Package: gatoRs 1.0.2

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_1.0.2.tar.gz
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gatoRs_1.0.2.tgz(r-4.5-any)gatoRs_1.0.2.tgz(r-4.4-any)gatoRs_1.0.2.tgz(r-4.3-any)
gatoRs_1.0.2.tar.gz(r-4.5-noble)gatoRs_1.0.2.tar.gz(r-4.4-noble)
gatoRs_1.0.2.tgz(r-4.4-emscripten)gatoRs_1.0.2.tgz(r-4.3-emscripten)
gatoRs.pdf |gatoRs.html✨
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 site:https://nataliepatten.github.io

On CRAN:

Conda:

6.16 score 11 stars 66 scripts 662 downloads 23 exports 152 dependencies

Last updated 11 months agofrom:c2c899018b. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 13 2025
R-4.5-winOKMar 13 2025
R-4.5-macOKMar 13 2025
R-4.5-linuxOKMar 13 2025
R-4.4-winOKMar 15 2025
R-4.4-macOKMar 13 2025
R-4.4-linuxOKMar 13 2025
R-4.3-winOKMar 13 2025
R-4.3-macOKMar 13 2025

Exports:%>%basic_locality_cleanbasis_cleancitation_bellowdata_chompfilter_fix_namesfix_columnsfix_namesfull_cleangators_downloadgators_mergeget_gbifget_idigbioneed_to_georeferenceneeded_recordsone_point_per_pixelprocess_flaggedremove_duplicatesremove_missingremove_redactedremove_skewedtaxa_cleanthin_points

Dependencies:askpassbackportsbase64encbitbit64blobbroombslibcachemcallrcellrangerclassclassIntclicliprcolorspaceconflictedCoordinateCleanercowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdeldirdigestdotCall64dplyrdtplyre1071evaluatefansifarverfastmapfieldsfontawesomeforcatsfsgarglegenericsgeosphereggplot2gluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttridsisobandjquerylibjsonlitekableExtraKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrmapsMASSMatrixmemoisemgcvmimemodelrmunsellnlmeoaiopensslparsedatepillarpkgconfigplyrpngpolyclipprettyunitsprocessxprogressproxypspurrrR6raggrappdirsrasterRColorBrewerRcppreadrreadxlrematchrematch2reprexrgbifridigbiorlangrmarkdownrnaturalearthrstudioapirvests2sassscalesselectrsfspspamspatstat.dataspatstat.geomspatstat.univarspatstat.utilsspThinstringistringrsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunxml2yaml

Introduction to gatoRs

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2024-05-17
Started: 2023-03-16

Many Downloads with gatoRs

Rendered fromManyDownloads.Rmdusingknitr::rmarkdownon Mar 13 2025.

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 iDigBio and GBIFgators_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 Biocollectionsget_idigbio
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
Taxonomic Cleaning - Filter and resolve taxon namestaxa_clean
Spatial Correction - Spatially thin recordsthin_points