Package: detect 0.5-1

detect: Analyzing Wildlife Data with Detection Error

Models for analyzing site occupancy and count data models with detection error, including single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>, Moreno et al. 2010 <doi:10.1890/09-1073.1>, Solymos et al. 2012 <doi:10.1002/env.1149>, Denes et al. 2016 <doi:10.1111/1365-2664.12818>), conditional distance sampling and time-removal models (QPAD) (Solymos et al. 2013 <doi:10.1111/2041-210X.12106>, Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>), and single bin QPAD (SQPAD) models (Lele & Solymos 2025 <doi:10.1093/ornithapp/duaf078>). Package development was supported by the Alberta Biodiversity Monitoring Institute and the Boreal Avian Modelling Project.

Authors:Peter Solymos [aut, cre], Monica Moreno [aut], Subhash R. Lele [aut], Steven L. Van Wilgenburg [ctb]

detect_0.5-1.tar.gz
detect_0.5-1.zip(r-4.7)detect_0.5-1.zip(r-4.6)detect_0.5-1.zip(r-4.5)
detect_0.5-1.tgz(r-4.6-any)detect_0.5-1.tgz(r-4.5-any)
detect_0.5-1.tar.gz(r-4.7-any)detect_0.5-1.tar.gz(r-4.6-any)
detect_0.5-1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
detect/json (API)

# Install 'detect' in R:
install.packages('detect', repos = c('https://psolymos.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/psolymos/detect/issues

Datasets:
  • databu - Simulated example for abundance model
  • datocc - Simulated example for occupancy model
  • josm - Bird point count data from Alberta's Oil Sands region
  • oven - Ovenbird abundances
  • paired - Example point count data set with paired human and ARU data

On CRAN:

Conda:

6.13 score 6 stars 150 scripts 582 downloads 6 mentions 25 exports 4 dependencies

Last updated from:68c644cc0b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK269
source / vignettesOK178
linux-release-x86_64OK264
macos-release-arm64OK149
macos-oldrel-arm64OK195
windows-develOK404
windows-releaseOK543
windows-oldrelOK430
wasm-releaseOK123

Exports:AUCbootstrapcmulticmulti.fitcmulti.fit0cmulti2.fitconvertEDRdrop.scope.svisitextractBOOTextractMLEhbootindexis.presentload_BAM_QPADpredictMCMCrocplotrtriangsqpadsqpad.fitsvabusvabu.fitsvabu.stepsvoccsvocc.fitsvocc.stepzif

Dependencies:FormulalatticeMatrixpbapply

Readme and manuals

Help Manual

Help pageTopics
Analyzing Wildlife Data with Detection Errordetect-package detect
AUC ROC plot for fitted modelsAUC rocplot
Do bootstrap and extract bootstrap resultsbootstrap extractBOOT
Conditional Multinomial Maximum Likelihood Estimationcmulti cmulti.fit cmulti2.fit fitted.cmulti model.frame.cmulti model.matrix.cmulti predict.cmulti
Conversion between truncated and unlimited effective detection distance (EDR)convertEDR
Simulated example for abundance modeldatabu
Simulated example for occupancy modeldatocc
Hierarchical bootstrap indiceshbootindex
Bird point count data from Alberta's Oil Sands regionjosm
Load BAM QPAD parameter estimates and support functionsload_BAM_QPAD
Ovenbird abundancesoven
Example point count data set with paired human and ARU datapaired
Single-bin QPAD (SQPAD)coef.sqpad fitted.sqpad logLik.sqpad predict.sqpad print.sqpad print.summary.sqpad rtriang sqpad sqpad.fit summary.sqpad vcov.sqpad
Single visit N-mixture abundance modelsis.present predictMCMC svabu svabu.fit svabu.step svabu_nb.fit zif
ZI Binomial model with single visitextractMLE svocc svocc.fit svocc.step