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datamuseum

Overview

datamuseum provides functions and practice data sets for the management and refinement of biological specimens with geographic and/or taxonomic information.

The package contents are organized into four main categories:

  • Coordinate functions (latlong_*) — refine geographic information associated with biological specimens

  • Taxonomic functions (taxon_*) — clean and validate taxonomies against the Global Biodiversity Information Facility (via rgbif) and the Integrated Taxonomic Information System (ITIS, via taxize)

  • Utilities — miscellaneous functions for data set management and improved graphical outputs

  • Example data — Japan-filtered occurrence records for specimens belonging to Superfamily Octopodoidea, compiled from the Global Biodiversity Information Facility (GBIF), Invert-E-Base (InvBase), the Biological Information System for Marine Life (BISMAL), the Ocean Biodiversity Information System (OBIS), and the National Museum of Nature and Science, Japan (NSMT), as well as the compiled data sets processed through datamuseum

Installation

Install the released version from CRAN:

install.packages("datamuseum")

Or install the development version from GitHub:

# install.packages("devtools")
devtools::install_github("btorgovitsky00/datamuseum")

Usage

datamuseum serves as a tool for researchers of all levels and backgrounds, as well as a pathway for improved data access from legacy sources like museum collections.

library(datamuseum)

# Remove duplicate catalogue numbers
df <- deduplicate(df, id_col = "catalogNumber", drop_na = TRUE)

# Filter occurrence data to a geographic bounding box
japan_data <- latlong_range(df, latitude = "Latitude", longitude = "Longitude",
                            lat_min = 25, lat_max = 50,
                            lon_min = 125, lon_max = 150)

# Clean taxonomic names
df <- taxon_cleaner(df, columns = "Genus", drop_na = TRUE)

# Validate against GBIF
df <- taxon_validate(df, column = "Genus", source = "gbif")

# Append higher taxonomic ranks
df <- taxon_add(df, column = "Genus", ranks = c("order", "phylum"))

# Append authorship strings
df <- taxon_cite(df, columns = c("Family", "Genus", "Genus"))

Getting help

Citation 

citation("datamuseum")

License

MIT © Bryson Y. Torgovitsky, Cheryl L. Ames

The datamuseum hex logo was designed by Sophie Collier.