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, 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.

Arguments

Image organisation and management

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. ll{ createStationFolders Create camera trap station directories for raw images timeShiftImages Apply time shifts to JPEG images imageRename Copy and rename images based on station ID and image creation date appendSpeciesNames Add or remove species names from image filenames --------------------------- ---------------------------------------------------------------------------------------------- }

Species / individual identification

These functions assist in species identification and prepare individual identification of animals. ll{ 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 --------------------------- ---------------------------------------------------------------------------------------------- }

Image 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{ 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) --------------------------- ---------------------------------------------------------------------------------------------- }

Data exploration and visualisation

These plots are generated from the record table and the camera trap table. ll{ 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 --------------------------- ---------------------------------------------------------------------------------------------- }

Data export

ll{ 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 --------------------------- ---------------------------------------------------------------------------------------------- }

Sample data

ll{ 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 --------------------------- ---------------------------------------------------------------------------------------------- }

Details

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.

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/