Package: gatoRs 2.0.0

Michelle L. Gaynor

gatoRs: Geographic and Taxonomic Occurrence R-Based Scrubbing

Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).

Authors:Natalie N. Patten [aut, cre], Michelle L. Gaynor [aut], Douglas E. Soltis [ctb], Pamela S. Soltis [ctb]

gatoRs_2.0.0.tar.gz
gatoRs_2.0.0.zip(r-4.7)gatoRs_2.0.0.zip(r-4.6)gatoRs_2.0.0.zip(r-4.5)
gatoRs_2.0.0.tgz(r-4.6-any)gatoRs_2.0.0.tgz(r-4.5-any)
gatoRs_2.0.0.tar.gz(r-4.7-any)gatoRs_2.0.0.tar.gz(r-4.6-any)
gatoRs_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
gatoRs/json (API)

# Install 'gatoRs' in R:
install.packages('gatoRs', repos = c('https://nataliepatten.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nataliepatten/gators/issues

Pkgdown/docs site:https://nataliepatten.github.io

On CRAN:

Conda:

6.08 score 13 stars 92 scripts 629 downloads 23 exports 107 dependencies

Last updated from:23e1fa0aae. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK299
source / vignettesOK314
linux-release-x86_64OK286
macos-release-arm64OK191
macos-oldrel-arm64OK184
windows-develOK204
windows-releaseOK209
windows-oldrelOK212
wasm-releaseOK186

Exports:%>%basic_locality_cleanbasis_cleancitation_bellowdata_chompfilter_fix_namesfix_columnsfix_namesfull_cleangators_downloadgators_mergeget_gbifget_idigbio_arcneed_to_georeferenceneeded_recordsone_point_per_pixelprocess_flaggedremove_duplicatesremove_missingremove_redactedremove_skewedtaxa_cleanthin_points

Dependencies:arrowaskpassassertthatbase64encbitbit64bslibcachemclassclassIntcliCoordinateCleanercpp11crosstalkcrulcurldata.tableDBIdeldirdigestdotCall64dplyrduckdbe1071evaluatefarverfastmapfieldsfontawesomefsgenericsgeosphereggplot2gluegtablehighrhtmltoolshtmlwidgetshttpcodehttrisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclemagrittrmapsMASSMatrixmemoisemimeoaiopensslparsedatepillarpkgconfigplyrpngpolyclipproxypurrrR6rappdirsrasterRColorBrewerRcpprgbifrlangrmarkdownrnaturalearths2S7sassscalessfspspamspatstat.dataspatstat.geomspatstat.univarspatstat.utilsspThinstringistringrsysterratibbletidyselecttinytextriebeardunitsurltoolsutf8vctrsviridisLitewhiskerwithrwkxfunxml2yaml

Introduction to gatoRs
Data Downloading | Identifying Synonyms | Download with gatoRs | Data Processing | Identify Records Missing Locality Information | Redacted Records | Records to Georeference | Merging Retained Records | Occurrence Data Cleaning | Resolve Taxon Names | Clean Locality | Basic Locality Clean | Find and Remove Flagged Points | Remove Duplicate Records | Remove Particular Record Bases | Spatial Correction | One Point Per Pixel | Spatial thining | Full Clean | Downstream Data Proccessing | Prepared data for MAXENT | Prepared data for publication
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2023-03-16

Many Downloads with gatoRs
Retry Function | Use the Retry Function
Rendered fromManyDownloads.Rmdusingknitr::rmarkdown

Last update: 2023-09-14
Started: 2023-09-12

Readme and manuals

Help Manual

Help pageTopics
Locality Cleaning - Remove missing and improbable coordinatesbasic_locality_clean
Basis Cleaning - Removes records with certain record basisbasis_clean
Cite Data - Get GBIF citationscitation_bellow
Subset Data - Get species, longitude, and latitude columnsdata_chomp
Used in gators_download() - Filter iDigBio results by scientific namefilter_fix_names
Used in gators_download() - Fill out taxonomic name columnsfix_columns
Used in gators_download() - Fix taxonomic name capitalizationfix_names
Full Cleaning - Wrapper function to speed cleanfull_clean
Download - Download specimen data from both GBIF and the iDigBio archivegators_download
Merge Retained Data - Combined original data set with georeferenced or retained records.gators_merge
Used in gators_download() - Download data from the Global Biodiversity Information Facilityget_gbif
Used in gators_download() - Download data from Integrated Digitized Biocollections that are not on GBIFget_idigbio_arc
Identify Missing Information - Find records which lack coordinate informationneed_to_georeference
Identify Missing Information - Find records with redacted or missing dataneeded_records
Spatial Correction - One point per pixelone_point_per_pixel
Locality Cleaning - Find possibly problematic occurrence recordsprocess_flagged
Remove Duplicates - Remove records with identical event dates and coordinatesremove_duplicates
Remove Missing Information - Prepare to merge a data frame with georeferenced and retrieved recordsremove_missing
Remove Redacted Information - Remove protected or private records prior to publicationremove_redacted
Used in basic_locality_clean() - Removed skewed localityremove_skewed
Used in gators_download() - Setting up local querysetupduckDB
Taxonomic Cleaning - Filter and resolve taxon namestaxa_clean
Spatial Correction - Spatially thin recordsthin_points