PresenceAbsence: Presence-Absence Model Evaluation.
Version 1.1.9

This package provides a set of functions useful when evaluating the results of presence-absence models. Package includes functions for calculating threshold dependent measures such as confusion matrices, pcc, sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It will calculate optimal threshold choice according to a choice of optimization criteria. It also includes functions to plot the threshold independent ROC curves along with the associated AUC (area under the curve).

AuthorElizabeth Freeman
Date of publication2012-08-17 18:47:44
MaintainerElizabeth Freeman <eafreeman@fs.fed.us>
LicenseUnlimited
Version1.1.9
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PresenceAbsence")

Popular man pages

calibration.plot: Calibration Plot
Kappa: Kappa
optimal.thresholds: Calculate Optimal Thresholds
pcc: Percent Correctly Classified
PresenceAbsence.package: Presence-Absence model evaluation
presence.absence.summary: Presence/Absence Summary Plots
specificity: Specificity
See all...

All man pages Function index File listing

Man pages

auc: Area Under the Curve
auc.roc.plot: AUC ROC Plot
calibration.plot: Calibration Plot
cmx: Confusion Matrix
error.threshold.plot: Error Threshold Plot
Kappa: Kappa
optimal.thresholds: Calculate Optimal Thresholds
pcc: Percent Correctly Classified
predicted.prevalence: Predicted Prevalence
presence.absence.accuracy: Accuracy Table for Presence/Absence Data
presence.absence.hist: Presence/Absence Histogram
PresenceAbsence.package: Presence-Absence model evaluation
presence.absence.simulation: Presence/Absence Data Simulation
presence.absence.summary: Presence/Absence Summary Plots
roc.plot.calculate: ROC Plot Calculations
sensitivity: Sensitivity
SIM3DATA: Simulated Presence-Absence Data
SPDATA: Species Presence/Absence Data
specificity: Specificity
SPPREV: Overall Preavalences for Species Presence/Absence Data

Functions

PresenceAbsence Man page
PresenceAbsence-package Man page
Kappa Man page Source code
SIM3DATA Man page
SPDATA Man page
SPPREV Man page
auc Man page Source code
auc.roc.plot Man page Source code
calibration.plot Man page Source code
cmx Man page Source code
error.threshold.plot Man page Source code
optimal.thresholds Man page Source code
pcc Man page Source code
predicted.prevalence Man page Source code
presence.absence.accuracy Man page Source code
presence.absence.hist Man page Source code
presence.absence.simulation Man page Source code
presence.absence.summary Man page Source code
roc.plot.calculate Man page Source code
sensitivity Man page Source code
specificity Man page Source code

Files

MD5
R
R/specificity.R
R/sensitivity.R
R/roc.plot.calculate.R
R/presence.absence.summary.R
R/presence.absence.simulation.R
R/presence.absence.hist.R
R/presence.absence.accuracy.R
R/predicted.prevalence.R
R/pcc.R
R/optimal.thresholds.R
R/Kappa.R
R/error.threshold.plot.R
R/cmx.R
R/calibration.plot.R
R/auc.roc.plot.R
R/auc.R
NAMESPACE
man
man/SPPREV.Rd
man/specificity.Rd
man/SPDATA.Rd
man/SIM3DATA.Rd
man/sensitivity.Rd
man/roc.plot.calculate.Rd
man/PresenceAbsence.package.Rd
man/presence.absence.summary.Rd
man/presence.absence.simulation.Rd
man/presence.absence.hist.Rd
man/presence.absence.accuracy.Rd
man/predicted.prevalence.Rd
man/pcc.Rd
man/optimal.thresholds.Rd
man/Kappa.Rd
man/error.threshold.plot.Rd
man/cmx.Rd
man/calibration.plot.Rd
man/auc.roc.plot.Rd
man/auc.Rd
inst
inst/CITATION
inst/CHANGELOG
DESCRIPTION
demo
demo/DemoSP.R
demo/DemoSIM.R
demo/00Index
data
data/SPPREV.txt.gz
data/SPDATA.txt.gz
data/SIM3DATA.txt.gz
COPYRIGHTS
PresenceAbsence documentation built on May 20, 2017, 3:45 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.