PresenceAbsence: Presence-Absence Model Evaluation.

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).

Author
Elizabeth Freeman
Date of publication
2012-08-17 18:47:44
Maintainer
Elizabeth Freeman <eafreeman@fs.fed.us>
License
Unlimited
Version
1.1.9

View on CRAN

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

Files in this package

PresenceAbsence
PresenceAbsence/MD5
PresenceAbsence/R
PresenceAbsence/R/specificity.R
PresenceAbsence/R/sensitivity.R
PresenceAbsence/R/roc.plot.calculate.R
PresenceAbsence/R/presence.absence.summary.R
PresenceAbsence/R/presence.absence.simulation.R
PresenceAbsence/R/presence.absence.hist.R
PresenceAbsence/R/presence.absence.accuracy.R
PresenceAbsence/R/predicted.prevalence.R
PresenceAbsence/R/pcc.R
PresenceAbsence/R/optimal.thresholds.R
PresenceAbsence/R/Kappa.R
PresenceAbsence/R/error.threshold.plot.R
PresenceAbsence/R/cmx.R
PresenceAbsence/R/calibration.plot.R
PresenceAbsence/R/auc.roc.plot.R
PresenceAbsence/R/auc.R
PresenceAbsence/NAMESPACE
PresenceAbsence/man
PresenceAbsence/man/SPPREV.Rd
PresenceAbsence/man/specificity.Rd
PresenceAbsence/man/SPDATA.Rd
PresenceAbsence/man/SIM3DATA.Rd
PresenceAbsence/man/sensitivity.Rd
PresenceAbsence/man/roc.plot.calculate.Rd
PresenceAbsence/man/PresenceAbsence.package.Rd
PresenceAbsence/man/presence.absence.summary.Rd
PresenceAbsence/man/presence.absence.simulation.Rd
PresenceAbsence/man/presence.absence.hist.Rd
PresenceAbsence/man/presence.absence.accuracy.Rd
PresenceAbsence/man/predicted.prevalence.Rd
PresenceAbsence/man/pcc.Rd
PresenceAbsence/man/optimal.thresholds.Rd
PresenceAbsence/man/Kappa.Rd
PresenceAbsence/man/error.threshold.plot.Rd
PresenceAbsence/man/cmx.Rd
PresenceAbsence/man/calibration.plot.Rd
PresenceAbsence/man/auc.roc.plot.Rd
PresenceAbsence/man/auc.Rd
PresenceAbsence/inst
PresenceAbsence/inst/CITATION
PresenceAbsence/inst/CHANGELOG
PresenceAbsence/DESCRIPTION
PresenceAbsence/demo
PresenceAbsence/demo/DemoSP.R
PresenceAbsence/demo/DemoSIM.R
PresenceAbsence/demo/00Index
PresenceAbsence/data
PresenceAbsence/data/SPPREV.txt.gz
PresenceAbsence/data/SPDATA.txt.gz
PresenceAbsence/data/SIM3DATA.txt.gz
PresenceAbsence/COPYRIGHTS