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#' Obtain species densities from transition matrices
#'
#' Using the vec-permutation approach as defined in:
#' Hunter and Caswell 2005, doi:10.1016/j.ecolmodel.2005.05.002,
#' Ozgul et al. 2009, doi: 10.1086/597225
#' In particular, it uses the arrangement by patches, and calculates
#' first demography, then dispersal (Table 1 of Hunter and Caswell 2005).
#'
#' @param focal.sp integer, focal species
#' @param vpm data structure holding all vector-permutation matrices; see
#' `vec_permutation_matrices`. If not in an appropriate format, it is likely
#' to fail without warning.
#' @param current.densities list of length sp, each element is a matrix sites*stages. If
#' not in that format, it is likely to fail without warning.
#'
#' @return matrix of sites x stages, each element is the density of a given life stage
#' (juvenile, non-reproductive adult, reproductive adult) at a given site.
#' @export
calculate_densities <- function(focal.sp,vpm,current.densities){
if(is.null(focal.sp) | is.null(vpm) | is.null(current.densities)){
message(paste("calculate_densities ERROR: one or more argumets are not specified",sep=""))
return(NULL)
}
# transform to numeric vector
dv <- c(t(current.densities[[focal.sp]]))
d2 <- t(vpm[["permutation"]][[focal.sp]])%*%vpm[["dispersal"]][[focal.sp]]%*%vpm[["permutation"]][[focal.sp]]%*%vpm[["demography"]][[focal.sp]]%*%dv
d3 <- matrix(d2,ncol = 3,byrow = T)
return(d3)
}
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