#
# plot_final_year_MERP_HTL_inshore_vs_offshore.R
#
#' Plot full time series of out
#'
#' Plot set of time series from model out
#'
#' @param model model object
#' @param results full model results
#'
#' @export
#
# most fixed/fitted parms etc are in the results$out from the ode
#
plot_final_year_MERP_HTL_inshore_vs_offshore <- function(model, results) {
build <- elt(results, "build")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
data <- elt(model, "data")
physical.parms <- elt(data, "physical.parameters")
si_depth <- elt(physical.parms, "si_depth")
so_depth <- elt(physical.parms, "so_depth")
d_depth <- elt(physical.parms, "d_depth")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
output <- elt(results, "output")
benthc_o <- elt(output, "benthc_o")
benthc_i <- elt(output, "benthc_i")
benthclar_o <- elt(output, "benthclar_o")
benthclar_i <- elt(output, "benthclar_i")
fishp_o <- elt(output, "fishp_o")
fishp_i <- elt(output, "fishp_i")
fishplar_o <- elt(output, "fishplar_o")
fishplar_i <- elt(output, "fishplar_i")
fishd_o <- elt(output, "fishd_o")
fishd_i <- elt(output, "fishd_i")
fishdlar_o <- elt(output, "fishdlar_o")
fishdlar_i <- elt(output, "fishdlar_i")
fishm_o <- elt(output, "fishm_o")
fishm_i <- elt(output, "fishm_i")
bird_o <- elt(output, "bird_o")
bird_i <- elt(output, "bird_i")
ceta_o <- elt(output, "ceta_o")
ceta_i <- elt(output, "ceta_i")
seal_o <- elt(output, "seal_o")
seal_i <- elt(output, "seal_i")
aggregates <- elt(results, "aggregates")
x_poros <- elt(aggregates, "x_poros")
x_depth <- elt(aggregates, "x_depth")
xvolume_si<-si_depth*x_shallowprop
xvolume_so<-so_depth*(1-x_shallowprop)
xd_volume<-d_depth*(1-x_shallowprop)
#Plot the final year of output
par(mfrow=c(3,3))
l1<-benthc_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-benthc_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Benthos c/s","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-benthclar_o[((nyears-1)*360+1):ndays]/(xvolume_so+xd_volume)
l2<-benthclar_i[((nyears-1)*360+1):ndays]/xvolume_si
tsplot22("Benthos c/s larvae","Nitrogen/m3","Offshore","Inshore",l1,l2)
l1<-fishp_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishp_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Pelagic fish","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-fishplar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishplar_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Pelagic fish larvae","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-fishd_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishd_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Demersal fish","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-fishdlar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishdlar_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Demersal fish larvae","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-fishm_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishm_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Migratory fish","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-bird_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-bird_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot22("Birds","Nitrogen/m2","Offshore","Inshore",l1,l2)
l1<-ceta_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-ceta_i[((nyears-1)*360+1):ndays]/x_shallowprop
l3<-seal_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l4<-seal_i[((nyears-1)*360+1):ndays]/x_shallowprop
tsplot44("Mammals","Nitrogen/m2","Ceatacean_o","Cetaceans_i", "Seals_o","Seals_i",l1,l2,l3,l4)
}
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