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#' Postprocess the Bream spatialized model results
#'
#' @param userpath the path where the working folder is located
#' @param output output list containing the output of the RK solver
#' @param times the vector containing informations on integration extremes
#' @param Dates the vector containing the date
#' @param CS the commercial size of Bream
#'
#' @return a list containing the model outputs saved by the main script to .nc; .csv and .asc files
#'
#' @import matrixStats plotrix rstudioapi
#'
#' @import grDevices graphics utils stats
#'
Bream_spatial_post<-function(userpath,output,times,Dates,CS) {
ti=times[1] # Integration beginning
tf=times[2] # Integration end
# Extracts outputs from the output list
weight=unlist(output[1])
exc=output[[2]]
wst=output[[3]]
ing=unlist(output[4])
ingvero=unlist(output[5])
Tfun=output[[6]]
metab=output[[7]]
O2=output[[8]]
NH4=output[[9]]
# Adjusts results acoording with integration extremes
# now day 1 coincides with ti
weightSave=weight[ti:tf]
excSave=exc[ti:tf,]
wstSave=wst[ti:tf,]
ingSave=ing[ti:tf]
ingveroSave=ingvero[ti:tf]
TfunSave=Tfun[ti:tf,]
metabSave=metab[ti:tf,]
O2Save=O2[ti:tf]
NH4Save=NH4[ti:tf]
# Days to commercial size
foo <- function(w,S){which(w>S)[1]}
arg=as.data.frame(weightSave)
days <- apply(arg,1,foo,S=CS)
days_L <- as.data.frame(days)
NonNAindex <- which(!is.na(days_L))
if (length(NonNAindex)==0) {
daysToSize=9999
}else{ daysToSize <- min(NonNAindex)
}
# daysToSize<-as.list(daysToSize)
output=list(weightSave,excSave,wstSave,ingSave,ingveroSave,metabSave,TfunSave, O2Save, NH4Save, daysToSize)
return(output)
}
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