Package: RuHere 1.0.1

Weverton C. F. Trindade

RuHere: Flags Spatial Errors in Biological Collection Data Using Specialists' Information

Automatically flags common spatial errors in biological collection data using metadata and specialists' information. RuHere implements a workflow to manage occurrence data through six steps: dataset merging, metadata flagging, validation against expert-derived distribution maps, visualization of flagged records, and sampling bias exploration. It specifically integrates specialist-curated range information to identify geographic errors and introductions that often escape standard automated validation procedures. For details on the methodology, see: Trindade & Caron (2026) <doi:10.64898/2026.02.02.703373>.

Authors:Weverton C. F. Trindade [aut, cre], Fernanda S. Caron [aut]

RuHere_1.0.1.tar.gz
RuHere_1.0.1.tar.gz(r-4.7-arm64)RuHere_1.0.1.tar.gz(r-4.7-x86_64)RuHere_1.0.1.tar.gz(r-4.6-arm64)RuHere_1.0.1.tar.gz(r-4.6-x86_64)
RuHere_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RuHere/json (API)
NEWS

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

Bug tracker:https://github.com/wevertonbio/ruhere/issues

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • country_dictionary - Country dictionary for standardizing country names and codes
  • cultivated - Dictionary of terms used to flag cultivated individuals
  • fake_data - Fake occurrence data for testing coordinate validation functions
  • flag_colors - Color palette for flagged records
  • flag_names - Flag name dictionary
  • occ_bien - Occurrence records of Yellow Trumpet Tree from BIEN
  • occ_flagged - Flagged occurrence records of _Araucaria angustifolia_
  • occ_gbif - Occurrence records of _Araucaria angustifolia_ from GBIF
  • occ_idig - Occurrence records of azure jay from iDigBio
  • occ_splink - Occurrence records of azure jay from SpeciesLink
  • occurrences - Integrated occurrence dataset for three example species
  • prepared_metadata - Metadata templates used internally by 'format_columns()'
  • puma_atlanticr - Occurrence records of _Puma concolor_ from AtlanticR
  • states - Administrative Units
  • states_dictionary - States dictionary for standardizing state and province names and codes
  • world - World Countries
  • worldclim - Bioclimatic Variables from WorldClim

On CRAN:

Conda:

openblascpp

3.48 score 12 scripts 201 downloads 56 exports 167 dependencies

Last updated from:46baa2e3eb. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK353
linux-devel-x86_64OK376
source / vignettesOK362
linux-release-arm64OK344
linux-release-x86_64OK372
wasm-releaseOK171

Exports:available_datasetsbien_herebind_herecheck_countriescheck_statescountry_from_coordscreate_metadatafaunabr_herefix_countriesfix_statesflag_bienflag_consensusflag_cultivatedflag_duplicatesflag_env_moranflag_faunabrflag_florabrflag_fossilflag_geo_moranflag_inaturalistflag_iucnflag_wcvpflag_yearflorabr_hereformat_columnsget_bienget_env_binsget_idigbioget_specieslinkggmap_hereggrid_hereimport_gbifiucn_heremap_heremoranfastplot_env_binsprepare_gbif_downloadrelocate_afterrelocate_beforeremove_accentremove_flaggedremove_invalid_coordinatesrequest_gbifrichness_hereset_gbif_credentialsset_iucn_credentialsset_specieslink_credentialsspatial_kdespatializestandardize_countriesstandardize_statesstates_from_coordssummarize_flagsthin_envthin_geowcvp_here

Dependencies:apeaskpassbackportsbase64encBIENbitbit64blobbrewbroombslibcachemcallrcellrangerclassclassIntclicliprcodetoolsconflictedcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdoParalleldoSNOWdotCall64dplyrdtplyre1071evaluatefarverfastmapfaunabrfieldsflorabrfontawesomeforcatsforeachfsgarglegenericsgeojsonsfgeometriesggnewscaleggplot2gluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttridsisobanditeratorsjquerylibjsonifyjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafemleafletleaflet.providersleafpoplifecyclelubridatemagrittrmapsmapviewMASSmemoisemimemodelrnlmeoaiopensslotelpillarpkgconfigplyrpngprettyunitsprocessxprogresspromisesproxypspurrrR6raggrapidjsonrrappdirsrasterRColorBrewerRcppRcppArmadilloreadrreadxlrematchrematch2reprexrgbifridigbiorlangrmarkdownRPostgreSQLrredlistrstudioapirvests2S7sasssatellitescalesselectrservrsfsfheaderssnowspspamstringistringrsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunXMLxml2yaml

Obtaining and preparing species occurrence data

Rendered fromobtaining_data.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-02-17
Started: 2026-02-17

Ensuring spatial consistency: countries, states, and coordinates

Rendered fromspatial_consistency.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-02-17
Started: 2026-02-17

Flagging Records Using Associated Information

Rendered fromflagging_records.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-02-17
Started: 2026-02-17

Flagging Records with Species List Information

Rendered fromflagging_records_species_list.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-02-17
Started: 2026-02-17

Reducing sampling bias

Rendered fromsampling_bias.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-02-17
Started: 2026-02-17

Readme and manuals

Help Manual

Help pageTopics
Check the available distribution datasets for a set of speciesavailable_datasets
Download species distribution information from BIENbien_here
Bind occurrences after standardizing columnsbind_here
Check if the records fall in the country assigned in the metadatacheck_countries
Check if the records fall in the state assigned in the metadatacheck_states
Country dictionary for standardizing country names and codescountry_dictionary
Extract country from coordinatescountry_from_coords
Create metadata templatecreate_metadata
Dictionary of terms used to flag cultivated individualscultivated
Fake occurrence data for testing coordinate validation functionsfake_data
Download the latest version of the Fauna do Brazil (Taxonomic Catalog of the Brazilian Fauna)faunabr_here
Identify and correct coordinates based on country informationfix_countries
Identify and correct coordinates based on state informationfix_states
Identify records outside natural ranges according to BIENflag_bien
Color palette for flagged recordsflag_colors
Get consensus across multiple flagsflag_consensus
Flag occurrence records of cultived individualsflag_cultivated
Flag duplicated recordsflag_duplicates
Select Environmentally Thinned Occurrences Using Moran's I Autocorrelationflag_env_moran
Identify records outside natural ranges according to Fauna do Brasilflag_faunabr
Identify records outside natural ranges according to Flora e Funga do Brasilflag_florabr
Flag fossil recordsflag_fossil
Select Spatially Thinned Occurrences Using Moran's I Autocorrelationflag_geo_moran
Flag occurrence records sourced from iNaturalistflag_inaturalist
Identify records outside natural ranges according to the IUCNflag_iucn
Flag name dictionaryflag_names
Identify records outside natural ranges according to the World Checklist of Vascular Plantsflag_wcvp
Flag records outside a year rangeflag_year
Download the latest version of Flora e Funga do Brasil databaseflorabr_here
Format and standardize column names and data types of an occurrence datasetformat_columns
Download occurrence records from BIENget_bien
Identify Environmental Blocks and Group Nearby Records in Environmental Spaceget_env_bins
get_idigbioget_idigbio
Download occurrence records from SpeciesLinkget_specieslink
Static Visualization of Occurrence Flags with ggplotggmap_here
Static Visualization of Richness and Trait Mapsggrid_here
Import a download requested from GBIFimport_gbif
Download species distribution information from IUCNiucn_here
Interactive Visualization of Occurrence Flags with mapviewmap_here
Fast Moran's I Autocorrelation Indexmoranfast
Occurrence records of Yellow Trumpet Tree from BIENocc_bien
Flagged occurrence records of _Araucaria angustifolia_occ_flagged
Occurrence records of _Araucaria angustifolia_ from GBIFocc_gbif
Occurrence records of azure jay from iDigBioocc_idig
Occurrence records of azure jay from SpeciesLinkocc_splink
Integrated occurrence dataset for three example speciesoccurrences
Plot Environmental Bins (2D Projection)plot_env_bins
Prepare data to request GBIF downloadprepare_gbif_download
Metadata templates used internally by 'format_columns()'prepared_metadata
Occurrence records of _Puma concolor_ from AtlanticRpuma_atlanticr
Relocate a column in a data framerelocate_after relocate_before
Remove accents and special characters from stringsremove_accent
Remove flagged recordsremove_flagged
Identify and remove invalid coordinatesremove_invalid_coordinates
Submit a request to download occurrence data from GBIF.request_gbif
Species Richness and Occurrence Summary Mappingrichness_here
Store GBIF credentialsset_gbif_credentials
Store SpeciesLink credentialset_iucn_credentials
Store SpeciesLink credentialset_specieslink_credentials
Kernel Density Estimation (Heatmap) for occurrence dataspatial_kde
Spatialize occurrence recordsspatialize
Standardize country namesstandardize_countries
Standardize state namesstandardize_states
Administrative Units (States, Provinces, and Regions)states
States dictionary for standardizing state and province names and codesstates_dictionary
Extract state from coordinatesstates_from_coords
Summarize flagssummarize_flags
Flag records that are close to each other in the enviromnetal spacethin_env
Flag records that are close to each other in the geographic spacethin_geo
Download distribution data from the World Checklist of Vascular Plants (WCVP)wcvp_here
World Countriesworld
Bioclimatic Variables from WorldClim (bio_1, bio_7, bio_12)worldclim