Reference

Overview

Overview of the camtrapR package

camtrapR-package camtrapR

Overview of the functions in the camtrapR package

Image organisation and management

Functions for image organisation and preprocessing

createStationFolders()

Create camera trap station directories for raw camera trap images

fixDateTimeOriginal()

Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire cameras

OCRdataFields()

Optical character recognition (OCR) from data fields in digital images

writeDateTimeOriginal()

Write values to DateTimeOriginal tag in image metadata

timeShiftImages()

Apply time shifts to JPEG image metadata

imageRename()

Copy and rename images based on camera trap station ID and creation date

addCopyrightTag()

Write a copyright tag into JPEG image metadata

appendSpeciesNames()

Add or remove species names from JPEG image filenames

Species / individual identification

Functions to assist identification of species and individuals

checkSpeciesNames()

Check species names against the ITIS taxonomic database

createSpeciesFolders()

Create species directories for species identification

checkSpeciesIdentification()

Consistency check on species image identification

getSpeciesImages()

Collect all images of a species

Image data extraction

Functions to extract and tabulate data from images

recordTable()

Generate a species record table from camera trap images and videos

recordTableIndividual()

Generate a single-species record table with individual identification from camera trap images or videos

exifTagNames()

Show Exif metadata of JPEG images or other image or video formats

addToPath()

Add a directory to PATH temporarily

filterRecordTable()

Filter species record table for temporal independence

Data exploration and visualisation

Functions for plotting species activity, detection maps and exporting shapefiles

detectionMaps()

Generate maps of observed species richness and species presences by station

activityHistogram()

Plot histogram of single-species activity

activityDensity()

Plot kernel density estimation of single-species activity

activityRadial()

Radial plots of single-species activity

activityOverlap()

Plot overlapping kernel densities of two-species activities

Data export

Functions to prepare occupancy and spatial capture-recapture analyses, and summarise surveys

cameraOperation()

Create a camera trap station operation matrix

detectionHistory()

Species detection histories for occupancy analyses

spatialDetectionHistory()

Generate a capthist object for spatial capture-recapture analyses from camera-trapping data

surveyReport()

Create a report about a camera trapping survey and species detections

communityModel()

Create a community (multi-species) occupancy model for JAGS or Nimble

surveyDashboard()

Shiny dashboard for summarizing and analyzing camera trap survey data

Community occupancy models

communityModel()

Create a community (multi-species) occupancy model for JAGS or Nimble

commOccu-class

commOccu objects

fit(<commOccu>)

Fit a community (multi-species) occupancy model

predict(<commOccu>)

Predictions from community occupancy models

summary(<commOccu>)

Summarize community occupancy model

plot_coef(<commOccu>)

Plot effect sizes of covariates in community occupancy model

plot_effects(<commOccu>)

Plot Marginal Effects of Covariates

Sample data

Sample data sets included in camtrapR

camtraps

Sample camera trap station information

recordTableSample

Sample species record table from camera trap images

recordTableIndividualSample

Sample single-species record table with custom metadata from camera trap images

camtrapsMultiSeason

Sample multi-season camera trap station information

recordTableSampleMultiSeason

Sample multi-season species record table from camera trap images

recordTableIndividualSampleMultiSeason

Sample single-species multi-season record table with custom metadata from camera trap images

timeShiftTable

Sample camera trap time shift table