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.

Install the latest version of this package by entering the following in R:
install.packages("camtrapR")
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 publication2017-03-21 15:20:23 UTC
MaintainerJuergen Niedballa <niedballa@izw-berlin.de>
LicenseGPL (>= 2)
Version0.99.8

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

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