Rocky Mountain Research Station

Title: PresenceAbsence: An R package for presence absence analysis

Author: Freeman, Elizabeth A.; Moisen, Gretchen

Date: 2008

Source: Journal of Statistical Software. 23(11): 31 p.

Description: 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.

Keywords: binary classification, ROC, AUC, sensitivity, specificity, threshold, species distribution models, diagnostic tests

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Citation

Freeman, Elizabeth A.; Moisen, Gretchen  2008.  PresenceAbsence: An R package for presence absence analysis.   Journal of Statistical Software. 23(11): 31 p..