Merge pull request #587 from ropensci/dev

Preparing for CRAN v3.7.5
ropensci · Dec 30, 2022 · 75d7cd8 · 75d7cd8
2 parents a6e7da4 + 4847634
commit 75d7cd8
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diff --git a/DESCRIPTION b/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: 3.7.4.3
+Version: 3.7.5
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut", comment = c(ORCID="0000-0003-1444-9135")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+rgbif 3.7.5
+===========
+
+### NEW FEATURES
+
+* `name_backbone_checklist()` now accepts `strict=TRUE`, meaning that only non-fuzzy matches are returned. (#565)
+* `name_backbone_checklist()` now accepts default values for high taxonomy, such as kingdom, phylum, family, ect. (#515)
+* `name_backbone_checklist()` now returns a column `is_alternative` when `verbose=TRUE`, which lets the user know if a name was originally considered to be an alternative choice by the name matcher. (#515)
+
+### DOCUMENTATION
+* Updated README to be more inviting to new users (#574)
+* Added data quality section to article [Getting Occurrence Data From GBIF](https://docs.ropensci.org/rgbif/articles/getting_occurrence_data.html). (#575)
+
+### MINOR IMPROVEMENTS
+* removed `sp` and `rgeos` dependencies. (#578)
+
 rgbif 3.7.4
 ===========
 
@@ -11,12 +27,12 @@ rgbif 3.7.4
 
 ### BUG FIXES
 
-* `dataset_gridded` bug fixed when inputing only one non-gridded dataset. (#546)
+* `dataset_gridded` bug fixed when inputting only one non-gridded dataset. (#546)
 
 ### MINOR IMPROVEMENTS
 
 * New CRAN checks badge URL. (#555)
-* Update min vcr requirment to (>= 1.2.0). (#559)
+* Update min vcr requirement to (>= 1.2.0). (#559)
 * Updated r-lib actions to v2 (#566)
 
 rgbif 3.7.3

diff --git a/codemeta.json b/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": "3.7.4",
+  "version": "3.7.5",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -101,30 +101,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=testthat"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "sp",
-      "name": "sp",
-      "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=sp"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "rgeos",
-      "name": "rgeos",
-      "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=rgeos"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "png",
@@ -394,7 +370,7 @@
   "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": "10899.16KB",
+  "fileSize": "10891.58KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -438,7 +414,7 @@
       ],
       "name": "rgbif: Interface to the Global Biodiversity Information Facility API",
       "url": "https://CRAN.R-project.org/package=rgbif",
-      "description": "R package version 3.7.4"
+      "description": "R package version 3.7.5"
     },
     {
       "@type": "ScholarlyArticle",

diff --git a/revdep/.gitignore b/revdep/.gitignore
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,22 +1,33 @@
 # Platform
 
-|field    |value                                       |
-|:--------|:-------------------------------------------|
-|version  |R version 4.0.2 Patched (2020-06-30 r78761) |
-|os       |macOS Catalina 10.15.5                      |
-|system   |x86_64, darwin17.0                          |
-|ui       |X11                                         |
-|language |(EN)                                        |
-|collate  |en_US.UTF-8                                 |
-|ctype    |en_US.UTF-8                                 |
-|tz       |US/Pacific                                  |
-|date     |2020-07-22                                  |
+|field    |value                                     |
+|:--------|:-----------------------------------------|
+|version  |R version 4.2.2 (2022-10-31 ucrt)         |
+|os       |Windows 10 x64 (build 19045)              |
+|system   |x86_64, mingw32                           |
+|ui       |RStudio                                   |
+|language |(EN)                                      |
+|collate  |Danish_Denmark.utf8                       |
+|ctype    |Danish_Denmark.utf8                       |
+|tz       |Europe/Paris                              |
+|date     |2022-12-30                                |
+|rstudio  |2022.07.2+576 Spotted Wakerobin (desktop) |
+|pandoc   |NA                                        |
 
 # Dependencies
 
-|package |old   |new      |Δ  |
-|:-------|:-----|:--------|:--|
-|rgbif   |3.1.0 |3.1.1.91 |*  |
+|package    |old   |new    |Δ  |
+|:----------|:-----|:------|:--|
+|rgbif      |3.7.4 |3.7.5  |*  |
+|cli        |NA    |3.5.0  |*  |
+|data.table |NA    |1.14.6 |*  |
+|isoband    |NA    |0.2.7  |*  |
+|jsonlite   |NA    |1.8.4  |*  |
+|openssl    |NA    |2.0.5  |*  |
+|stringr    |NA    |1.5.0  |*  |
+|vctrs      |NA    |0.5.1  |*  |
+|whisker    |NA    |0.4.1  |*  |
+|wk         |NA    |0.7.1  |*  |
 
 # Revdeps
 
diff --git a/revdep/check.R b/revdep/check.R
diff --git a/revdep/checks.rds b/revdep/checks.rds
diff --git a/revdep/email.yml b/revdep/email.yml
@@ -1,5 +1,5 @@
-release_date: ???
-rel_release_date: ???
-my_news_url: ???
-release_version: ???
-release_details: ???
+release_date: ???
+rel_release_date: ???
+my_news_url: ???
+release_version: ???
+release_details: ???
diff --git a/tests/fixtures/occ_facet.yml b/tests/fixtures/occ_facet.yml
@@ -17,14 +17,14 @@ http_interactions:
       status: HTTP/1.1 200 OK
       content-type: application/json
     body:
-      encoding: UTF-8
+      encoding: ''
       file: no
-      string: '{"offset":0,"limit":0,"endOfRecords":false,"count":2184797352,"results":[],"facets":[{"field":"COUNTRY","counts":[{"name":"US","count":808302991},{"name":"CA","count":131806867},{"name":"GB","count":108057716},{"name":"AU","count":107917235},{"name":"SE","count":107632259},{"name":"FR","count":100666945},{"name":"NL","count":77444744},{"name":"ES","count":54442678},{"name":"DE","count":49855461},{"name":"DK","count":47888195}]}]}'
-  recorded_at: 2022-04-08 13:39:23 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: '{"offset":0,"limit":0,"endOfRecords":false,"count":2298098025,"results":[],"facets":[{"field":"COUNTRY","counts":[{"name":"US","count":820028047},{"name":"FR","count":135859403},{"name":"CA","count":133937135},{"name":"SE","count":118149141},{"name":"AU","count":114128644},{"name":"GB","count":111294920},{"name":"NL","count":87954359},{"name":"ES","count":55634531},{"name":"DE","count":51158570},{"name":"DK","count":50011653}]}]}'
+  recorded_at: 2022-12-30 08:43:33 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
-    uri: https://api.gbif.org/v1/occurrence/search?facetMincount=50000000&limit=0&facet=country
+    uri: https://api.gbif.org/v1/occurrence/search?facetMincount=100000000&limit=0&facet=country
     body:
       encoding: ''
       string: ''
@@ -40,8 +40,8 @@ http_interactions:
       status: HTTP/1.1 200 OK
       content-type: application/json
     body:
-      encoding: UTF-8
+      encoding: ''
       file: no
-      string: '{"offset":0,"limit":0,"endOfRecords":false,"count":2184797352,"results":[],"facets":[{"field":"COUNTRY","counts":[{"name":"US","count":808302991},{"name":"CA","count":131806867},{"name":"GB","count":108057716},{"name":"AU","count":107917235},{"name":"SE","count":107632259},{"name":"FR","count":100666945},{"name":"NL","count":77444744},{"name":"ES","count":54442678}]}]}'
-  recorded_at: 2022-04-08 13:39:23 GMT
-  recorded_with: vcr/1.0.2, webmockr/0.8.0
+      string: '{"offset":0,"limit":0,"endOfRecords":false,"count":2298098025,"results":[],"facets":[{"field":"COUNTRY","counts":[{"name":"US","count":820028047},{"name":"FR","count":135859403},{"name":"CA","count":133937135},{"name":"SE","count":118149141},{"name":"AU","count":114128644},{"name":"GB","count":111294920}]}]}'
+  recorded_at: 2022-12-30 08:43:33 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.8.2
diff --git a/tests/testthat/test-occ_facet.R b/tests/testthat/test-occ_facet.R
@@ -4,7 +4,7 @@ test_that("occ_facet works", {
   vcr::use_cassette("occ_facet", {
     aa <- occ_facet(facet = "country")
     # facetMincount
-    bb <- occ_facet(facet = "country", facetMincount = 50000000L)
+    bb <- occ_facet(facet = "country", facetMincount = 100000000L)
   })
 
   expect_is(aa, "list")

diff --git a/vignettes/getting_occurrence_data.Rmd b/vignettes/getting_occurrence_data.Rmd
@@ -236,7 +236,7 @@ occ_download(pred_within(large_wkt),format = "SIMPLE_CSV"))
 
 ## Data Quality 
 
-GBIF is a large data aggregator. It mediates occurrences occurrence records from a large variety of sources: 
+GBIF is a large data aggregator. It mediates occurrences records from a large variety of sources: 
 
 * Museums
 * eDNA
@@ -259,8 +259,9 @@ For this reason, not all of the occurrences from GBIF are "fit for use", meaning
 * Any-Zero Coordinates
 * Gridded Datasets 
 
-Please see the following resources for cleaning or post-processing your downloads from GBIF: 
+Since **rgbif** is not a data cleaning package, please see the following resources for post-processing your occurrence downloads: 
 
 * [Common things to look out for when post-processing GBIF downloads](https://data-blog.gbif.org/post/gbif-filtering-guide/)
 * [CoordinateCleaner](https://docs.ropensci.org/CoordinateCleaner/)
 * [Data Quality Webinar](https://www.gbif.org/event/2CAcHI4oxVK5ZgMnFszNUD/data-use-club-practical-sessions-data-quality)
+