| camtrapR-package {camtrapR} | R Documentation |
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.
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.
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.
createStationFolders | Create camera trap station directories for raw images |
fixDateTimeOriginal | Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire cameras |
OCRdataFields | Optical character recognition (OCR) from data fields in images |
writeDateTimeOriginal | Write values to DateTimeOriginal tag in image metadata |
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 |
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 and videos |
recordTableIndividual | Create a single-species record table from camera trap images and videos with individual IDs |
exifTagNames | Return Exif metadata tags and tag names from JPEG images |
addToPath | Add the directory containing exiftool.exe to PATH temporarily (Windows only) |
filterRecordTable | Filter existing record table for temporal independence. |
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, export shapefiles |
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 |
Prepare occupancy and spatial capture-recapture analyses, and summarise surveys
cameraOperation | Create a camera operation matrix |
detectionHistory | Species detection histories for occupancy analyses (single and multi-season) |
spatialDetectionHistory | Detection histories of individuals for spatial capture-recapture analyses |
surveyReport | Create a report about camera trap surveys and species detections |
surveyDashboard | Shiny dashboard for summarizing and analyzing camera trap survey data |
Community (multi-species) occupancy models
communityModel | Create a community (multi-species) occupancy model for JAGS or Nimble |
commOccu-class | commOccu objects |
fit,commOccu-method | Fit a community (multi-species) occupancy model |
predict,commOccu-method | Predictions from community occupancy models |
summary,commOccu-method | Summarize community occupancy model |
plot_coef | Plot effect sizes of covariates in community occupancy model |
plot_effects | Plot Marginal Effects of Covariates |
Sample data
camtraps | Sample camera trap station information table |
recordTableSample | Sample species record table |
recordTableIndividualSample | Single-species record table with individual IDs |
camtrapsMultiSeason | Sample multi season camera trap station information table |
recordTableSampleMultiSeason | Sample multi season species record table |
recordTableIndividualSampleMultiSeason | Single-species multi season record table with individual IDs |
timeShiftTable | Sample camera trap time shift information |
Vignettes
Author(s)
Juergen Niedballa
Maintainer:Juergen Niedballa <camtrapr@gmail.com>
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