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R/CredInt_make_aamass_results.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
CredInt_make_aamass_results
#
# CredInt_make_aamass_results.R
#
#' Save current set of fitted parameters to file
#'
#' @param model model object
#' @param inshoreaamassstore inshore annual flux data
#' @param offshoreaamassstore offshore annual flux data
#' @param wholeaamassstore whole annual flux data
#' @param csv.output (TRUE or FALSE, default=TRUE) Set to FALSE to disable writing of CSV output files - useful for testing
#'
#' @importFrom graphics abline bxp
#'
#' @noRd
#
# ------------------------------------------------------------------------------
CredInt_make_aamass_results <- function(model, inshoreaamassstore, offshoreaamassstore, wholeaamassstore,csv.output) {
pkg.env$csv.output <- csv.output # controls writing of CSV files
setup <- elt(model, "setup")
resultsdir <- elt(setup, "resultsdir")
identifier <- elt(setup, "model.ident")
credpath <- makepath(resultsdir, CREDINT_DIR)
# names(offshoreaamassstore)
# [1] "iteration" "likelihood"
# [3] "Surface_layer_detritus" "Deep_layer_detritus"
# [5] "Sediment_labile_plus_refractory_detritus" "Sediment_refractory_detritus"
# [7] "Fishery_discards" "Corpses"
# [9] "Macrophyte_debris" "Surface_layer_ammonia"
#[11] "Deep_layer_ammonia" "Sediment_porewater_ammonia"
#[13] "Surface_layer_nitrate" "Deep_layer_nitrate"
#[15] "Sediment_porewater_nitrate" "Macrophyte_nitrogen"
#[17] "Surface_layer_phytoplankton" "Deep_layer_phytoplankton"
#[19] "Omnivorous_zooplankton" "Carnivorous_zooplankton"
#[21] "Benthos_susp/dep_feeders_larvae" "Benthos_susp/dep_feeders"
#[23] "Benthos_carn/scav_feeders_larvae" "Benthos_carn/scav_feeders"
#[25] "Planktivorous_fish_larvae" "Planktivorous_fish"
#[27] "Migratory_fish" "Demersal_fish_larvae"
#[29] "Demersal_fish" "Bird"
#[31] "Pinnipeds" "Cetaceans"
#[33] "Total_nitrogen_mass" "Area_proportion_of_inshore_zone"
#[35] "Thickness_of_inshore_surface_layer" "Thickness_of_offshore_surface_layer"
#[37] "Thickness_of_offshore_deep_layer" "Area_proportion_inshore_rock"
#[39] "Area_proportion_inshore_sediment_s1" "Area_proportion_inshore_sediment_s2"
#[41] "Area_proportion_inshore_sediment_s3" "Area_proportion_offshore_rock"
#[43] "Area_proportion_offshore_sediment_d1" "Area_proportion_offshore_sediment_d2"
#[45] "Area_proportion_offshore_sediment_d3" "Thickness_of_inshore_sediment_layer_s1"
#[47] "Thickness_of_inshore_sediment_layer_s2" "Thickness_of_inshore_sediment_layer_s3"
#[49] "Thickness_of_offshore_sediment_layer_d1" "Thickness_of_offshore_sediment_layer_d2"
#[51] "Thickness_of_offshore_sediment_layer_d3" "Porosity_of_inshore_sediment_layer_s1"
#[53] "Porosity_of_inshore_sediment_layer_s2" "Porosity_of_inshore_sediment_layer_s3"
#[55] "Porosity_of_offshore_sediment_layer_d1" "Porosity_of_offshore_sediment_layer_d2"
#[57] "Porosity_of_offshore_sediment_layer_d3"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Just need the values of the constant xR detritus to subtract from the total x-detritus figures here
xRdetritus_i <- inshoreaamassstore$Sediment_refractory_detritus[1]
xRdetritus_o <- offshoreaamassstore$Sediment_refractory_detritus[1]
xRdetritus_w <- wholeaamassstore$Sediment_refractory_detritus[1]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xLdetritus_i <- inshoreaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_i
xLdetritus_o <- offshoreaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_o
xLdetritus_w <- wholeaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_w
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
total_labile_detritus_i <- xLdetritus_i + inshoreaamassstore$Surface_layer_detritus + inshoreaamassstore$Corpses + inshoreaamassstore$Fishery_discards + inshoreaamassstore$Macrophyte_debris
total_labile_detritus_o <- xLdetritus_o + offshoreaamassstore$Surface_layer_detritus + offshoreaamassstore$Deep_layer_detritus + offshoreaamassstore$Corpses + offshoreaamassstore$Fishery_discards
total_labile_detritus_w <- xLdetritus_w + wholeaamassstore$Surface_layer_detritus + wholeaamassstore$Deep_layer_detritus + wholeaamassstore$Corpses + wholeaamassstore$Fishery_discards + wholeaamassstore$Macrophyte_debris
offshoreaamassstore$total_labile_detritus_bd<-total_labile_detritus_o/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$kelp_bd<-(offshoreaamassstore$Macrophyte_nitrogen)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$phyt_bd<-(offshoreaamassstore$Surface_layer_phytoplankton+offshoreaamassstore$Deep_layer_phytoplankton)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
#offshoreaamassstore$benth_susp_bd<-(offshoreaamassstore$Benthos_susp/dep_feeders+offshoreaamassstore$Benthos_susp/dep_feeders_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$benth_susp_bd<-(offshoreaamassstore[,21]+offshoreaamassstore[,22])/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$omni_bd<-offshoreaamassstore$Omnivorous_zooplankton/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
#offshoreaamassstore$benth_carn_bd<-(offshoreaamassstore$Benthos_carn/scav_feeders+offshoreaamassstore$Benthos_carn/scav_feeders_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$benth_carn_bd<-(offshoreaamassstore[,23]+offshoreaamassstore[,24])/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$carn_bd<-offshoreaamassstore$Carnivorous_zooplankton/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$plankfish_bd<-(offshoreaamassstore$Planktivorous_fish+offshoreaamassstore$Planktivorous_fish_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$migfish_bd<-offshoreaamassstore$Migratory_fish/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$demfish_bd<-(offshoreaamassstore$Demersal_fish+offshoreaamassstore$Demersal_fish_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$bird_bd<-offshoreaamassstore$Bird/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$seal_bd<-offshoreaamassstore$Pinnipeds/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$ceta_bd<-offshoreaamassstore$Cetaceans/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$total_labile_detritus_bd<-total_labile_detritus_i/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$kelp_bd<-(inshoreaamassstore$Macrophyte_nitrogen)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$phyt_bd<-(inshoreaamassstore$Surface_layer_phytoplankton)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
#inshoreaamassstore$benth_susp_bd<-(inshoreaamassstore$Benthos_susp/dep_feeders+inshoreaamassstore$Benthos_susp/dep_feeders_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$benth_susp_bd<-(inshoreaamassstore[,21]+inshoreaamassstore[,22])/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$omni_bd<-inshoreaamassstore$Omnivorous_zooplankton/(inshoreaamassstore$Area_proportion_of_inshore_zone)
#inshoreaamassstore$benth_carn_bd<-(inshoreaamassstore$Benthos_carn/scav_feeders+inshoreaamassstore$Benthos_carn/scav_feeders_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$benth_carn_bd<-(inshoreaamassstore[,23]+inshoreaamassstore[,24])/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$carn_bd<-inshoreaamassstore$Carnivorous_zooplankton/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$plankfish_bd<-(inshoreaamassstore$Planktivorous_fish+inshoreaamassstore$Planktivorous_fish_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$migfish_bd<-inshoreaamassstore$Migratory_fish/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$demfish_bd<-(inshoreaamassstore$Demersal_fish+inshoreaamassstore$Demersal_fish_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$bird_bd<-inshoreaamassstore$Bird/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$seal_bd<-inshoreaamassstore$Pinnipeds/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$ceta_bd<-inshoreaamassstore$Cetaceans/(inshoreaamassstore$Area_proportion_of_inshore_zone)
wholeaamassstore$total_labile_detritus_bd<-total_labile_detritus_w
wholeaamassstore$kelp_bd<-(wholeaamassstore$Macrophyte_nitrogen)
wholeaamassstore$phyt_bd<-(wholeaamassstore$Surface_layer_phytoplankton+wholeaamassstore$Deep_layer_phytoplankton)
#wholeaamassstore$benth_susp_bd<-(wholeaamassstore$Benthos_susp/dep_feeders+wholeaamassstore$Benthos_susp/dep_feeders_larvae)
wholeaamassstore$benth_susp_bd<-(wholeaamassstore[,21]+wholeaamassstore[,22])
wholeaamassstore$omni_bd<-wholeaamassstore$Omnivorous_zooplankton
#wholeaamassstore$benth_carn_bd<-(wholeaamassstore$Benthos_carn/scav_feeders+wholeaamassstore$Benthos_carn/scav_feeders_larvae)
wholeaamassstore$benth_carn_bd<-(wholeaamassstore[,23]+wholeaamassstore[,24])
wholeaamassstore$carn_bd<-wholeaamassstore$Carnivorous_zooplankton
wholeaamassstore$plankfish_bd<-(wholeaamassstore$Planktivorous_fish+wholeaamassstore$Planktivorous_fish_larvae)
wholeaamassstore$migfish_bd<-wholeaamassstore$Migratory_fish
wholeaamassstore$demfish_bd<-(wholeaamassstore$Demersal_fish+wholeaamassstore$Demersal_fish_larvae)
wholeaamassstore$bird_bd<-wholeaamassstore$Bird
wholeaamassstore$seal_bd<-wholeaamassstore$Pinnipeds
wholeaamassstore$ceta_bd<-wholeaamassstore$Cetaceans
Nind<-13
cols2use<-58:(58-1+Nind)
creds<-c(0.005,0.25,0.5,0.75,0.995) # This can be any lenth of vector in any order. All values must be between 0 and 1
O_results<-data.frame(rep(0,(length(creds)+1)))
rownames(O_results)<-c("maxlik","lowlimit","lowquart","median","uppquart","upplimit")
for(jj in 2:Nind){
O_results[,jj]<-rep(0,(length(creds)+1))
}
colnames(O_results)<-names(offshoreaamassstore[cols2use])
I_results<-O_results
W_results<-O_results
O_results[1,]<-offshoreaamassstore[1,cols2use]
I_results[1,]<-inshoreaamassstore[1,cols2use]
W_results[1,]<-wholeaamassstore[1,cols2use]
for(jj in 1:Nind){
if(jj==1 || jj>2){ # Exception here for kelp where offshore values are all zero
Result<-offshoreaamassstore[,cols2use[jj]]
Likelihood<-offshoreaamassstore$likelihood
#message("\n","Processing offshore ",colnames(O_results)[jj]," data ")
O_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(O_results)[jj],plotgraph=FALSE)
}
Result<-inshoreaamassstore[,cols2use[jj]]
Likelihood<-inshoreaamassstore$likelihood
#message("\n","Processing inshore ",colnames(I_results)[jj]," data ")
I_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(I_results)[jj],plotgraph=FALSE)
Result<-wholeaamassstore[,cols2use[jj]]
Likelihood<-wholeaamassstore$likelihood
#message("\n","Processing whole domain ",colnames(W_results)[jj]," data ")
W_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(W_results)[jj],plotgraph=FALSE)
}
O_results
I_results
W_results
writecsv(O_results, csvname(credpath, "CredInt_processed_AAMresults_offshore", identifier), row.names=TRUE)
writecsv(I_results, csvname(credpath, "CredInt_processed_AAMresults_inshore", identifier), row.names=TRUE)
writecsv(W_results, csvname(credpath, "CredInt_processed_AAMresults_whole", identifier), row.names=TRUE)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output_data<-list(offshore = O_results,
inshore = I_results,
whole = W_results)
output_data
}
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Defines functions CredInt_make_aamass_results
#
# CredInt_make_aamass_results.R
#
#' Save current set of fitted parameters to file
#'
#' @param model model object
#' @param inshoreaamassstore inshore annual flux data
#' @param offshoreaamassstore offshore annual flux data
#' @param wholeaamassstore whole annual flux data
#' @param csv.output (TRUE or FALSE, default=TRUE) Set to FALSE to disable writing of CSV output files - useful for testing
#'
#' @importFrom graphics abline bxp
#'
#' @noRd
#
# ------------------------------------------------------------------------------
CredInt_make_aamass_results <- function(model, inshoreaamassstore, offshoreaamassstore, wholeaamassstore,csv.output) {
pkg.env$csv.output <- csv.output # controls writing of CSV files
setup <- elt(model, "setup")
resultsdir <- elt(setup, "resultsdir")
identifier <- elt(setup, "model.ident")
credpath <- makepath(resultsdir, CREDINT_DIR)
# names(offshoreaamassstore)
# [1] "iteration" "likelihood"
# [3] "Surface_layer_detritus" "Deep_layer_detritus"
# [5] "Sediment_labile_plus_refractory_detritus" "Sediment_refractory_detritus"
# [7] "Fishery_discards" "Corpses"
# [9] "Macrophyte_debris" "Surface_layer_ammonia"
#[11] "Deep_layer_ammonia" "Sediment_porewater_ammonia"
#[13] "Surface_layer_nitrate" "Deep_layer_nitrate"
#[15] "Sediment_porewater_nitrate" "Macrophyte_nitrogen"
#[17] "Surface_layer_phytoplankton" "Deep_layer_phytoplankton"
#[19] "Omnivorous_zooplankton" "Carnivorous_zooplankton"
#[21] "Benthos_susp/dep_feeders_larvae" "Benthos_susp/dep_feeders"
#[23] "Benthos_carn/scav_feeders_larvae" "Benthos_carn/scav_feeders"
#[25] "Planktivorous_fish_larvae" "Planktivorous_fish"
#[27] "Migratory_fish" "Demersal_fish_larvae"
#[29] "Demersal_fish" "Bird"
#[31] "Pinnipeds" "Cetaceans"
#[33] "Total_nitrogen_mass" "Area_proportion_of_inshore_zone"
#[35] "Thickness_of_inshore_surface_layer" "Thickness_of_offshore_surface_layer"
#[37] "Thickness_of_offshore_deep_layer" "Area_proportion_inshore_rock"
#[39] "Area_proportion_inshore_sediment_s1" "Area_proportion_inshore_sediment_s2"
#[41] "Area_proportion_inshore_sediment_s3" "Area_proportion_offshore_rock"
#[43] "Area_proportion_offshore_sediment_d1" "Area_proportion_offshore_sediment_d2"
#[45] "Area_proportion_offshore_sediment_d3" "Thickness_of_inshore_sediment_layer_s1"
#[47] "Thickness_of_inshore_sediment_layer_s2" "Thickness_of_inshore_sediment_layer_s3"
#[49] "Thickness_of_offshore_sediment_layer_d1" "Thickness_of_offshore_sediment_layer_d2"
#[51] "Thickness_of_offshore_sediment_layer_d3" "Porosity_of_inshore_sediment_layer_s1"
#[53] "Porosity_of_inshore_sediment_layer_s2" "Porosity_of_inshore_sediment_layer_s3"
#[55] "Porosity_of_offshore_sediment_layer_d1" "Porosity_of_offshore_sediment_layer_d2"
#[57] "Porosity_of_offshore_sediment_layer_d3"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Just need the values of the constant xR detritus to subtract from the total x-detritus figures here
xRdetritus_i <- inshoreaamassstore$Sediment_refractory_detritus[1]
xRdetritus_o <- offshoreaamassstore$Sediment_refractory_detritus[1]
xRdetritus_w <- wholeaamassstore$Sediment_refractory_detritus[1]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xLdetritus_i <- inshoreaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_i
xLdetritus_o <- offshoreaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_o
xLdetritus_w <- wholeaamassstore$Sediment_labile_plus_refractory_detritus-xRdetritus_w
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
total_labile_detritus_i <- xLdetritus_i + inshoreaamassstore$Surface_layer_detritus + inshoreaamassstore$Corpses + inshoreaamassstore$Fishery_discards + inshoreaamassstore$Macrophyte_debris
total_labile_detritus_o <- xLdetritus_o + offshoreaamassstore$Surface_layer_detritus + offshoreaamassstore$Deep_layer_detritus + offshoreaamassstore$Corpses + offshoreaamassstore$Fishery_discards
total_labile_detritus_w <- xLdetritus_w + wholeaamassstore$Surface_layer_detritus + wholeaamassstore$Deep_layer_detritus + wholeaamassstore$Corpses + wholeaamassstore$Fishery_discards + wholeaamassstore$Macrophyte_debris
offshoreaamassstore$total_labile_detritus_bd<-total_labile_detritus_o/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$kelp_bd<-(offshoreaamassstore$Macrophyte_nitrogen)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$phyt_bd<-(offshoreaamassstore$Surface_layer_phytoplankton+offshoreaamassstore$Deep_layer_phytoplankton)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
#offshoreaamassstore$benth_susp_bd<-(offshoreaamassstore$Benthos_susp/dep_feeders+offshoreaamassstore$Benthos_susp/dep_feeders_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$benth_susp_bd<-(offshoreaamassstore[,21]+offshoreaamassstore[,22])/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$omni_bd<-offshoreaamassstore$Omnivorous_zooplankton/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
#offshoreaamassstore$benth_carn_bd<-(offshoreaamassstore$Benthos_carn/scav_feeders+offshoreaamassstore$Benthos_carn/scav_feeders_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$benth_carn_bd<-(offshoreaamassstore[,23]+offshoreaamassstore[,24])/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$carn_bd<-offshoreaamassstore$Carnivorous_zooplankton/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$plankfish_bd<-(offshoreaamassstore$Planktivorous_fish+offshoreaamassstore$Planktivorous_fish_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$migfish_bd<-offshoreaamassstore$Migratory_fish/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$demfish_bd<-(offshoreaamassstore$Demersal_fish+offshoreaamassstore$Demersal_fish_larvae)/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$bird_bd<-offshoreaamassstore$Bird/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$seal_bd<-offshoreaamassstore$Pinnipeds/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
offshoreaamassstore$ceta_bd<-offshoreaamassstore$Cetaceans/(1-offshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$total_labile_detritus_bd<-total_labile_detritus_i/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$kelp_bd<-(inshoreaamassstore$Macrophyte_nitrogen)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$phyt_bd<-(inshoreaamassstore$Surface_layer_phytoplankton)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
#inshoreaamassstore$benth_susp_bd<-(inshoreaamassstore$Benthos_susp/dep_feeders+inshoreaamassstore$Benthos_susp/dep_feeders_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$benth_susp_bd<-(inshoreaamassstore[,21]+inshoreaamassstore[,22])/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$omni_bd<-inshoreaamassstore$Omnivorous_zooplankton/(inshoreaamassstore$Area_proportion_of_inshore_zone)
#inshoreaamassstore$benth_carn_bd<-(inshoreaamassstore$Benthos_carn/scav_feeders+inshoreaamassstore$Benthos_carn/scav_feeders_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$benth_carn_bd<-(inshoreaamassstore[,23]+inshoreaamassstore[,24])/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$carn_bd<-inshoreaamassstore$Carnivorous_zooplankton/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$plankfish_bd<-(inshoreaamassstore$Planktivorous_fish+inshoreaamassstore$Planktivorous_fish_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$migfish_bd<-inshoreaamassstore$Migratory_fish/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$demfish_bd<-(inshoreaamassstore$Demersal_fish+inshoreaamassstore$Demersal_fish_larvae)/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$bird_bd<-inshoreaamassstore$Bird/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$seal_bd<-inshoreaamassstore$Pinnipeds/(inshoreaamassstore$Area_proportion_of_inshore_zone)
inshoreaamassstore$ceta_bd<-inshoreaamassstore$Cetaceans/(inshoreaamassstore$Area_proportion_of_inshore_zone)
wholeaamassstore$total_labile_detritus_bd<-total_labile_detritus_w
wholeaamassstore$kelp_bd<-(wholeaamassstore$Macrophyte_nitrogen)
wholeaamassstore$phyt_bd<-(wholeaamassstore$Surface_layer_phytoplankton+wholeaamassstore$Deep_layer_phytoplankton)
#wholeaamassstore$benth_susp_bd<-(wholeaamassstore$Benthos_susp/dep_feeders+wholeaamassstore$Benthos_susp/dep_feeders_larvae)
wholeaamassstore$benth_susp_bd<-(wholeaamassstore[,21]+wholeaamassstore[,22])
wholeaamassstore$omni_bd<-wholeaamassstore$Omnivorous_zooplankton
#wholeaamassstore$benth_carn_bd<-(wholeaamassstore$Benthos_carn/scav_feeders+wholeaamassstore$Benthos_carn/scav_feeders_larvae)
wholeaamassstore$benth_carn_bd<-(wholeaamassstore[,23]+wholeaamassstore[,24])
wholeaamassstore$carn_bd<-wholeaamassstore$Carnivorous_zooplankton
wholeaamassstore$plankfish_bd<-(wholeaamassstore$Planktivorous_fish+wholeaamassstore$Planktivorous_fish_larvae)
wholeaamassstore$migfish_bd<-wholeaamassstore$Migratory_fish
wholeaamassstore$demfish_bd<-(wholeaamassstore$Demersal_fish+wholeaamassstore$Demersal_fish_larvae)
wholeaamassstore$bird_bd<-wholeaamassstore$Bird
wholeaamassstore$seal_bd<-wholeaamassstore$Pinnipeds
wholeaamassstore$ceta_bd<-wholeaamassstore$Cetaceans
Nind<-13
cols2use<-58:(58-1+Nind)
creds<-c(0.005,0.25,0.5,0.75,0.995) # This can be any lenth of vector in any order. All values must be between 0 and 1
O_results<-data.frame(rep(0,(length(creds)+1)))
rownames(O_results)<-c("maxlik","lowlimit","lowquart","median","uppquart","upplimit")
for(jj in 2:Nind){
O_results[,jj]<-rep(0,(length(creds)+1))
}
colnames(O_results)<-names(offshoreaamassstore[cols2use])
I_results<-O_results
W_results<-O_results
O_results[1,]<-offshoreaamassstore[1,cols2use]
I_results[1,]<-inshoreaamassstore[1,cols2use]
W_results[1,]<-wholeaamassstore[1,cols2use]
for(jj in 1:Nind){
if(jj==1 || jj>2){ # Exception here for kelp where offshore values are all zero
Result<-offshoreaamassstore[,cols2use[jj]]
Likelihood<-offshoreaamassstore$likelihood
#message("\n","Processing offshore ",colnames(O_results)[jj]," data ")
O_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(O_results)[jj],plotgraph=FALSE)
}
Result<-inshoreaamassstore[,cols2use[jj]]
Likelihood<-inshoreaamassstore$likelihood
#message("\n","Processing inshore ",colnames(I_results)[jj]," data ")
I_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(I_results)[jj],plotgraph=FALSE)
Result<-wholeaamassstore[,cols2use[jj]]
Likelihood<-wholeaamassstore$likelihood
#message("\n","Processing whole domain ",colnames(W_results)[jj]," data ")
W_results[2:(length(creds)+1),jj]<-GetCredInt(Result,Likelihood,creds,var=colnames(W_results)[jj],plotgraph=FALSE)
}
O_results
I_results
W_results
writecsv(O_results, csvname(credpath, "CredInt_processed_AAMresults_offshore", identifier), row.names=TRUE)
writecsv(I_results, csvname(credpath, "CredInt_processed_AAMresults_inshore", identifier), row.names=TRUE)
writecsv(W_results, csvname(credpath, "CredInt_processed_AAMresults_whole", identifier), row.names=TRUE)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output_data<-list(offshore = O_results,
inshore = I_results,
whole = W_results)
output_data
}
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