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#' Enters the prorated results into the bootstrap.results array
#'
#' @param n index of the current bootstrap iteration
#' @param bootstrap.results list of 4-dimensional arrays containing the
#' bootstrap results
#' @param formatted.results list of data objects similar to the dht class
#' @param clusters boolean are the observations clusters of individuals
#' bootstrap results
#' @return list of 4-dimensional arrays containing the updated
#' @author Laura Marshall
#'
accumulate.results <- function(n, bootstrap.results, formatted.results, clusters){
#
# execute.multi.analysis - function for dealing with model uncertainty, covariate uncertainty and unidentified species in Distance Sampling
#
# Arguments:
# n - iteration number
# bootstrap.results - list of 4-dimensional arrays
# prorated.results - list of data objects similar to the dht class
#
# Value:
# returns the updated list of 4-dimensional arrays
#
# Function Calls: none
#
species.name <- names(formatted.results)
#fill in results for each species
for(sp in seq(along=species.name)){
#Fill in individual results
bootstrap.results$individual.summary[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$individual$summary[,2:6])
bootstrap.results$individual.N[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$individual$N[,2:4])
}
if(clusters){
for(sp in seq(along=species.name)){
#Fill in individual results
bootstrap.results$clusters.summary[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$clusters$summary[,2:7])
bootstrap.results$clusters.N[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$clusters$N[,2:4])
#this can be changed back after dht is fixed
#bootstrap.results$Expected.S[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$Expected.S[,2:3])
bootstrap.results$Expected.S[,,n,species.name[sp]] <- as.matrix(formatted.results[[species.name[sp]]]$Expected.S[1:(dim(as.matrix(formatted.results[[species.name[sp]]]$clusters$N[,2:4]))[1]),2:3])
}
}
return(bootstrap.results)
}
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