R/wildlifeDI-package.r

In jedalong/wildlifeDI: Calculate Indices of Dynamic Interaction for Wildlife Tracking Data

# This is package documentation for wildlifeDI. roxygen will use this file to create a NAMESPACE file. Of importance is the @import command, as it lists package dependencies.

#' @title wildlifeDI: Calculate Indices of Dynamic Interaction for Wildlife Tracking Data
#'
#' @description Dynamic interaction refers to spatial-temporal associations in the movements of two (or more) animals. This package provides tools for calculating a suite of indices used for quantifying dynamic interaction with wildlife telemetry data. For more information on each of the methods employed see the references within. The package (as of version 0.3) also has new tools for automating contact analysis in large tracking datasets. In the most recent update the package (v1.0 onwards) has switched and now uses the new 'move2' class of trajectory objects. There is support for converting ltraj objects to move2 objects.
#'
#' @details The package \code{wildlifeDI} allows users to compute a number of currently available indices of dynamic 
#' interaction useful for wildlife telemetry studies. The currently available methods include:
#' \itemize{
#'    \item{Prox - Proximity analysis (Bertrand et al. 1996)}
#'    \item{Ca - Coefficient of Association (Bauman 1998)}
#'    \item{Don - Doncaster's measure of dynamic interaction (Doncaster 1990)}
#'    \item{Lixn - Minta's measures of spatial-temporal interaction (Minta 1992)}
#'    \item{Cs - Coefficient of Sociality (Kenward et al. 1993)}
#'    \item{HAI - Half-weight Association Index (Atwood and Weeks Jr. 2003)}
#'    \item{Cr - Correlation coefficient (Shirabe 2006)}
#'    \item{DI - Dynamic interaction index (Long and Nelson 2013)}
#'    \item{IAB - Interaction statistic (Benhamou et al. 2014)} 
#' }
#' The package \code{wildlifeDI} also provides useful functionality for identifying which fixes are temporally simultaneous, required for many of the above methods, using the function \code{GetSimultaneous}, along with other functions for exploring spatial-temporal interactions patterns in wildlife telemetry data.
#' 
#' When citing this package please use citation('wildlifeDI), also please cite the appropriate papers associated with individual methods being used.
#' 
#' As of version 0.4.1 the package also includes a number of new functions for performing contact analysis with larger tracking datasets. These functions use a prefix 'con' to distinguish them from other functions in the package.
#' 
#' As of version 1.0 the package has completely switched to use the more modern \code{move2} trajectory objects. This has rendered many of the helper and summary functions unnecessary and they have been removed from the package. See the vignettes for guidance on how to leverage the new move2 objects for studying dynamic interactions in wildlife tracking data.
#' 
#' The functions in \code{wildlifeDI} utilize the \code{move2} objects from the package \code{move2}. For more information on objects of this type see \code{help(mt_as_move2)}.
#'
#' @author Jed Long
#' 
#' @import move2 
#' @import sf 
#' @import graphics
#' @import dplyr
#' @import units
#' @importFrom adehabitatLT as.ltraj ld
#' @importFrom sp CRS
#' @importFrom lwgeom st_geod_azimuth
#' @importFrom stats chisq.test embed pchisq wilcox.test sd ave
#' 
#' @docType package
#' @name wildlifeDI-package
NULL