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

Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.

AuthorJuergen 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], Andreas Wilting [ctb, ths]
Date of publication2016-12-20 00:55:26
MaintainerJuergen Niedballa <niedballa@izw-berlin.de>
LicenseGPL (>= 2)
Version0.99.6

View on CRAN

Man pages

activityDensity: Plot kernel density estimation of single-species activity

activityHistogram: Plot histogram of single-species activity

activityOverlap: Plot overlapping kernel densities of two-species activities

activityRadial: Radial plots of single-species activity

addCopyrightTag: Write a copyright tag into JPEG image metadata

appendSpeciesNames: Add or remove species names from JPEG image filenames

cameraOperation: Create a camera trap station operability matrix

camtrapR-defunct: Consistency check on species image identification

camtrapR-package: Overview of the functions in the camtrapR package

camtraps: Sample camera trap station information

checkSpeciesIdentification: Consistency check on species image identification

checkSpeciesNames: Check species names against the ITIS taxonomic database

createSpeciesFolders: Create species directories for species identification

createStationFolders: Create camera trap station directories for raw camera trap...

detectionHistory: Species detection histories for occupancy analyses

detectionMaps: Generate maps of observed species richness and species...

exifTagNames: Show Exif metadata tags and tag names from JPEG images

exiftoolPath: Add a directory to PATH temporarily

fixDateTimeOriginal: Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire...

getSpeciesImages: Collect all images of a species

imageRename: Copy and rename images based on camera trap station ID and...

recordTable: Generate a species record table from camera trap images

recordTableIndividual: Generate a single-species record table with individual...

recordTableIndividualSample: Sample single-species record table with custom metadata from...

recordTableSample: Sample species record table from camera trap images

spatialDetectionHistory: Generate a 'capthist' object for spatial capture-recapture...

surveyReport: Create a report about a camera trapping survey and species...

timeShiftImages: Apply time shifts to JPEG image metadata

timeShiftTable: Sample camera trap time shift table

Files in this package

camtrapR
camtrapR/inst
camtrapR/inst/pictures
camtrapR/inst/pictures/sample_images_tagged
camtrapR/inst/pictures/sample_images_tagged/LeopardCat
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-14__23-30-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-23__03-33-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-05-05__18-24-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-10__04-07-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-04-22__20-19-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-07__00-23-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-05-07__18-47-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-05__00-11-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-25__04-33-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-04-22__20-21-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-24__22-54-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-04-23__00-07-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-06__03-00-00(2).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-04-23__00-09-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-14__23-30-00(2).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-05__23-13-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-06__03-00-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-23__03-34-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-25__04-33-00(2).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-04-21__00-40-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-10__04-08-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-05-05__18-25-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-05-14__02-11-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationC__2009-04-18__22-57-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationA__2009-05-07__17-11-00(1).JPG
camtrapR/inst/pictures/sample_images_tagged/LeopardCat/StationB__2009-04-14__06-13-00(1).JPG
camtrapR/inst/pictures/raw_images
camtrapR/inst/pictures/raw_images/StationB
camtrapR/inst/pictures/raw_images/StationB/IMG0003.JPG
camtrapR/inst/pictures/raw_images/StationB/IMG0002.JPG
camtrapR/inst/pictures/raw_images/StationB/IMG0001.JPG
camtrapR/inst/pictures/raw_images/StationA
camtrapR/inst/pictures/raw_images/StationA/IMG0003.JPG
camtrapR/inst/pictures/raw_images/StationA/IMG0002.JPG
camtrapR/inst/pictures/raw_images/StationA/IMG0001.JPG
camtrapR/inst/pictures/sample_images
camtrapR/inst/pictures/sample_images/StationC
camtrapR/inst/pictures/sample_images/StationC/VTA
camtrapR/inst/pictures/sample_images/StationC/VTA/StationC__2009-04-24__02-57-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-14__23-30-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-23__03-33-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-05-05__18-24-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-05-07__18-47-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-06__03-00-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-14__23-30-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-06__03-00-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-23__03-34-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-05-05__18-25-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/PBE/StationC__2009-04-18__22-57-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-25__03-09-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-23__02-27-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-27__00-17-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-05-02__03-35-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-23__02-25-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-06__03-49-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-05-02__03-36-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-12__20-26-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/EGY/StationC__2009-04-12__20-26-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/Thumbs.db
camtrapR/inst/pictures/sample_images/StationC/TRA
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-12__02-34-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-02__00-11-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-14__00-18-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-01__20-10-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-27__00-20-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-13__22-38-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-27__00-19-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-24__19-26-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-13__22-38-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-11__21-46-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-24__19-27-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-12__02-32-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-11__21-44-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-01__20-12-00(1).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-14__00-18-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-04-11__21-46-00(2).JPG
camtrapR/inst/pictures/sample_images/StationC/TRA/StationC__2009-05-02__00-10-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB
camtrapR/inst/pictures/sample_images/StationB/NO_ID
camtrapR/inst/pictures/sample_images/StationB/NO_ID/StationB__2009-05-07__18-45-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/VTA
camtrapR/inst/pictures/sample_images/StationB/VTA/StationB__2009-04-15__19-12-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/VTA/Thumbs.db
camtrapR/inst/pictures/sample_images/StationB/VTA/StationB__2009-04-27__05-07-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-10__04-07-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-07__00-23-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-05__00-11-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-25__04-33-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-24__22-54-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-05__23-13-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/Thumbs.db
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-25__04-33-00(2).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-10__04-08-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-05-14__02-11-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/PBE/StationB__2009-04-14__06-13-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/Thumbs.db
camtrapR/inst/pictures/sample_images/StationB/MNE
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-15__07-23-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-49-00(3).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-48-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-48-00(3).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-49-00(2).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-48-00(2).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-15__07-21-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-49-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-47-00(1).JPG
camtrapR/inst/pictures/sample_images/StationB/MNE/StationB__2009-04-28__17-47-00(2).JPG
camtrapR/inst/pictures/sample_images/StationA
camtrapR/inst/pictures/sample_images/StationA/VTA
camtrapR/inst/pictures/sample_images/StationA/VTA/StationA__2009-04-10__05-07-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/VTA/StationA__2009-05-06__19-06-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-04-22__20-19-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-04-22__20-21-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-04-23__00-07-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-04-23__00-09-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-04-21__00-40-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/PBE/StationA__2009-05-07__17-11-00(1).JPG
camtrapR/inst/pictures/sample_images/StationA/Thumbs.db
camtrapR/inst/doc
camtrapR/inst/doc/DataExploration.Rmd
camtrapR/inst/doc/DataExtraction.Rmd
camtrapR/inst/doc/SpeciesIndividualIdentification.Rmd
camtrapR/inst/doc/DataExploration.html
camtrapR/inst/doc/SpeciesIndividualIdentification.R
camtrapR/inst/doc/DataExtraction.html
camtrapR/inst/doc/ImageOrganisation.Rmd
camtrapR/inst/doc/ImageOrganisation.html
camtrapR/inst/doc/DataExtraction.R
camtrapR/inst/doc/ImageOrganisation.R
camtrapR/inst/doc/DataExploration.R
camtrapR/inst/doc/SpeciesIndividualIdentification.html
camtrapR/NAMESPACE
camtrapR/NEWS
camtrapR/data
camtrapR/data/recordTableIndividualSample.rda
camtrapR/data/camtraps.rda
camtrapR/data/recordTableSample.rda
camtrapR/data/timeShiftTable.rda
camtrapR/R
camtrapR/R/spatialDetectionHistory.R camtrapR/R/recordTable.R camtrapR/R/detectionMaps.R camtrapR/R/checkSpeciesNames.R camtrapR/R/variousOtherHelperFunctions.R camtrapR/R/variousPlottingHelperFunctions.R camtrapR/R/onAttach.R camtrapR/R/timeShiftImages.R camtrapR/R/getSpeciesImages.R camtrapR/R/activityRadial.R camtrapR/R/imageRename.R camtrapR/R/recordTableIndividual.R camtrapR/R/cameraOperation.R camtrapR/R/createStationFolders.R camtrapR/R/addCopyrightTag.R camtrapR/R/createSpeciesFolders.R camtrapR/R/appendSpeciesNames.R camtrapR/R/activityOverlap.R camtrapR/R/fixDateTimeOriginal.R camtrapR/R/exifTagNames.R camtrapR/R/surveyReport.R camtrapR/R/activityHistogram.R camtrapR/R/checkSpeciesIdentification.R camtrapR/R/exiftoolPath.R camtrapR/R/activityDensity.R camtrapR/R/detectionHistory.R
camtrapR/vignettes
camtrapR/vignettes/DataExploration.Rmd
camtrapR/vignettes/DataExtraction.Rmd
camtrapR/vignettes/SpeciesIndividualIdentification.Rmd
camtrapR/vignettes/ImageOrganisation.Rmd
camtrapR/vignettes/SpeciesID_digiKam.png
camtrapR/MD5
camtrapR/build
camtrapR/build/vignette.rds
camtrapR/DESCRIPTION
camtrapR/man
camtrapR/man/checkSpeciesIdentification.Rd camtrapR/man/exifTagNames.Rd camtrapR/man/checkSpeciesNames.Rd camtrapR/man/createStationFolders.Rd camtrapR/man/camtraps.Rd camtrapR/man/detectionMaps.Rd camtrapR/man/timeShiftTable.Rd camtrapR/man/recordTableIndividual.Rd camtrapR/man/activityHistogram.Rd camtrapR/man/surveyReport.Rd camtrapR/man/recordTable.Rd camtrapR/man/activityRadial.Rd camtrapR/man/addCopyrightTag.Rd camtrapR/man/activityDensity.Rd camtrapR/man/camtrapR-defunct.Rd camtrapR/man/imageRename.Rd camtrapR/man/createSpeciesFolders.Rd camtrapR/man/detectionHistory.Rd camtrapR/man/fixDateTimeOriginal.Rd camtrapR/man/recordTableIndividualSample.Rd camtrapR/man/activityOverlap.Rd camtrapR/man/getSpeciesImages.Rd camtrapR/man/exiftoolPath.Rd camtrapR/man/cameraOperation.Rd camtrapR/man/recordTableSample.Rd camtrapR/man/camtrapR-package.Rd camtrapR/man/timeShiftImages.Rd camtrapR/man/appendSpeciesNames.Rd camtrapR/man/spatialDetectionHistory.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.