The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
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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A probability threshold value for predicting terra preta presence and absence was generated based on maximizing the percentage of sites correctly classified.
“A probability threshold value for predicting terra preta presence and absence was generated based on maximizing the percentage of sites correctly classified [51].”
From Predicting pre-columbian anthropogenic soils in amazonia (2014) · cites this paper as [51]
Citations
Cites
DeLong, E. R., DeLong, D. M., & Clarke-Pearson, D. L. (1988) · Biometrics · doi:10.2307/2531595 · Cited by 22,649
limma: Linear Models for Microarray Data
Smyth, G. K. (2005) · Statistics for Biology and Health · doi:10.1007/0-387-29362-0_23 · Cited by 5,796
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A tutorial on calibration measurements and calibration models for clinical prediction models
Huang, Y., Li, W., Macheret, F., Gabriel, R. A., & Ohno-Machado, L. (2020) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocz228 · Cited by 486
Predicting pre-columbian anthropogenic soils in amazonia
McMichael, C. H., Palace, M. W., Bush, M. B., Braswell, B., Hagen, S., Neves, E. G., Silman, M. R., Tamanaha, E. K., & Czarnecki, C. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2013.2475 · Cited by 179
Testing species assemblage predictions from stacked and joint species distribution models
Zurell, D., Zimmermann, N. E., Gross, H., Baltensweiler, A., Sattler, T., & Wüest, R. O. (2020) · Journal of Biogeography · doi:10.1111/jbi.13608 · Cited by 153
Metadata
- Authors
- Freeman, E. A., & Moisen, G.
- Venue
- Journal of Statistical Software
- Publisher
- Foundation for Open Access Statistic
- Published
- 2008
- Volume
- 23
- Issue
- 11
- ISSN
- 1548-7660
- Cited by
- 461
- References
- 2
- Language
- en
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