camtrapR (version 0.99.2)

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.

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.

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.

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).

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.

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

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

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/

See Also

overlap unmarked secr plotrix taxize