Package: camtrapR 3.0.3

Juergen Niedballa

camtrapR: Camera Trap Data Management and Analysis Framework

Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.

Authors:Juergen Niedballa [aut, cre], Alexandre Courtiol [aut], Rahel Sollmann [aut], John Mathai [ctb], Seth Timothy Wong [ctb], An The Truong Nguyen [ctb], Azlan bin Mohamed [ctb], Andrew Tilker [ctb], Roshan Guharajan [ctb], Ioannis Alexiou [ctb], Andreas Wilting [ctb, ths]

camtrapR_3.0.3.tar.gz
camtrapR_3.0.3.zip(r-4.7)camtrapR_3.0.3.zip(r-4.6)camtrapR_3.0.3.zip(r-4.5)
camtrapR_3.0.3.tgz(r-4.6-any)camtrapR_3.0.3.tgz(r-4.5-any)
camtrapR_3.0.3.tar.gz(r-4.7-any)camtrapR_3.0.3.tar.gz(r-4.6-any)
camtrapR_3.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
camtrapR/json (API)

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

Bug tracker:https://github.com/jniedballa/camtrapr/issues

Pkgdown/docs site:https://jniedballa.github.io

Datasets:

On CRAN:

Conda:

occupancy-modelingspatial-capture-recapturewildlife

9.83 score 45 stars 206 scripts 1.6k downloads 14 mentions 40 exports 96 dependencies

Last updated from:e31f2da91d. Checks:8 OK, 1 NOTE. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK493
source / vignettesOK354
linux-release-x86_64OK460
macos-release-arm64OK429
macos-oldrel-arm64NOTE266
windows-develOK515
windows-releaseOK551
windows-oldrelOK500
wasm-releaseOK231

Exports:activityDensityactivityHistogramactivityOverlapactivityRadialaddCopyrightTagaddToPathaggregateStationsappendSpeciesNamescameraOperationcheckSpeciesIdentificationcheckSpeciesNamescommunityModelcreateCovariatescreateSpeciesFolderscreateStationFoldersdetectionHistorydetectionMapsexifTagNamesfilterRecordTablefitfixDateTimeOriginalgetSpeciesImagesimageRenameOCRdataFieldsplot_coefplot_effectsPPC.communityPPC.residualspredictreadcamtrapDPreadWildlifeInsightsrecordTablerecordTableIndividualspatialDetectionHistoryspeciesAccumsummarysurveyDashboardsurveyReporttimeShiftImageswriteDateTimeOriginal

Dependencies:abindbase64encBHbslibcachemclassclassIntclicommonmarkcpp11crosstalkdata.tableDBIdigestdplyrDTe1071evaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemvtnormnlmeotelpillarpkgconfigpngpromisesproxyR6rappdirsrasterRColorBrewerRcppRcppEigenRcppNumericalRcppParallelrlangrmarkdowns2S7sassscalessecrsecrfuncsfshinyshinyBSshinydashboardshinyjssourcetoolsspstringistringrterratibbletidyselecttimechangetinytexunitsutf8vctrsviridisLitewithrwkxfunxtableyaml

Organising raw camera trap images in camtrapR
Introduction | Camera trap station information | Organising raw camera trap images
Rendered fromcamtrapr1.pdf.asisusingR.rsp::asis

Last update: 2021-12-16
Started: 2021-12-16

Species and Individual Identification
Methods for species and individual identification - General | Species identification | Individual identification
Rendered fromcamtrapr2.pdf.asisusingR.rsp::asis

Last update: 2021-12-16
Started: 2021-12-16

Data Extraction from Images and videos, creating occupancy & secr input
Tabulating species and individual records: the recordTable functions | Camera Operation | Input for subsequent analyses (single-season) | Input for subsequent analyses (multi-season)
Rendered fromcamtrapr3.pdf.asisusingR.rsp::asis

Last update: 2021-12-16
Started: 2021-12-16

Data exploration and visualisation
Overview | Species presence maps | Visualising species activity data | Survey summary report
Rendered fromcamtrapr4.pdf.asisusingR.rsp::asis

Last update: 2021-12-16
Started: 2021-12-16

Multi-species occupancy models
5. Multi-species occupancy models | Overview | Warning | Limitations | Parameter naming convention | Quick example | Data preparation | Fit model in JAGS | Models in Nimble | More complete example | Prepare data | JAGS Model | Nimble Model | Missing values in detection histories | Further possibilies | Fixed effects | Priors | Data augmentation | Categorical covariates | Random effects other than species | Nested random effects | Species and site random effect on detection | Quadratic covariate effects | WAIC | Species richness | Spatial predictions | Percentage of area occupied (by species) | bayesplot | Model diagnostics | Royle-Nichols model | Single-species occupancy models
Rendered fromcamtrapr5.html.asisusingR.rsp::asis

Last update: 2021-12-16
Started: 2021-12-16

Readme and manuals

Help Manual

Help pageTopics
Overview of the functions in the camtrapR packagecamtrapR-package camtrapR
Plot kernel density estimation of single-species activityactivityDensity
Plot histogram of single-species activityactivityHistogram
Plot overlapping kernel densities of two-species activitiesactivityOverlap
Radial plots of single-species activityactivityRadial
Write a copyright tag into JPEG image metadataaddCopyrightTag
Add a directory to PATH temporarilyaddToPath
Aggregate Camera Trap Table to Station LevelaggregateStations
Add or remove species names from JPEG image filenamesappendSpeciesNames
Create a camera trap station operation matrixcameraOperation
Sample camera trap station informationcamtraps
Sample multi-season camera trap station informationcamtrapsMultiSeason
Consistency check on species image identificationcheckSpeciesIdentification
Check species names against the ITIS taxonomic databasecheckSpeciesNames
commOccu objectscommOccu-class
Create a community (multi-species) occupancy model for JAGS or NimblecommunityModel
Extract covariate values from spatial rasters and prepare rasters for spatial predictionscreateCovariates
Create species directories for species identificationcreateSpeciesFolders
Create camera trap station directories for raw camera trap imagescreateStationFolders
Species detection histories for occupancy analysesdetectionHistory
Generate maps of observed species richness and species presences by stationdetectionMaps
Show Exif metadata of JPEG images or other image or video formatsexifTagNames
Filter species record table for temporal independencefilterRecordTable
Fit a community (multi-species) occupancy modelfit,commOccu-method
Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire camerasfixDateTimeOriginal
Collect all images of a speciesgetSpeciesImages
Copy and rename images based on camera trap station ID and creation dateimageRename
Optical character recognition (OCR) from data fields in digital imagesOCRdataFields
Plot effect sizes of covariates in community occupancy modelplot_coef plot_coef,commOccu-method
Plot Marginal Effects of Covariatesplot_effects plot_effects,commOccu-method
Calculate Community-Level Posterior Predictive Checks for Occupancy ModelsPPC.community
Calculate Residuals from MCMC Output of Occupancy ModelsPPC.residuals
Predictions from community occupancy modelspredict predict,commOccu-method
Convert Camtrap DP format data to camtrapR formatreadcamtrapDP
Import Wildlife Insights data to camtrapRreadWildlifeInsights
Generate a species record table from camera trap images and videosrecordTable
Generate a single-species record table with individual identification from camera trap images or videosrecordTableIndividual
Sample single-species record table with custom metadata from camera trap imagesrecordTableIndividualSample
Sample single-species multi-season record table with custom metadata from camera trap imagesrecordTableIndividualSampleMultiSeason
Sample species record table from camera trap imagesrecordTableSample
Sample multi-season species record table from camera trap imagesrecordTableSampleMultiSeason
Generate a 'capthist' object for spatial capture-recapture analyses from camera-trapping dataspatialDetectionHistory
Species Accumulation Curves for Camera Trap DataspeciesAccum
Summarize community occupancy modelsummary,commOccu-method
Survey Dashboard for Camera Trap Data AnalysissurveyDashboard
Create a report about a camera trapping survey and species detectionssurveyReport
Apply time shifts to JPEG image metadatatimeShiftImages
Sample camera trap time shift tabletimeShiftTable
Write values to DateTimeOriginal tag in image metadatawriteDateTimeOriginal