#' Tool to extract geographic and geometric measures of ecotones for R.
#'
#' @section Methods to locate a transect:
#'
#' \enumerate{
#' \item Select random points in edge cells of vegetation 1
#' \item Locate a second point within a neighborhood of specified size by one of four methods:
#' \itemize{
#' \item at the highest elevation (\code{\linkS4class{EcotonerSettings@transect_type == 1}})
#' \item following the steepest slope outside a minimum distance (\code{\linkS4class{EcotonerSettings@transect_type == 2}})
#' \item by the flowpath (\code{\linkS4class{EcotonerSettings@transect_type == 3}})
#' \item by sufficient area of homogeneous aspect (\code{\linkS4class{EcotonerSettings@transect_type == 4}})
#' }
#' \item Extend line connecting these two points in both directions
#' \item Trim line to the section between the lowest and highest elevation
#' }
#'
#' @section Determine if transect is a suitable ecotone / ecological boundary:
#'
#' \enumerate{
#' \item Transect is empty (i.e., trivial condition)
#' \item Definition of 'zone of ecotone / ecological boundary' is not met
#' }
#'
#' @section Definition of 'zone of ecotone / ecological boundary':
#'
#' Operational definition of zone of ecological boundary (v5):
#' Process:
#' \enumerate{
#' \item Apply definition to vegetation 1 and 2
#' \item Apply definition to majority type of vegetation 1 and majority type of vegetation 2
#' }
#' Definition:
#' \itemize{
#' \item Transect orientation (from low to high elevation, i.e., from left to right)
#' \item Density = rolling mean [over 90 m = 3 cell widths] of the mean column density (over the 200 cell wide band) at a 0.01 resolution
#' \item Overall start :=
#' \itemize{
#' \item Leftmost position within minimum zone (= first run of sufficiently low values, <= \code{\linkS4class{EcotonerSettings@vegDefiningDensityTransect_low}}) of veg2 such that
#' \item There is at least one point of the maximum zone (= last run of sufficiently high values, >= \code{\linkS4class{EcotonerSettings@vegDefiningDensityTransect_high}}) of veg1 to the right and that
#' \item All of veg1 between overall start and the rightmost point of the maximum zone of veg1 have sufficient density (i.e., > \code{\linkS4class{EcotonerSettings@vegDefiningDensityTransectExtended_min}})
#' }
#' \item Overall end :=
#' \itemize{
#' \item Rightmost position within minimum zone (=last low run after the last high run) of veg1 such that
#' \item Overall start is on the left,
#' \item There is at least one point of the maximum zone (=first high run after the last low run) of veg2 to the left and that
#' \item All of veg2 between the lefmost point of the maximum zone of veg1 and overall end have sufficient density (i.e., > \code{\linkS4class{EcotonerSettings@vegDefiningDensityTransectExtended_min}})
#' }
#' \item No remaining BSE or TF vegetation should attain a maximal density (i.e., < \code{\linkS4class{EcotonerSettings@vegDefiningDensityTransectExtended_min}})
#' \item Zone of ecological boundary := from overall start to overall end
#' }
#'
#' @docType package
#' @name ecotoner
NULL
##------ Package level variables
etr_vars <- new.env()
##------ Package uses S4 classes - they are defined in package:methods
#' @importFrom methods setClass setGeneric setMethod setValidity slot setReplaceMethod new initialize validObject
NULL
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