"nubCoveragePct":100,"colCoveragePct":85,"countByConstituent":{},"countByKingdom":{"ANIMALIA":7},"countByRank":{"KINGDOM":1,"PHYLUM":1,"CLASS":1,"ORDER":1,"FAMILY":1,"GENUS":1,"SPECIES":1},"countNamesByLanguage":{},"countExtRecordsByExtension":{"DESCRIPTION":7,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0,"VERNACULAR_NAME":0},"countByOrigin":{"DENORMED_CLASSIFICATION":6,"SOURCE":1},"countByIssue":{"NOMENCLATURAL_STATUS_INVALID":1},"otherCount":{},"downloaded":"2022-07-09T23:51:15.843+00:00"}'
-  recorded_at: 2022-07-12 12:28:01 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: '{"key":1806059,"datasetKey":"863e6d6b-f602-4495-ac30-881482b6f799","usagesCount":7,"synonymsCount":0,"distinctNamesCount":7,"nubMatchingCount":7,"colMatchingCount":6,"nubCoveragePct":100,"colCoveragePct":85,"countByConstituent":{},"countByKingdom":{"ANIMALIA":7},"countByRank":{"KINGDOM":1,"PHYLUM":1,"CLASS":1,"ORDER":1,"FAMILY":1,"GENUS":1,"SPECIES":1},"countNamesByLanguage":{},"countExtRecordsByExtension":{"DESCRIPTION":7,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0,"VERNACULAR_NAME":0},"countByOrigin":{"DENORMED_CLASSIFICATION":6,"SOURCE":1},"countByIssue":{"NOMENCLATURAL_STATUS_INVALID":1},"otherCount":{},"downloaded":"2022-12-09T11:32:03.702+00:00"}'
+  recorded_at: 2023-03-22 11:30:52 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
     uri: https://api.gbif.org/v1/dataset/66dd0960-2d7d-46ee-a491-87b9adcfe7b1/metrics
@@ -63,8 +63,8 @@ http_interactions:
       status: HTTP/1.1 200 OK
       content-type: application/json
     body:
-      encoding: UTF-8
+      encoding: ''
       file: no
-      string: '{"key":1285697,"datasetKey":"66dd0960-2d7d-46ee-a491-87b9adcfe7b1","usagesCount":138248,"synonymsCount":59906,"distinctNamesCount":138122,"nubMatchingCount":131967,"colMatchingCount":113479,"nubCoveragePct":95,"colCoveragePct":82,"countByConstituent":{},"countByKingdom":{"PLANTAE":72457,"INCERTAE_SEDIS":1},"countByRank":{"SPECIES":52563,"GENUS":12880,"VARIETY":4810,"SUBSPECIES":4462,"SERIES":1077,"TRIBE":844,"FAMILY":509,"SUBTRIBE":327,"SUBFAMILY":303,"SUBGENUS":240,"FORM":238,"SECTION":82,"SUBVARIETY":5,"KINGDOM":1},"countNamesByLanguage":{"ENGLISH":32165,"SWEDISH":7284,"GERMAN":4882,"SPANISH":4157,"FRENCH":3783,"PORTUGUESE":1141,"ITALIAN":663,"AFRIKAANS":450,"ARABIC":182,"INDONESIAN":153,"MALAY":139,"SWAHILI":72,"DUTCH":50,"MALAGASY":41,"DANISH":21,"FIJIAN":17,"HINDI":15,"SOMALI":11,"TURKISH":8,"NEPALI":7,"POLISH":7,"CZECH":4,"KOREAN":4,"TAJIK":4,"CATALAN":3,"FINNISH":3,"JAVANESE":3,"ROMANIAN":3,"VIETNAMESE":3,"YORUBA":3,"AYMARA":2,"CHINESE":2,"SAMOAN":2,"ALBANIAN":1,"BISLAMA":1,"HUNGARIAN":1,"LAO":1,"MONGOLIAN":1,"NORWEGIAN":1,"QUECHUA":1,"RUSSIAN":1,"SANSKRIT":1,"TAMIL":1,"THAI":1,"TONGA":1,"TURKMEN":1},"countExtRecordsByExtension":{"VERNACULAR_NAME":64900,"DESCRIPTION":0,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0},"countByOrigin":{"SOURCE":138246,"DENORMED_CLASSIFICATION":1,"MISSING_ACCEPTED":1},"countByIssue":{"SCIENTIFIC_NAME_ASSEMBLED":128661,"BACKBONE_MATCH_NONE":6281,"VERNACULAR_NAME_INVALID":5501,"CHAINED_SYNOYM":522,"PARENT_NAME_USAGE_ID_INVALID":48,"PARTIALLY_PARSABLE":7,"PARENT_CYCLE":1},"otherCount":{},"downloaded":"2022-07-10T01:53:07.909+00:00"}'
-  recorded_at: 2022-07-12 12:28:01 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: '{"key":1809611,"datasetKey":"66dd0960-2d7d-46ee-a491-87b9adcfe7b1","usagesCount":138248,"synonymsCount":59906,"distinctNamesCount":138122,"nubMatchingCount":131965,"colMatchingCount":116603,"nubCoveragePct":95,"colCoveragePct":84,"countByConstituent":{},"countByKingdom":{"PLANTAE":72437,"INCERTAE_SEDIS":17},"countByRank":{"SPECIES":52563,"GENUS":12880,"VARIETY":4810,"SUBSPECIES":4462,"SERIES":1077,"TRIBE":844,"FAMILY":509,"SUBTRIBE":327,"SUBFAMILY":303,"SUBGENUS":240,"FORM":238,"SECTION":82,"SUBVARIETY":5,"KINGDOM":1},"countNamesByLanguage":{"ENGLISH":32165,"SWEDISH":7284,"GERMAN":4882,"SPANISH":4157,"FRENCH":3783,"PORTUGUESE":1141,"ITALIAN":663,"AFRIKAANS":450,"ARABIC":182,"INDONESIAN":153,"MALAY":139,"SWAHILI":72,"DUTCH":50,"MALAGASY":41,"DANISH":21,"FIJIAN":17,"HINDI":15,"SOMALI":11,"TURKISH":8,"NEPALI":7,"POLISH":7,"CZECH":4,"KOREAN":4,"TAJIK":4,"CATALAN":3,"FINNISH":3,"JAVANESE":3,"ROMANIAN":3,"VIETNAMESE":3,"YORUBA":3,"AYMARA":2,"CHINESE":2,"SAMOAN":2,"ALBANIAN":1,"BISLAMA":1,"HUNGARIAN":1,"LAO":1,"MONGOLIAN":1,"NORWEGIAN":1,"QUECHUA":1,"RUSSIAN":1,"SANSKRIT":1,"TAMIL":1,"THAI":1,"TONGA":1,"TURKMEN":1},"countExtRecordsByExtension":{"VERNACULAR_NAME":64900,"DESCRIPTION":0,"DISTRIBUTION":0,"IDENTIFIER":0,"MULTIMEDIA":0,"REFERENCE":0,"SPECIES_PROFILE":0,"TYPES_AND_SPECIMEN":0},"countByOrigin":{"SOURCE":138246,"DENORMED_CLASSIFICATION":1,"MISSING_ACCEPTED":1},"countByIssue":{"SCIENTIFIC_NAME_ASSEMBLED":128661,"BACKBONE_MATCH_NONE":6283,"VERNACULAR_NAME_INVALID":5501,"CHAINED_SYNOYM":522,"PARENT_NAME_USAGE_ID_INVALID":48,"PARTIALLY_PARSABLE":7,"PARENT_CYCLE":1},"otherCount":{},"downloaded":"2023-01-22T18:36:41.107+00:00"}'
+  recorded_at: 2023-03-22 11:30:52 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.8.2