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camtrapR (version 2.3.0)

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 (and videos), 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 or ubms packages, 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 is 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

User support

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.

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.

createStationFoldersCreate camera trap station directories for raw images
fixDateTimeOriginalFix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire cameras
OCRdataFieldsOptical character recognition (OCR) from data fields in images
writeDateTimeOriginalWrite values to DateTimeOriginal tag in image metadata
timeShiftImagesApply time shifts to JPEG images
imageRenameCopy and rename images based on station ID and image creation date
addCopyrightTagWrite a copyright tag into JPEG image metadata
appendSpeciesNamesAdd or remove species names from image filenames

Species / individual identification

These functions assist in species identification and prepare individual identification of animals.

checkSpeciesNamesCheck species names against the ITIS taxonomic database
createSpeciesFoldersCreate directories for species identification
checkSpeciesIdentificationConsistency check on species image identification
getSpeciesImagesGather 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).

recordTableCreate a species record table from camera trap images and videos
recordTableIndividualCreate a single-species record table from camera trap images and videos with individual IDs
exifTagNamesReturn Exif metadata tags and tag names from JPEG images
addToPathAdd the directory containing exiftool.exe to PATH temporarily (Windows only)
filterRecordTableFilter existing record table for temporal independence.

Data exploration and visualisation

These plots are generated from the record table and the camera trap table.

detectionMapsGenerate maps of species richness and species presence by station, export shapefiles
activityHistogramSingle-species diel activity histograms
activityDensitySingle-species diel activity kernel density estimation plots
activityRadialSingle-species diel activity radial plot
activityOverlapTwo-species diel activity overlap plots and estimates

Prepare occupancy and spatial capture-recapture analyses, and summarise surveys

cameraOperationCreate a camera operation matrix
detectionHistorySpecies detection histories for occupancy analyses (single and multi-season)
spatialDetectionHistoryDetection histories of individuals for spatial capture-recapture analyses
surveyReportCreate a report about camera trap surveys and species detections
surveyDashboardShiny dashboard for summarizing and analyzing camera trap survey data

Community (multi-species) occupancy models

communityModelCreate a community (multi-species) occupancy model for JAGS or Nimble
commOccu-classcommOccu objects
fit,commOccu-methodFit a community (multi-species) occupancy model
predict,commOccu-methodPredictions from community occupancy models
summary,commOccu-methodSummarize community occupancy model
plot_coefPlot effect sizes of covariates in community occupancy model
plot_effectsPlot Marginal Effects of Covariates

Sample data

camtrapsSample camera trap station information table
recordTableSampleSample species record table
recordTableIndividualSampleSingle-species record table with individual IDs
camtrapsMultiSeasonSample multi season camera trap station information table
recordTableSampleMultiSeasonSample multi season species record table
recordTableIndividualSampleMultiSeasonSingle-species multi season record table with individual IDs
timeShiftTableSample camera trap time shift information

Author

Juergen Niedballa

Maintainer:Juergen Niedballa <camtrapr@gmail.com>

Details

Image metadata (such as date and time or user-assigned tags) are extracted from the images using Phil Harvey's ExifTool (available from https://exiftool.org/) 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 a matrix 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

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). https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12600

camtrapR Google Group https://groups.google.com/forum/#!forum/camtrapr

Phil Harvey's ExifTool https://exiftool.org/

See Also

overlap unmarked ubms secr wiqid