Package: camtrapR 2.3.0

camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Management of and data extraction from camera trap data in wildlife studies. The package provides a workflow for storing and sorting camera trap photos (and videos), tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it can visualise species activity data and provides simple mapping functions with GIS export.

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]

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camtrapR.pdf |camtrapR.html✨
camtrapR/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

occupancy-modelingspatial-capture-recapturewildlife

7.80 score 32 stars 148 scripts 1.1k downloads 33 exports 56 dependencies

Last updated 8 months agofrom:c6776115ef. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:activityDensityactivityHistogramactivityOverlapactivityRadialaddCopyrightTagaddToPathappendSpeciesNamescameraOperationcheckSpeciesIdentificationcheckSpeciesNamescommunityModelcreateSpeciesFolderscreateStationFoldersdetectionHistorydetectionMapsexifTagNamesfilterRecordTablefitfixDateTimeOriginalgetSpeciesImagesimageRenameOCRdataFieldsplot_coefplot_effectspredictrecordTablerecordTableIndividualspatialDetectionHistorysummarysurveyDashboardsurveyReporttimeShiftImageswriteDateTimeOriginal

Dependencies:abindBHclassclassIntclicolorspacecpp11data.tableDBIe1071fansifarvergenericsggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigproxyR6rasterRColorBrewerRcppRcppEigenRcppNumericalRcppParallelrlangs2scalessecrsfspstringistringrterratibbletimechangeunitsutf8vctrsviridisLitewithrwk

Organising raw camera trap images in camtrapR

Rendered fromcamtrapr1.pdf.asisusingR.rsp::asison Oct 30 2024.

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

Species and Individual Identification

Rendered fromcamtrapr2.pdf.asisusingR.rsp::asison Oct 30 2024.

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

Data Extraction from Images and videos, creating occupancy & secr input

Rendered fromcamtrapr3.pdf.asisusingR.rsp::asison Oct 30 2024.

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

Data exploration and visualisation

Rendered fromcamtrapr4.pdf.asisusingR.rsp::asison Oct 30 2024.

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

Multi-species occupancy models

Rendered fromcamtrapr5.html.asisusingR.rsp::asison Oct 30 2024.

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
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
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
Predictions from community occupancy modelspredict predict,commOccu-method
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
Summarize community occupancy modelsummary,commOccu-method
Shiny dashboard for summarizing and analyzing camera trap survey datasurveyDashboard
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