Package: PresenceAbsence 1.1.11
Elizabeth Freeman
PresenceAbsence: Presence-Absence Model Evaluation
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).
Authors:
PresenceAbsence_1.1.11.tar.gz
PresenceAbsence_1.1.11.tar.gz(r-4.5-noble)PresenceAbsence_1.1.11.tar.gz(r-4.4-noble)
PresenceAbsence_1.1.11.tgz(r-4.4-emscripten)PresenceAbsence_1.1.11.tgz(r-4.3-emscripten)
PresenceAbsence.pdf |PresenceAbsence.html✨
PresenceAbsence/json (API)
| # Install 'PresenceAbsence' in R: |
| install.packages('PresenceAbsence', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:231cfc9e54. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 25 2024 |
| R-4.5-linux | OK | Aug 25 2024 |
Exports:aucauc.roc.plotcalibration.plotcmxerror.threshold.plotKappaoptimal.thresholdspccpredicted.prevalencepresence.absence.accuracypresence.absence.histpresence.absence.simulationpresence.absence.summaryroc.plot.calculatesensitivityspecificity
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Presence-Absence model evaluation | PresenceAbsence-package PresenceAbsence |
| Area Under the Curve | auc |
| AUC ROC Plot | auc.roc.plot |
| Calibration Plot | calibration.plot |
| Confusion Matrix | cmx |
| Error Threshold Plot | error.threshold.plot |
| Kappa | Kappa |
| Calculate Optimal Thresholds | optimal.thresholds |
| Percent Correctly Classified | pcc |
| Predicted Prevalence | predicted.prevalence |
| Accuracy Table for Presence/Absence Data | presence.absence.accuracy |
| Presence/Absence Histogram | presence.absence.hist |
| Presence/Absence Data Simulation | presence.absence.simulation |
| Presence/Absence Summary Plots | presence.absence.summary |
| ROC Plot Calculations | roc.plot.calculate |
| Sensitivity | sensitivity |
| Simulated Presence-Absence Data | SIM3DATA |
| Species Presence/Absence Data | SPDATA |
| Specificity | specificity |
| Overall Preavalences for Species Presence/Absence Data | SPPREV |