Package: datamuseum 0.1.0

Bryson Y. Torgovitsky

datamuseum: Spatial and Taxonomic Data Utilities for Specimen Datasets

A management tool for specimen data ranging from public museum collections to private specimen repositories. The main types of data addressed are spatial (coordinates, longitude and latitude) and taxonomic data (ranking and nomenclature validity) with some additional options for user-determined dataset refinement. Combined or individual calls to the online repositories of the Global Biodiversity Information Facility (GBIF) via 'rgbif' and the Integrated Taxonomic Information System (ITIS) via 'taxize' enable built-in taxonomic checks.

Authors:Bryson Y. Torgovitsky [aut, cre], Cheryl L. Ames [aut]

datamuseum_0.1.0.tar.gz
datamuseum_0.1.0.zip(r-4.7)datamuseum_0.1.0.zip(r-4.6)datamuseum_0.1.0.zip(r-4.5)
datamuseum_0.1.0.tgz(r-4.6-any)datamuseum_0.1.0.tgz(r-4.5-any)
datamuseum_0.1.0.tar.gz(r-4.7-any)datamuseum_0.1.0.tar.gz(r-4.6-any)
datamuseum_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
datamuseum/json (API)

# Install 'datamuseum' in R:
install.packages('datamuseum', repos = c('https://btorgovitsky00.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/btorgovitsky00/datamuseum/issues

Pkgdown/docs site:https://btorgovitsky00.github.io

Datasets:
  • BISMAL_Japan - Japan-filtered BISMAL Octopodoidea occurrence records
  • GBIF_Japan - Japan-filtered GBIF Octopodoidea occurrence records
  • InvBase_Japan - Japan-filtered InvBase Octopodoidea occurrence records
  • museum - Combined Japan Octopodoidea occurrence records
  • museum_taxon - Taxonomically validated and enriched Japan Octopodoidea records
  • NSMT_Japan - Japan-filtered NSMT Octopodoidea occurrence records
  • OBIS_Japan - Japan-filtered OBIS Octopodoidea occurrence records

On CRAN:

Conda:

4.78 score 407 downloads 23 exports 95 dependencies

Last updated from:166b0f4bdc. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK197
source / vignettesOK266
linux-release-x86_64OK193
macos-release-arm64OK119
macos-oldrel-arm64OK203
windows-develOK90
windows-releaseOK103
windows-oldrelOK96
wasm-releaseOK152

Exports:deduplicateduplicateitalicizelatlong_columnlatlong_combinelatlong_convertlatlong_filterlatlong_formatlatlong_hemispherelatlong_limitslatlong_rangelatlong_regionlatlong_splittaxon_addtaxon_citetaxon_cleanertaxon_columntaxon_combinetaxon_ranktaxon_sorttaxon_spellchecktaxon_splittaxon_validate

Dependencies:apeaskpasscachemclassclassIntclicodetoolscpp11crayoncrulcurldata.tableDBIdigestdplyre1071farverfastmapfastmatchfurrrfuturegenericsggplot2globalsgluegtablehmshttpcodehttrigraphisobandjsonliteKernSmoothlabelinglatticelazyevallifecyclelistenvmagrittrMASSMatrixmemoisemimenatservnlmeoaiopensslparallellyphangornpillarpkgconfigplyrprettyunitsprogressproxypurrrquadprogR6RColorBrewerRcpprentrezrgbifritisrlangrnaturalearthrnclrotlrredlists2S7scalessfsolriumstringistringrsystaxizeterratibbletidyselecttriebeardunitsurltoolsutf8vctrsviridisLitewhiskerWikipediRwikitaxawithrwkworrmsXMLxml2zoo

Accessing GitHub Data
Description
Rendered fromgithub_data.Rmdusingknitr::rmarkdown

Last update: 2026-04-22
Started: 2026-04-21

Octopodoidea in Japan
Description | Individual Data Sets | Global Biodiversity Information Facility (GBIF) Data | Invert-E-Base (InvBase) Data | Biological Information System for Marine Life (BISMAL) Data | Ocean Biodiversity Information System (OBIS) | National Museum of Nature and Science, Japan (NSMT) | Concatenated Data Sets | Japan Octopodoidea Data Set, museum | Japan Octopodoidea Data Set, museum_taxon
Rendered fromoctopodoidea_japan.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2026-04-07

Get Started
Geographic Data | Taxonomic Data | Example Data | Utilities
Rendered fromdatamuseum.Rmdusingknitr::rmarkdown

Last update: 2026-04-08
Started: 2026-04-07

Publications
Rendered frompublications.Rmdusingknitr::rmarkdown

Last update: 2026-04-07
Started: 2026-04-07

Readme and manuals

Help Manual

Help pageTopics
Japan-filtered BISMAL Octopodoidea occurrence recordsBISMAL_Japan
Remove duplicate rowsdeduplicate
Duplicate rows by a count columnduplicate
Japan-filtered GBIF Octopodoidea occurrence recordsGBIF_Japan
Japan-filtered InvBase Octopodoidea occurrence recordsInvBase_Japan
Format taxonomic names for italic display in ggplot2italicize
Identify coordinate columns in a data framelatlong_column
Combine separate coordinate columns into onelatlong_combine
Convert coordinate formatslatlong_convert
Filter rows by real-world coordinate validitylatlong_filter
Check the format of coordinate columnslatlong_format
Assign hemispheres to coordinateslatlong_hemisphere
Report coordinate limits of a data framelatlong_limits
Filter rows by coordinate rangelatlong_range
Filter rows by geographic regionlatlong_region
Split a combined coordinate column into separate columnslatlong_split
Combined Japan Octopodoidea occurrence recordsmuseum
Taxonomically validated and enriched Japan Octopodoidea recordsmuseum_taxon
Japan-filtered NSMT Octopodoidea occurrence recordsNSMT_Japan
Japan-filtered OBIS Octopodoidea occurrence recordsOBIS_Japan
Add higher taxonomic rank columnstaxon_add
Append authorship and year to taxonomic name columnstaxon_cite
Clean taxonomic name formattingtaxon_cleaner
Identify taxonomic columnstaxon_column
Combine genus and epithet columns into a binomial nametaxon_combine
Detect the taxonomic rank of a columntaxon_rank
Sort columns into standard taxonomic rank ordertaxon_sort
Check and correct taxonomic name spellingtaxon_spellcheck
Split a binomial name column into genus and epithettaxon_split
Validate taxonomic names against ITIS and GBIFtaxon_validate