This package provides a streamlined workflow for processing data generated in camera trap-based wildlife studies and prepares input for further analyses, particularly in occupancy and spatial capture-recapture frameworks.
It suggests a simple data structure and provides functions for managing digital camera trap photographs, generating record tables, maps of species richness and species detections and species activity diagrams. It further helps prepare subsequent analyses by creating detection/non-detection matrices for occupancy analyses, e.g. in the unmarked package, and capthist objects for spatial capture-recapture analyses in the secr package. In addition, basic survey statistics are computed. The functions build on one another in a logical sequence.
The only manual input needed it species (and individual) identification, which is achieved by moving images into species directories or by tagging images in image management software. Besides, a table holding basic information about camera trap station IDs, locations and trapping periods must be created in spreadsheet software.
The camtrapR Google group is an online support and help forum for camtrapR users. You can find it here: https://groups.google.com/forum/#!forum/camtrapr.
The functions in this section set up a directory structure for storing camera trap images and identifying species and individuals from images. They build on one another and can be run in sequential order as needed.
createStationFolders |
Create camera trap station directories for raw images |
fixDateTimeOriginal |
Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire cameras |
timeShiftImages |
Apply time shifts to JPEG images |
imageRename |
Copy and rename images based on station ID and image creation date |
addCopyrightTag |
Write a copyright tag into JPEG image metadata |
appendSpeciesNames |
Add or remove species names from image filenames |
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These functions assist in species identification and prepare individual identification of animals.
checkSpeciesNames |
Check species names against the ITIS taxonomic database |
createSpeciesFolders |
Create directories for species identification |
checkSpeciesIdentification |
Consistency check on species image identification |
getSpeciesImages |
Gather all images of a species in a new directory |
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These function use the directory structure built above (Section 'Image management workflow') and a table containing basic information about camera traps and/or stations (IDs, location, trapping period).
recordTable |
Create a species record table from camera trap images |
recordTableIndividual |
Create a single-species record table from camera trap images with individual IDs |
exifTagNames |
Return Exif metadata tags and tag names from JPEG images |
exiftoolPath |
Add the directory containing exiftool.exe to PATH temporarily (Windows only) |
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These plots are generated from the record table and the camera trap table.
detectionMaps |
Generate maps of species richness and species presence by station |
activityHistogram |
Single-species diel activity histograms |
activityDensity |
Single-species diel activity kernel density estimation plots |
activityRadial |
Single-species diel activity radial plot |
activityOverlap |
Two-species diel activity overlap plots and estimates |
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cameraOperation |
Create a camera operability matrix |
detectionHistory |
Species detection histories for occupancy analyses |
spatialDetectionHistory |
Detection histories of individuals for spatial capture-recapture analyses |
surveyReport |
Create a report about camera trap surveys and species detections |
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camtraps |
Sample camera trap station information table |
recordTableSample |
Sample species record table |
recordTableIndividualSample |
Single-species record table with individual IDs |
timeShiftTable |
Sample camera trap time shift information |
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Image metadata (such as date and time or user-assigned tags) are extracted from the images using Phil Harvey's ExifTool (available from http://www.sno.phy.queensu.ca/~phil/exiftool/) and the information is stored in a record table. An adjustable criterion for temporal independence of records can be applied. Maps of species presence and species richness can be generated. Several functions are available for plotting single- and two-species activity patterns. Information about the camera-specific trapping periods (and periods of malfunction) are summarized into information about camera trap operability. These, together with the record table, are used to generate species detection histories for occupancy and spatial capture-recapture analyses. The user has considerable freedom in generating the detection histories; sampling occasion length, beginning date and and occasion start times are adjustable. In addition, trapping effort (i.e. active trap nights per station and occasion) can be computed for use as a covariate / offset on detection probability.
Niedballa, J., Sollmann, R., Courtiol, A., Wilting, A. (2016): camtrapR: an R package for efficient camera trap data management. Methods in Ecology and Evolution, 7(12). http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12600/full
camtrapR Google Group https://groups.google.com/forum/#!forum/camtrapr
Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4): 8-12.
Mike Meredith and Martin Ridout (2014). overlap: Estimates of coefficient of overlapping for animal activity patterns. R package version 0.2.4. https://CRAN.R-project.org/package=overlap
Phil Harvey's ExifTool http://www.sno.phy.queensu.ca/~phil/exiftool/
overlap unmarked secr plotrix taxize ritis