datamuseum: an R package for managing and refining biological specimen data

datamuseum (R package ver 0.1.0) is a newly published R Package which provides accessible management and refinement of biological specimen data through dedicated taxonomic and spatial data utilities to researchers at all levels of coding and taxonomy. datamuseum provides users with a robust taxonomic validation backbone via GBIF (Global Biodiversity Information Facility) and ITIS (Integrated Taxonomic Information System), and an accessible framework intended for access to researchers at all levels of taxonomic and coding expertise. Within datamuseum, there are three major function types: spatial, taxonomic, and utilities for overall data set management. The inclusion of these utilities within a single R package, a high level of user customizability, and step-by-step outputs distinguish datamuseum as an introduction tool for newcomers to these key fields. The package also hosts data for specimens of Superfamily Octopodoidea d’Orbigny, 1839 compiled from five research-grade repositories: BISMaL, GBIF, Invert-E-Base, NSMT, and OBIS. Here, an example workflow refines those separate data sets spatially around Japan, combines them, and updates included taxonomic information to its valid nomenclature. This is followed by additional data cleaning to a readily analyzable and publishable format. From an initial collection of nearly 180,000 specimen data points, which included 49 apparent genera, 21 genera were successfully validated across 5,118 refined specimens through a recursive framework original to datamuseum. Comparisons with similar packages highlight the unique applications of datamuseum as a unique new tool for the management of biological specimen metadata in R.