diff --git a/DESCRIPTION b/DESCRIPTION index 436daef9..5e45666d 100644 --- 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 index c0e6b439..8e3b6cd4 100644 --- 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 index f38904ae..f8f1021f 100644 --- 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 deleted file mode 100644 index 44b4b36a..00000000 --- a/revdep/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -checks -library -checks.noindex -library.noindex -cloud.noindex -data.sqlite -*.html diff --git a/revdep/README.md b/revdep/README.md index bdddf9ee..a48a20fd 100644 --- 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 deleted file mode 100644 index 84f59e67..00000000 --- a/revdep/check.R +++ /dev/null @@ -1,2 +0,0 @@ -revdepcheck::revdep_reset() -revdepcheck::revdep_check(num_workers = 2) diff --git a/revdep/checks.rds b/revdep/checks.rds deleted file mode 100644 index 47b309bf..00000000 Binary files a/revdep/checks.rds and /dev/null differ diff --git a/revdep/email.yml b/revdep/email.yml index f7340fa4..0c5cef87 100644 --- 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 index 1160af19..5fe5f750 100644 --- 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 index d0cef747..61a72c93 100644 --- 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 index caaf4f08..25316912 100644 --- 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) +