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 publication2017-01-31 14:16:48
MaintainerJuergen Niedballa <niedballa@izw-berlin.de>
LicenseGPL (>= 2)
Version0.99.7

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

Functions

activityDensity Man page
activityHistogram Man page
activityOverlap Man page
activityRadial Man page
addCopyrightTag Man page
appendSpeciesNames Man page
cameraOperation Man page
camtrapR Man page
camtrapR-defunct Man page
camtrapR-package Man page
camtraps Man page
checkSpeciesIdentification Man page
checkSpeciesNames Man page
createSpeciesFolders Man page
createStationFolders Man page
detectionHistory Man page
detectionMaps Man page
exifTagNames Man page
exiftoolPath Man page
fixDateTimeOriginal Man page
getSpeciesImages Man page
imageRename Man page
recordTable Man page
recordTableIndividual Man page
recordTableIndividualSample Man page
recordTableSample Man page
spatialDetectionHistory Man page
surveyReport Man page
timeShiftImages Man page
timeShiftTable Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

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