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camtrapR

camtrapR is a package for camera trap data management in R.

Installation

You can install the release version of camtrapR from CRAN:

install.packages("camtrapR")

or the latest GitHub version (containing recent changes and new features) via:

# install.packages("remotes")
# install.packages("R.rsp")
remotes::install_github("jniedballa/camtrapR", build_vignettes = TRUE)

For installation from GitHub make sure package R.rsp is available. build_vignettes = TRUE is necessary since v 2.1.1. due to the new static vignettes.

You can also install a previous version (e.g. if a recent update broke the code you need to run urgently) via:

remotes::install_version(package = "camtrapR", version = "2.0.3")

Exiftool

Numerous important camtrapR functions read EXIF metadata from JPG images (and videos). This is done via Exiftool, a free and open-source sofware tool developed by Phil Harvey and available for Windows, MacOS and Linux.

To make full use of camtrapR, you will need Exiftool on your system. You can download it from the Exiftool homepage. Please follow the installation instruction in vignette 1 and the Exiftool website.

You may not need Exiftool if you do not work with image files, but only use camtrapR to create input for occupancy or spatial capture-recapture models from existing record tables.

Help and Support

Google Group

There is a Google Group for all questions and problems regarding camtrapR. Please feel free to join the discussion there.

GitHub issues

Alternatively, you can report bugs and problems as issues on GitHub (here).

Further reading

See the Article in Methods in Ecology and Evolution for an overview of the package. The five vignettes provide examples for the entire workflow.

Citation

To cite camtrapR, please use:

Jürgen Niedballa, Rahel Sollmann, Alexandre Courtiol, Andreas Wilting (2016). camtrapR: an R package for efficient camera trap data management. Methods in Ecology and Evolution 7(12), 1457-1462, https://doi.org/10.1111/2041-210X.12600, URL: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12600

or see citation("camtrapR")

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Version

Install

install.packages('camtrapR')

Monthly Downloads

1,614

Version

2.2.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/jniedballa/camtrapR

Homepage

https://jniedballa.github.io/camtrapR/

Maintainer

Juergen Niedballa

Last Published

May 11th, 2022

Functions in camtrapR (2.2.0)

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

camtrapR-package

Overview of the functions in the camtrapR package

Radial plots of single-species activity

activityOverlap

Plot overlapping kernel densities of two-species activities

addCopyrightTag

Write a copyright tag into JPEG image metadata

activityHistogram

Plot histogram of single-species activity

activityDensity

Plot kernel density estimation of single-species activity

appendSpeciesNames

Add or remove species names from JPEG image filenames

cameraOperation

Create a camera trap station operability matrix

Sample camera trap station information

Generate maps of observed species richness and species presences by station

commOccu objects

checkSpeciesNames

Check species names against the ITIS taxonomic database

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

recordTableIndividual

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

createSpeciesFolders

Create species directories for species identification

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

Generate a species record table from camera trap images and videos

Add a directory to PATH temporarily

createStationFolders

Create camera trap station directories for raw camera trap images

detectionHistory

Species detection histories for occupancy analyses

fit,commOccu-method

Fit a community (multi-species) occupancy model

predict,commOccu-method

Spatial predictions from community occupancy models

plot_effects,commOccu-method

Plot Marginal Effects of Covariates

recordTableIndividualSample

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

timeShiftImages

Apply time shifts to JPEG image metadata

Create a report about a camera trapping survey and species detections

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

recordTableIndividualSampleMultiSeason

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

recordTableSampleMultiSeason

Sample multi-season species record table from camera trap images

recordTableSample

Sample species record table from camera trap images

summary,commOccu-method

Summarize community occupancy model

plot_coef,commOccu-method

Plot effect sizes of covariates in community occupancy model

spatialDetectionHistory

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

camtrapsMultiSeason

Sample multi-season camera trap station information

fixDateTimeOriginal

Fix DateTimeOriginal Exif metadata tag in Reconyx Hyperfire cameras

getSpeciesImages

Collect all images of a species

checkSpeciesIdentification

Consistency check on species image identification

writeDateTimeOriginal

Write values to DateTimeOriginal tag in image metadata

Sample camera trap time shift table