Package: RuHere 1.0.1

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
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RuHere_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RuHere/json (API)

# Install 'RuHere' in R:
install.packages('RuHere', repos = c('https://wevertonbio.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:
  • atlantic_amphibians - Amphibian communities from the Atlantic Forest
  • 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

6.37 score 3 stars 12 scripts 242 downloads 57 exports 163 dependencies

Last updated from:e1fe28a9c6. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
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source / vignettesOK367
linux-release-arm64OK319
linux-release-x86_64OK356
macos-release-arm64OK271
macos-release-x86_64OK573
macos-oldrel-arm64OK188
macos-oldrel-x86_64OK454
windows-develOK385
windows-releaseOK367
windows-oldrelOK370
wasm-releaseOK219

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_gbifinventory_completenessiucn_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:askpassbackportsbase64encbitbit64blobbrewbroombslibcachemcallrcellrangerclassclassIntclicliprcodetoolsconflictedcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdoSNOWdotCall64dplyrdtplyre1071evaluatefarverfastmapfaunabrfieldsflorabrfontawesomeforcatsforeachfsgarglegenericsgeojsonsfgeometriesggnewscaleggplot2gluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttridsisobanditeratorsjquerylibjsonifyjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafemleafletleaflet.providersleafpoplifecyclelubridatemagrittrmapsmapviewMASSmemoisemimemodelroaiopensslotelpillarpkgconfigplyrpngprettyunitsprocessxprogresspromisesproxypspurrrR6raggrapidjsonrrappdirsrasterRColorBrewerRcppRcppArmadilloreadrreadxlrematchrematch2reprexrgbifridigbiorlangrmarkdownRPostgreSQLrredlistrstudioapirvests2S7sasssatellitescalesselectrservrsfsfheaderssnowspspamstringistringrsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsviridisLitevroomwhiskerwithrwkxfunXMLxml2yaml

Flagging Records with Species List Information
Introduction | Proposed workflow | Overview of the functions: | Getting ready | Downloading distribution datasets | World Checklist of Vascular Plants (WCVP) | Botanical Information and Ecology Network (BIEN) | IUCN | Brazilian Flora and Funga (florabr) | Taxonomic Catalog of the Brazilian Fauna (faunabr) | Checking data availability | Flagging with expert information | Using World Checklist of Vascular Plants (WCVP) | Using IUCN | Using Botanical Information and Ecology Network (BIEN) | Using Brazilian Flora and Funga (florabr) | Using Taxonomic Catalog of the Brazilian Fauna (faunabr) | Map of occurrence flags | Summarizing flags
Rendered fromflagging_records_species_list.Rmdusingknitr::rmarkdown

Last update: 2026-02-11
Started: 2025-12-18

Flagging Records Using Associated Information
Introduction | Proposed workflow | Overview of the functions: | Getting ready | Removing invalid coordinates (remove_invalid_coordinates()) | Flagging based on metadata information | Fossil records | Cultivated individuals | Records from iNaturalist | Records outside a year range | Flagging duplicates | Spatial cleaning (CoordinateCleaner) | Implement flags from CoordinateCleaner | Map of occurrence flags | Get consensus across multiple flags | Removing flagged records | Summarizing flags | Spatial aggregation of records and flags | Mapping species richness and record density | Mapping data quality flags
Rendered fromflagging_records.Rmdusingknitr::rmarkdown

Last update: 2026-02-02
Started: 2025-12-18

Reducing sampling bias
Introduction | Heatmap for occurrence data | Thinning in geographic space | Selecting the best distance to thin records | Thinning in environmental space | Selecting the best number of environmental bins | Consensus between environmental and geographic thinning
Rendered fromsampling_bias.Rmdusingknitr::rmarkdown

Last update: 2026-01-27
Started: 2025-12-10

Obtaining and preparing species occurrence data
Introduction | Overview of the functions: | Setting up credentials | GBIF | SpeciesLink | Data acquisition | SpeciesLink, BIEN, and iDigBio | Standardization and unification | Standardizing columns (format_columns) | Customizing Metadata (create_metadata) | Spatialization (spatialize)
Rendered fromobtaining_data.Rmdusingknitr::rmarkdown

Last update: 2026-01-15
Started: 2025-12-18

Ensuring spatial consistency: countries, states, and coordinates
Introduction | Overview of the functions: | Standardizing country and state names | Occurrence data | Standardizing countries (standardize_countries) | Standardizing states (standardize_states) | Imputing geographic information from coordinates | Extracting country from coordinates (country_from_coords) | Extracting state from coordinates (states_from_coords) | Checking and fixing spatial inconsistencies | Checking country consistency (check_countries) | Checking state consistency (check_states) | Fixing coordinate errors explicitly (fix_countries)
Rendered fromspatial_consistency.Rmdusingknitr::rmarkdown

Last update: 2025-12-25
Started: 2025-12-18

Readme and manuals

Help Manual

Help pageTopics
Amphibian communities from the Atlantic Forestatlantic_amphibians
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
Estimation of inventory completeness and coverage deficitinventory_completeness
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