Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Elizabeth A. Freeman, Gretchen Moisen
Title: PresenceAbsence: An R Package for Presence Absence Analysis
Abstract: The PresenceAbsence package for R provides a set of functions useful when evaluating the results of presence-absence analysis, for example, models of species distribution or the analysis of diagnostic tests. The package provides a toolkit for selecting the optimal threshold for translating a probability surface into presence-absence maps specifically tailored to their intended use. The package includes functions for calculating threshold dependent measures such as confusion matrices, percent correctly classified (PCC), sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It also includes functions to plot the Receiver Operator Characteristic (ROC) curve and calculates the associated area under the curve (AUC), a threshold independent measure of model quality. Finally, the package computes optimal thresholds by multiple criteria, and plots these optimized thresholds on the graphs.

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Paper: PresenceAbsence: An R Package for Presence Absence Analysis     Download PDF (Downloads: 14230)
Supplements:
PresenceAbsence_1.1.1.tar.gz: R source package Download (Downloads: 1358; 129KB)
v23i11.R: R example code from the paper Download (Downloads: 1869; 19KB)
DOI: 10.18637/jss.v023.i11

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.