R/ADePTR.R

In bsmity13/ADePTR: Acoustic Detection Processing and Visualization Tool in R

#' ADePTR: Acoustic Detection Processing and Visualization Tool in R
#'
#' ADePTR is package developed to streamline processing and visualization
#' of animal movement data from a passive acoustic array.
#'
#' @docType package
#' @name ADePTR
#'
#' @details
#'
#' This package was designed with the following workflow in mind:
#'
#' \enumerate{
#'   \item Process input files
#'   \item Filter erroneous detections
#'   \item Calculate centers of activity
#'   \item Summarize detections on a grid of the study area
#'   \item Interpolate locations and animate
#' }
#'
#' For each step of the workflow, there are both possible inputs and
#' possible outputs. The package is designed to work well with minimal
#' user input (\emph{i.e.}, most arguments have defaults), but it is also
#' designed to allow a high level of customization. Advanced users should
#' be able to edit the outputs of any step before passsing it to the next
#' step, or alternatively, to enter the workflow with their own data at
#' any point.
#'
#' @section Step 1. Process Inputs:
#'
#' The primary functions available for this step are:
#' \itemize{
#'   \item \code{\link{proc_dets}()} -- uses station/receiver information to
#'   georeference the detections
#'   \item \code{\link{plot_sta_history}()} -- makes a summary plot of
#'   detections over time by station
#'   \item \code{\link{map_dets}()} -- makes a map showing the number of
#'   detections by station
#' }
#'
#' @section Step 2. Filter:
#'
#' The primary functions available for this step are:
#' \itemize{
#'   \item \code{\link{spd_filter}()} -- filters detections that would imply
#'   an unrealistic swim speed
#'   \item \code{\link{singleton_filter}()} -- filters single detections of
#'   an individual ID at an individual station over a given time period
#' }
#'
#' @section Step 3. COAs:
#'
#' The primary functions available for this step are:
#' \itemize{
#'   \item \code{\link{coa_locs}()} -- calculates centers of activity (COAs)
#'   using either arithmetic or harmonic means
#'   \item \code{\link{map_coas}()} -- makes a map showing the COAs on top of
#'   detections by station
#' }
#'
#' @section Step 4. Summarize on Grid:
#'
#' The primary functions available for this step are:
#' \itemize{
#'   \item \code{\link{init_raster}()} -- initializes a template raster for
#'   future functions
#'   \item \code{\link{rasterize_dets}()} -- converts detection data to counts
#'   of detections by raster cells
#'   \item \code{\link{raster_pres}()} -- converts a detections raster to a
#'   presence-only raster
#'   \item \code{\link{raster_overlap}()} -- sums the input presence-only or
#'   presence-absence layers to show overlapping individuals or species
#' }
#'
#' @section Step 5. Interpolate and Animate:
#'
#' The primary functions available for this step are:
#' \itemize{
#'   \item \code{\link{str_paths}()} -- connects locations with straight paths
#'   \item \code{\link{lc_paths}()} -- connects locations with least
#'   cost paths
#'   \item \code{\link{regular_points}()} -- interpolates regular points along
#'   a straight path or least cost path
#'   \item \code{\link{animate_points}()} -- creates an animation from regular
#'   points
#' }
#'
#' @section More details:
#'
#' For more details on the usage of this package, see the package vignette.
#'
#' The package has a GitHub repository at
#' \url{https://github.com/bjsmith-usgs/ADePTR}.
#'
#'
#' @encoding UTF-8
#'
#' @import dplyr
#' @import sf
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