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United States Department of Agriculture

Agricultural Research Service

Research Project: SYSTEMATICS, GENETIC DIVERSITY ASSESSMENT, AND ACQUISITION OF POTATOES, CARROTS, AND THEIR RELATED WILD RELATIVES

Location: Vegetable Crops Research Unit

Title: A new R function, exsic, to assist taxonomists in creating indices

Authors
item Simon, Reinhard -
item Spooner, David

Submitted to: Applications in Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 23, 2013
Publication Date: June 7, 2013
Repository URL: http://handle.nal.usda.gov/10113/56841
Citation: Simon, R., Spooner, D.M. 2013. A new R function, exsic, to assist taxonomists in creating indices. Applications in Plant Sciences. 1(6):1-4.

Interpretive Summary: A taxonomic monograph is a book-length compilation of many facts of a natural group of species, that includes 1) the history of the genus in the literature, 2) facts about the interrelationships of the species, 3) tools to identify the species (called taxonomic keys), 4) species illustrations, 5) species descriptions, 6) lists of all names that have been published for the species, 7) maps of the distribution of the species, 8) lists the geographic occurrence of species, who collected the specimens documenting these collections, dates of these collections, and where the specimen records (herbarium sheets) are deposited, and 9) indices to associate collectors and collector numbers from herbarium sheets to identifications, a format technically termed an exsiccate list. For factors 8 and 9, are typically initiated by entering data into a database, and then converted into text files suitable for publication. This conversion process is done by hand and is time-consuming, cumbersome, and error-prone. We constructed a software tool to automate procedures 8 and 9 that greatly increases the speed and accuracy of these two processes and deposited it for free use in the “R” library of computer software. This paper describes this software tool and provides instructions in its use.

Technical Abstract: Taxonomists manage large amounts of specimen data. This is usually initiated in spreadsheets and then converted for publication into locality lists and in indices to associate collectors and collector numbers from herbarium sheets to identifications, a format technically termed an exsiccate list. This conversion process is done by hand and is time-consuming, cumbersome, and error-prone. We constructed a tool, ‘exsic’, based on the statistical software R and tools for reproducible research. The exsic function is part of the R library ‘mcpd’ and produces locality lists and exsiccate conforming to the format used by Systematic Botany Monographs. The tool increases speed, efficiency, and accuracy to convert raw databases to publication-ready content.

Last Modified: 4/16/2014
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