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
gatoRs_1.0.2.zip(r-4.5)gatoRs_1.0.2.zip(r-4.4)gatoRs_1.0.2.zip(r-4.3)
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'))

Peer review:

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

Datasets:

    On CRAN:

    6.46 score 11 stars 66 scripts 587 downloads 23 exports 152 dependencies

    Last updated 6 months agofrom:c2c899018b. Checks:OK: 7. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 14 2024
    R-4.5-winOKOct 14 2024
    R-4.5-linuxOKOct 14 2024
    R-4.4-winOKOct 14 2024
    R-4.4-macOKOct 14 2024
    R-4.3-winOKOct 14 2024
    R-4.3-macOKOct 14 2024

    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 Oct 14 2024.

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

    Many Downloads with gatoRs

    Rendered fromManyDownloads.Rmdusingknitr::rmarkdownon Oct 14 2024.

    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