You are here: Home
/ Publication Information
Title: PresenceAbsence: An R package for presence absence analysis
Author: Freeman, Elizabeth A.; Moisen, Gretchen;
Source: Journal of Statistical Software. 23(11): 31 p.
Publication Series: Miscellaneous Publication
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
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
- You may send email to firstname.lastname@example.org to request a hard copy of this publication. (Please specify exactly which publication you are requesting and your mailing address.)
XML: View XML
Freeman, Elizabeth A.; Moisen, Gretchen 2008. PresenceAbsence: An R package for presence absence analysis. Journal of Statistical Software. 23(11): 31 p.
Get the latest version of the Adobe Acrobat reader or Acrobat Reader for Windows with Search and Accessibility