camtrapR-package: Overview of the functions in the camtrapR package
Description
This package provides a streamlined workflow for processing data generated in camera trap-based wildlife studies and prepares input for further analyses.
It suggests a simple data structure and provides functions for managing digital camera trap photographs, generating record databases, maps of species richness and species detections, species activity diagrams and detection/non-detection matrices for occupancy analyses, e.g. in the unmarked package. Further, basic survey statistics are computed. The function build on one another in a logical sequence.
Apart from species identification, which is achieved by moving images into species directories, and the creation of a table holding basic information about camera trap station IDs, locations and trapping periods, no manual input is required.Image management workflow
The functions in this section build on one another and can be run in sequential order as needed.
ll{
imageRename Copy and rename images based on camera trap station ID and creation date
createSpeciesFolders Create species directories for species identification
checkSpeciesFolders Consistency check on species image identification
appendSpeciesNames Add or remove species names from image filenames
}Data extraction
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).
ll{
recordDatabase Create a species record database from camera trap images
detectionMaps Generate maps of species richness and species presence by station
cameraOperation Create a camera operability matrix
detectionHistory Species detection histories for occupancy analyses
surveyReport Create a report about camera trap surveys and species detections
}Species activity plots
These plots are generated from the record database.
ll{
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
}Additional functions
ll{
exiftoolPath Add a directory to PATH temporarily (for exiftool.exe under Windows)
exifTagNames Extract Exif metadata tag names from jpg images
timeShiftImages Apply time shifts to jpg image metadata
getSpeciesImages Copy all images of a species to a new directory
}Details
Images are renamed automatically and stored in a directory structure of camera trap station directories. Within each of these camera trap station directories, species subdirectories contain the species images. Image metadata are extracted from the images in that directory structure using Phil Harvey's Exiftool (available from http://www.sno.phy.queensu.ca/~phil/exiftool/) and the information is stored in a record database. 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 database are used to generate species detection histories. The user has considerable freedom in generating the detection histories; data format, session lengths, and session start times are adjustable. In addition, trapping effort (i.e. active trap nights per station and session) can be computed for use as a observation covariate in occupancy models.References
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. http://CRAN.R-project.org/package=overlap
Phil Harvey's Exiftool http://www.sno.phy.queensu.ca/~phil/exiftool/