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.

Author
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], Andreas Wilting [ctb, ths]
Date of publication
2016-10-06 19:17:40
Maintainer
Juergen Niedballa <niedballa@izw-berlin.de>
License
GPL (>= 2)
Version
0.99.5

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-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
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 s 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/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/imageRename.Rd
camtrapR/man/createSpeciesFolders.Rd
camtrapR/man/detectionHistory.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