R/camtrapR-package.R

In camtrapR: Camera Trap Data Management and Analysis Framework

#' Overview of the functions in the camtrapR package
#' 
#' 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
#' \pkg{unmarked} or \pkg{ubms} packages, and \code{capthist} objects for
#' spatial capture-recapture analyses in the \pkg{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.
#' 
#' Image metadata (such as date and time or user-assigned tags) are extracted
#' from the images using Phil Harvey's ExifTool (available from
#' \url{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.
#' 
#' @name camtrapR-package
#' @aliases camtrapR-package camtrapR
#' @docType package
#' 
#' @section User support: The camtrapR Google group is an online support and
#' help forum for camtrapR users. You can find it here:
#' \url{https://groups.google.com/forum/#!forum/camtrapr}.
#' 
#' @author Juergen Niedballa
#' 
#' Maintainer:Juergen Niedballa <camtrapr@@gmail.com>
#' 
#' @seealso \pkg{overlap} \pkg{unmarked} \pkg{ubms} \pkg{secr} \pkg{wiqid}
#' 
#' @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).
#' \url{https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12600}
#' \cr
#' 
#' camtrapR Google Group \url{https://groups.google.com/forum/#!forum/camtrapr}
#' \cr
#' 
#' Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News,
#' 6(4): 8-12. \cr
#' 
#' Mike Meredith and Martin Ridout (2018). overlap: Estimates of coefficient of
#' overlapping for animal activity patterns. R package version 0.3.2.
#' \url{https://CRAN.R-project.org/package=overlap} \cr
#' 
#' Phil Harvey's ExifTool \url{https://exiftool.org/} \cr
#' @keywords internal
"_PACKAGE"