Nothing
R/plot_final_year_time_series_data_with_ci.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
plot_final_year_time_series_data_with_ci
#
# plot_final_year_time_series_data_with_ci.R
#
#' Create multi-panel plots showing the credible intervals of state variable densities over the final year of a simulation generated by the Monte Carlo e2e_run_mc() function
#'
#' Each panel of the plot shows a time-series of the densities (per unit sea surface area or layer volume) of a
#' state variable over the final year of a run. The data displayed are the solution to the basic model, together with
#' centiles of the distribution of credible values. The distribution of credible values is derived from
#' a Monte Carlo simulation scheme performed by the e2e_run_mc() function.
#'
#' Daily interval post-processed data from the Monte Carlo function are stored in the file
#' /results/Modelname/Variantname/CredInt/CredInt_processed_daily_mass-*.csv, where * represents the model run identifier
#' (model.ident) text embedded in the R-list object created by the e2e_read() function.
#' The function described here loads these stored data. Depending on the value set for the 'selection' argument in the function,
#' different groups of variables are extracted for plotting in each multi-panel page.
#'
#' Optionally the function can read an example data set for one of the two North Sea model variants supplied with the package.
#'
#' In each plot the x-axis represents day of the year over an annual cycle. The y-axis represents mass density of a state variable
#' (mMN/m2 or mMN/m3). Results from the basic model are shown by a red line. The median of the credible values distribution
#' is shown my a solid black line. A grey-shaded area indicates the 50% credible interval (spanning quartiles of the cumulative likelihood
#' of simulated values). Black dashed lines span the 99% credible interval.
#'
#' For details of how the distribution of credible output values from StrathE2E are calculated see help(e2e_run_mc).
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param selection Text string from a list identifying the group of model output variables to be plotted. Select from: "NUT_PHYT", "SEDIMENT", "ZOOPLANKTON", "FISH", "BENTHOS", "PREDATORS", "CORP_DISC", "MACROPHYTE", Remember to include the phrase within "" quotes.
#' @param use.example Logical. If TRUE then use pre-computed example data from the internal North Sea model rather than user-generated data (default=FALSE)
#'
#' @return Graphical display in a new graphics window
#'
#' @importFrom graphics polygon
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_final_year_time_series_data_with_ci <- function(model, selection, use.example=FALSE) {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
resultsdir <- elt(model, "setup", "resultsdir")
model.ident <- elt(model, "setup", "model.ident")
model.name <- elt(model, "setup", "model.name")
model.variant <- elt(model, "setup", "model.variant")
corefilename<-"CredInt_processed_daily_mass"
if(use.example==TRUE){
Result_data_store <- get.example.results(model.name, model.variant, corefilename, CREDINT_DIR)
}
if(use.example==FALSE){
credpath <- makepath(resultsdir, CREDINT_DIR)
credfile <- csvname(credpath, corefilename, model.ident)
message("Reading credible interval processed data from '", credfile, "'")
Result_data_store <- readcsv(credfile, row.names=1)
#showall("row.names()", row.names(Result_data_store))
}
# ---------------------------------------------------------------------------------
# Function to find joint y axis maximum across several plots
findyaxmax<-function(VtoGet){
for(jjj in 1:(length(VtoGet))){
if(jjj==1) alldata<-as.numeric(Result_data_store[VtoGet[jjj],])
if(jjj>1) alldata<-c(alldata,as.numeric(Result_data_store[VtoGet[jjj],]))
}
yaxmax<- max(alldata,na.rm=TRUE)
yaxmax
}
# ---------------------------------------------------------------------------------
# Function to plot cred int data
tsplotCI<-function(tspmain,axtitle,VtoGet,ymax){
#In each set:
#Row1 = maximum likelihood model result
#Row2 = 0.005 centile
#Row3 = lower quartile
#Row4 = median
#Row5 = upper quartile
#Row6 = 0.995 centile
#
par(mar=c(3.5,3.8,2.1,0.7))
message("Plot", tspmain, "and", axtitle)
yml<-as.numeric(Result_data_store[VtoGet[1],])
yll<-as.numeric(Result_data_store[VtoGet[2],])
ylq<-as.numeric(Result_data_store[VtoGet[3],])
ymd<-as.numeric(Result_data_store[VtoGet[4],])
yuq<-as.numeric(Result_data_store[VtoGet[5],])
yul<-as.numeric(Result_data_store[VtoGet[6],])
# showall("data", VtoGet)
# showall("yml", yml)
# showall("yll", yll)
# showall("ylq", ylq)
# showall("ymd", ymd)
# showall("yuq", yuq)
# showall("yul", yul)
poly_y<-c(ylq,yuq[361:1],ylq[1])
poly_x<-c(seq(0,360),seq(360,0,by=-1),0)
if(ymax>0) y_max<-ymax
if(ymax==0) y_max<-1.1*max(yul)
plot(seq(0,360),yul,ylim=c(0,y_max),type="l",lty="dashed",lwd=1,col="black",xaxt="n",yaxt="n",ann=FALSE,main=tspmain)
polygon(poly_x,poly_y,col="grey",border="grey")
lines(seq(0,360),yll,type="l",lty="dashed",lwd=1,col="black")
lines(seq(0,360),ymd,type="l",lwd=2,col="black")
lines(seq(0,360),yml,type="l",lwd=1,col="red")
axis(side=1,at=c(0,60,120,180,240,300,360),las=1,cex.axis=0.9)
axis(side=2,las=1,cex.axis=0.9)
mtext("Days",cex=0.7,side=1,line=2)
mtext(axtitle,cex=0.7,side=2,line=2.8)
mtext(tspmain,cex=0.7,side=3,line=0.7)
}
# ---------------------------------------------------------------------------------
if (selection == "NUT_PHYT") {
#WATER COLUMN NUTRIENTS DETRITUS AND PHYTOPLANKTON
Surface_detritus_offshore_id <-grep("Surface_detritus_offshore",row.names(Result_data_store))
Surface_ammonia_offshore_id <-grep("Surface_ammonia_offshore",row.names(Result_data_store))
Surface_nitrate_offshore_id <-grep("Surface_nitrate_offshore",row.names(Result_data_store))
Surface_phytoplankton_offshore_id <-grep("Surface_phytoplankton_offshore",row.names(Result_data_store))
Deep_detritus_offshore_id <-grep("Deep_detritus_offshore",row.names(Result_data_store))
Deep_ammonia_offshore_id <-grep("Deep_ammonia_offshore",row.names(Result_data_store))
Deep_nitrate_offshore_id <-grep("Deep_nitrate_offshore",row.names(Result_data_store))
Deep_phytoplankton_offshore_id <-grep("Deep_phytoplankton_offshore",row.names(Result_data_store))
Surface_detritus_inshore_id <-grep("Surface_detritus_inshore",row.names(Result_data_store))
Surface_ammonia_inshore_id <-grep("Surface_ammonia_inshore",row.names(Result_data_store))
Surface_nitrate_inshore_id <-grep("Surface_nitrate_inshore",row.names(Result_data_store))
Surface_phytoplankton_inshore_id <-grep("Surface_phytoplankton_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Surface_detritus_offshore_id,
Deep_detritus_offshore_id,
Surface_detritus_inshore_id))
C2max<-1.2*findyaxmax(c(Surface_ammonia_offshore_id,
Deep_ammonia_offshore_id,
Surface_ammonia_inshore_id))
C3max<-1.2*findyaxmax(c(Surface_nitrate_offshore_id,
Deep_nitrate_offshore_id,
Surface_nitrate_inshore_id))
C4max<-1.2*findyaxmax(c(Surface_phytoplankton_offshore_id,
Deep_phytoplankton_offshore_id,
Surface_phytoplankton_inshore_id))
unitsize<-0.5
unitline<- -0.3
unitadj<- -0.7
par(mfrow=c(3,4))
VtoGet<-Surface_detritus_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_ammonia_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_nitrate_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_phytoplankton_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_detritus_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_ammonia_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_nitrate_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_phytoplankton_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_detritus_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_ammonia_inshore_id
tspmain<-"Inshore zone"
axtitle<-" Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_nitrate_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_phytoplankton_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "SEDIMENT") {
#SEABED DETRITUS AND NUTRIENTS
Sediment_detritus_N_by_weight_offshore_mud_id <-grep("Sediment_detritus_N%_by_weight_offshore_mud",row.names(Result_data_store))
Sediment_detritus_N_by_weight_offshore_sand_id <-grep("Sediment_detritus_N%_by_weight_offshore_sand",row.names(Result_data_store))
Sediment_detritus_N_by_weight_inshore_mud_id <-grep("Sediment_detritus_N%_by_weight_inshore_mud",row.names(Result_data_store))
Sediment_detritus_N_by_weight_inshore_sand_id <-grep("Sediment_detritus_N%_by_weight_inshore_sand",row.names(Result_data_store))
Porewater_nitrate_offshore_mud_id <-grep("Porewater_nitrate_offshore_mud",row.names(Result_data_store))
Porewater_nitrate_offshore_sand_id <-grep("Porewater_nitrate_offshore_sand",row.names(Result_data_store))
Porewater_nitrate_inshore_mud_id <-grep("Porewater_nitrate_inshore_mud",row.names(Result_data_store))
Porewater_nitrate_inshore_sand_id <-grep("Porewater_nitrate_inshore_sand",row.names(Result_data_store))
Porewater_ammonia_offshore_mud_id <-grep("Porewater_ammonia_offshore_mud",row.names(Result_data_store))
Porewater_ammonia_offshore_sand_id <-grep("Porewater_ammonia_offshore_sand",row.names(Result_data_store))
Porewater_ammonia_inshore_mud_id <-grep("Porewater_ammonia_inshore_mud",row.names(Result_data_store))
Porewater_ammonia_inshore_sand_id <-grep("Porewater_ammonia_inshore_sand",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Sediment_detritus_N_by_weight_offshore_mud_id,
Sediment_detritus_N_by_weight_offshore_sand_id,
Sediment_detritus_N_by_weight_inshore_mud_id,
Sediment_detritus_N_by_weight_inshore_sand_id))
C2max<-1.2*findyaxmax(c(Porewater_nitrate_offshore_mud_id,
Porewater_nitrate_offshore_sand_id,
Porewater_nitrate_inshore_mud_id,
Porewater_nitrate_inshore_sand_id))
C3max<-1.2*findyaxmax(c(Porewater_ammonia_offshore_mud_id,
Porewater_ammonia_offshore_sand_id,
Porewater_ammonia_inshore_mud_id,
Porewater_ammonia_inshore_sand_id))
unitsize<-0.55
unitline<-0.35
unitadj<- -0.25
par(mfrow=c(4,3))
VtoGet<-Sediment_detritus_N_by_weight_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "ZOOPLANKTON") {
#ZOOPLANKTON
Omnivorous_zooplankton_offshore_id <-grep("Omnivorous_zooplankton_offshore",row.names(Result_data_store))
Omnivorous_zooplankton_inshore_id <-grep("Omnivorous_zooplankton_inshore",row.names(Result_data_store))
Carnivorous_zooplankton_offshore_id <-grep("Carnivorous_zooplankton_offshore",row.names(Result_data_store))
Carnivorous_zooplankton_inshore_id <-grep("Carnivorous_zooplankton_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Omnivorous_zooplankton_offshore_id,
Omnivorous_zooplankton_inshore_id))
C2max<-1.2*findyaxmax(c(Carnivorous_zooplankton_offshore_id,
Carnivorous_zooplankton_inshore_id))
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Omnivorous_zooplankton_offshore_id
tspmain<-"Offshore zone "
axtitle<-"Omnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivorous_zooplankton_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Omnivorous_zooplankton_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Omnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivorous_zooplankton_inshore_id
tspmain<-"Inshore zone "
axtitle<-"Carnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "FISH") {
#FISH AND FISH LARVAE
Planktivorous_fish_offshore_id <-grep("Planktivorous_fish_offshore",row.names(Result_data_store))
Planktivorous_fish_larvae_offshore_id <-grep("Planktivorous_fish_larvae_offshore",row.names(Result_data_store))
Demersal_fish_offshore_id <-grep("Demersal_fish_offshore",row.names(Result_data_store))
Demersal_fish_larvae_offshore_id <-grep("Demersal_fish_larvae_offshore",row.names(Result_data_store))
Planktivorous_fish_inshore_id <-grep("Planktivorous_fish_inshore",row.names(Result_data_store))
Planktivorous_fish_larvae_inshore_id <-grep("Planktivorous_fish_larvae_inshore",row.names(Result_data_store))
Demersal_fish_inshore_id <-grep("Demersal_fish_inshore",row.names(Result_data_store))
Demersal_fish_larvae_inshore_id <-grep("Demersal_fish_larvae_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Planktivorous_fish_offshore_id,
Planktivorous_fish_inshore_id))
C2max<-1.2*findyaxmax(c(Planktivorous_fish_larvae_offshore_id,
Planktivorous_fish_larvae_inshore_id))
C3max<-1.2*findyaxmax(c(Demersal_fish_offshore_id,
Demersal_fish_inshore_id))
C4max<-1.2*findyaxmax(c(Demersal_fish_larvae_offshore_id,
Demersal_fish_larvae_inshore_id))
unitsize<-0.55
unitline<- -0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Planktivorous_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Planktivorous fish"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Planktivorous fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Demersal fish"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Demersal fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Planktivorous fish"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Planktivorous fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Demersal fish"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Demersal fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "BENTHOS") {
#BENTHOS AND BENTHOS LARVAE
Suspension_deposit_benthos_offshore_id <-grep("Suspension_deposit_benthos_offshore",row.names(Result_data_store))
Suspension_deposit_benthos_larvae_offshore_id <-grep("Suspension_deposit_benthos_larvae_offshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_offshore_id <-grep("Carnivore_scavenge_benthos_offshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_larvae_offshore_id <-grep("Carnivore_scavenge_benthos_larvae_offshore",row.names(Result_data_store))
Suspension_deposit_benthos_inshore_id <-grep("Suspension_deposit_benthos_inshore",row.names(Result_data_store))
Suspension_deposit_benthos_larvae_inshore_id <-grep("Suspension_deposit_benthos_larvae_inshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_inshore_id <-grep("Carnivore_scavenge_benthos_inshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_larvae_inshore_id <-grep("Carnivore_scavenge_benthos_larvae_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Suspension_deposit_benthos_offshore_id,
Suspension_deposit_benthos_inshore_id))
C2max<-1.2*findyaxmax(c(Suspension_deposit_benthos_larvae_offshore_id,
Suspension_deposit_benthos_larvae_inshore_id))
C3max<-1.2*findyaxmax(c(Carnivore_scavenge_benthos_offshore_id,
Carnivore_scavenge_benthos_inshore_id))
C4max<-1.2*findyaxmax(c(Carnivore_scavenge_benthos_larvae_offshore_id,
Carnivore_scavenge_benthos_larvae_inshore_id))
unitsize<-0.55
unitline<- - 0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Suspension_deposit_benthos_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Susp./dep. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Susp./dep. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carn./scav. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carn./scav. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Susp./dep. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Susp./dep. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Carn./scav. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Carn./scav. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "PREDATORS") {
#BIRDS/MAMMALS, MIGRATORY FISH
Birds_offshore_id <-grep("Birds_offshore",row.names(Result_data_store))
Seals_offshore_id <-grep("Pinnipeds_offshore",row.names(Result_data_store))
Cetaceans_offshore_id <-grep("Cetaceans_offshore",row.names(Result_data_store))
Migratory_fish_inshore_id <-grep("Migratory_fish_inshore",row.names(Result_data_store))
Birds_inshore_id <-grep("Birds_inshore",row.names(Result_data_store))
Seals_inshore_id <-grep("Pinnipeds_inshore",row.names(Result_data_store))
Cetaceans_inshore_id <-grep("Cetaceans_inshore",row.names(Result_data_store))
Migratory_fish_offshore_id <-grep("Migratory_fish_offshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Birds_offshore_id,
Birds_inshore_id))
C2max<-1.2*findyaxmax(c(Seals_offshore_id,
Seals_inshore_id))
C3max<-1.2*findyaxmax(c(Cetaceans_offshore_id,
Cetaceans_inshore_id))
C4max<-1.2*findyaxmax(c(Migratory_fish_inshore_id,
Migratory_fish_offshore_id))
unitsize<-0.55
unitline<- - 0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Birds_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Birds"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Seals_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Pinnipeds"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Cetaceans_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Cetaceans"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Migratory_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Migratory fish"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Birds_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Birds"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Seals_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Pinnipeds"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Cetaceans_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Cetaceans"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Migratory_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Migratory fish"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "CORP_DISC") {
#CORPSES and DISCARDS
Corpses_offshore_id <-grep("Corpses_offshore",row.names(Result_data_store))
Discards_offshore_id <-grep("Discards_offshore",row.names(Result_data_store))
Corpses_inshore_id <-grep("Corpses_inshore",row.names(Result_data_store))
Discards_inshore_id <-grep("Discards_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Corpses_offshore_id,
Corpses_inshore_id))
C2max<-1.2*findyaxmax(c(Discards_offshore_id,
Discards_inshore_id))
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Corpses_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Seabed corpses"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Discards_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Fishery discards"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Corpses_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Seabed corpses"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Discards_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Fishery discards"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "MACROPHYTE") {
#KELP and KELP DEBRIS
Kelp_inshore_id <-grep("Macrophytes_inshore",row.names(Result_data_store))
Kelp_debris_inshore_id <-grep("Macrophyte_debris_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(Kelp_inshore_id)
C2max<-1.2*findyaxmax(Kelp_debris_inshore_id)
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Kelp_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Macrophytes"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Kelp_debris_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Macrophyte debris"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else {
stop("Error: unknown plot selection '", selection, "' !\n")
}
}
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Defines functions plot_final_year_time_series_data_with_ci
#
# plot_final_year_time_series_data_with_ci.R
#
#' Create multi-panel plots showing the credible intervals of state variable densities over the final year of a simulation generated by the Monte Carlo e2e_run_mc() function
#'
#' Each panel of the plot shows a time-series of the densities (per unit sea surface area or layer volume) of a
#' state variable over the final year of a run. The data displayed are the solution to the basic model, together with
#' centiles of the distribution of credible values. The distribution of credible values is derived from
#' a Monte Carlo simulation scheme performed by the e2e_run_mc() function.
#'
#' Daily interval post-processed data from the Monte Carlo function are stored in the file
#' /results/Modelname/Variantname/CredInt/CredInt_processed_daily_mass-*.csv, where * represents the model run identifier
#' (model.ident) text embedded in the R-list object created by the e2e_read() function.
#' The function described here loads these stored data. Depending on the value set for the 'selection' argument in the function,
#' different groups of variables are extracted for plotting in each multi-panel page.
#'
#' Optionally the function can read an example data set for one of the two North Sea model variants supplied with the package.
#'
#' In each plot the x-axis represents day of the year over an annual cycle. The y-axis represents mass density of a state variable
#' (mMN/m2 or mMN/m3). Results from the basic model are shown by a red line. The median of the credible values distribution
#' is shown my a solid black line. A grey-shaded area indicates the 50% credible interval (spanning quartiles of the cumulative likelihood
#' of simulated values). Black dashed lines span the 99% credible interval.
#'
#' For details of how the distribution of credible output values from StrathE2E are calculated see help(e2e_run_mc).
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param selection Text string from a list identifying the group of model output variables to be plotted. Select from: "NUT_PHYT", "SEDIMENT", "ZOOPLANKTON", "FISH", "BENTHOS", "PREDATORS", "CORP_DISC", "MACROPHYTE", Remember to include the phrase within "" quotes.
#' @param use.example Logical. If TRUE then use pre-computed example data from the internal North Sea model rather than user-generated data (default=FALSE)
#'
#' @return Graphical display in a new graphics window
#'
#' @importFrom graphics polygon
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_final_year_time_series_data_with_ci <- function(model, selection, use.example=FALSE) {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
resultsdir <- elt(model, "setup", "resultsdir")
model.ident <- elt(model, "setup", "model.ident")
model.name <- elt(model, "setup", "model.name")
model.variant <- elt(model, "setup", "model.variant")
corefilename<-"CredInt_processed_daily_mass"
if(use.example==TRUE){
Result_data_store <- get.example.results(model.name, model.variant, corefilename, CREDINT_DIR)
}
if(use.example==FALSE){
credpath <- makepath(resultsdir, CREDINT_DIR)
credfile <- csvname(credpath, corefilename, model.ident)
message("Reading credible interval processed data from '", credfile, "'")
Result_data_store <- readcsv(credfile, row.names=1)
#showall("row.names()", row.names(Result_data_store))
}
# ---------------------------------------------------------------------------------
# Function to find joint y axis maximum across several plots
findyaxmax<-function(VtoGet){
for(jjj in 1:(length(VtoGet))){
if(jjj==1) alldata<-as.numeric(Result_data_store[VtoGet[jjj],])
if(jjj>1) alldata<-c(alldata,as.numeric(Result_data_store[VtoGet[jjj],]))
}
yaxmax<- max(alldata,na.rm=TRUE)
yaxmax
}
# ---------------------------------------------------------------------------------
# Function to plot cred int data
tsplotCI<-function(tspmain,axtitle,VtoGet,ymax){
#In each set:
#Row1 = maximum likelihood model result
#Row2 = 0.005 centile
#Row3 = lower quartile
#Row4 = median
#Row5 = upper quartile
#Row6 = 0.995 centile
#
par(mar=c(3.5,3.8,2.1,0.7))
message("Plot", tspmain, "and", axtitle)
yml<-as.numeric(Result_data_store[VtoGet[1],])
yll<-as.numeric(Result_data_store[VtoGet[2],])
ylq<-as.numeric(Result_data_store[VtoGet[3],])
ymd<-as.numeric(Result_data_store[VtoGet[4],])
yuq<-as.numeric(Result_data_store[VtoGet[5],])
yul<-as.numeric(Result_data_store[VtoGet[6],])
# showall("data", VtoGet)
# showall("yml", yml)
# showall("yll", yll)
# showall("ylq", ylq)
# showall("ymd", ymd)
# showall("yuq", yuq)
# showall("yul", yul)
poly_y<-c(ylq,yuq[361:1],ylq[1])
poly_x<-c(seq(0,360),seq(360,0,by=-1),0)
if(ymax>0) y_max<-ymax
if(ymax==0) y_max<-1.1*max(yul)
plot(seq(0,360),yul,ylim=c(0,y_max),type="l",lty="dashed",lwd=1,col="black",xaxt="n",yaxt="n",ann=FALSE,main=tspmain)
polygon(poly_x,poly_y,col="grey",border="grey")
lines(seq(0,360),yll,type="l",lty="dashed",lwd=1,col="black")
lines(seq(0,360),ymd,type="l",lwd=2,col="black")
lines(seq(0,360),yml,type="l",lwd=1,col="red")
axis(side=1,at=c(0,60,120,180,240,300,360),las=1,cex.axis=0.9)
axis(side=2,las=1,cex.axis=0.9)
mtext("Days",cex=0.7,side=1,line=2)
mtext(axtitle,cex=0.7,side=2,line=2.8)
mtext(tspmain,cex=0.7,side=3,line=0.7)
}
# ---------------------------------------------------------------------------------
if (selection == "NUT_PHYT") {
#WATER COLUMN NUTRIENTS DETRITUS AND PHYTOPLANKTON
Surface_detritus_offshore_id <-grep("Surface_detritus_offshore",row.names(Result_data_store))
Surface_ammonia_offshore_id <-grep("Surface_ammonia_offshore",row.names(Result_data_store))
Surface_nitrate_offshore_id <-grep("Surface_nitrate_offshore",row.names(Result_data_store))
Surface_phytoplankton_offshore_id <-grep("Surface_phytoplankton_offshore",row.names(Result_data_store))
Deep_detritus_offshore_id <-grep("Deep_detritus_offshore",row.names(Result_data_store))
Deep_ammonia_offshore_id <-grep("Deep_ammonia_offshore",row.names(Result_data_store))
Deep_nitrate_offshore_id <-grep("Deep_nitrate_offshore",row.names(Result_data_store))
Deep_phytoplankton_offshore_id <-grep("Deep_phytoplankton_offshore",row.names(Result_data_store))
Surface_detritus_inshore_id <-grep("Surface_detritus_inshore",row.names(Result_data_store))
Surface_ammonia_inshore_id <-grep("Surface_ammonia_inshore",row.names(Result_data_store))
Surface_nitrate_inshore_id <-grep("Surface_nitrate_inshore",row.names(Result_data_store))
Surface_phytoplankton_inshore_id <-grep("Surface_phytoplankton_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Surface_detritus_offshore_id,
Deep_detritus_offshore_id,
Surface_detritus_inshore_id))
C2max<-1.2*findyaxmax(c(Surface_ammonia_offshore_id,
Deep_ammonia_offshore_id,
Surface_ammonia_inshore_id))
C3max<-1.2*findyaxmax(c(Surface_nitrate_offshore_id,
Deep_nitrate_offshore_id,
Surface_nitrate_inshore_id))
C4max<-1.2*findyaxmax(c(Surface_phytoplankton_offshore_id,
Deep_phytoplankton_offshore_id,
Surface_phytoplankton_inshore_id))
unitsize<-0.5
unitline<- -0.3
unitadj<- -0.7
par(mfrow=c(3,4))
VtoGet<-Surface_detritus_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_ammonia_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_nitrate_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_phytoplankton_offshore_id
tspmain<-"Offshore zone upper layer"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_detritus_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_ammonia_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_nitrate_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Deep_phytoplankton_offshore_id
tspmain<-"Offshore zone lower layer"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_detritus_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Suspended bact & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_ammonia_inshore_id
tspmain<-"Inshore zone"
axtitle<-" Ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_nitrate_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Surface_phytoplankton_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Phytoplankton"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "SEDIMENT") {
#SEABED DETRITUS AND NUTRIENTS
Sediment_detritus_N_by_weight_offshore_mud_id <-grep("Sediment_detritus_N%_by_weight_offshore_mud",row.names(Result_data_store))
Sediment_detritus_N_by_weight_offshore_sand_id <-grep("Sediment_detritus_N%_by_weight_offshore_sand",row.names(Result_data_store))
Sediment_detritus_N_by_weight_inshore_mud_id <-grep("Sediment_detritus_N%_by_weight_inshore_mud",row.names(Result_data_store))
Sediment_detritus_N_by_weight_inshore_sand_id <-grep("Sediment_detritus_N%_by_weight_inshore_sand",row.names(Result_data_store))
Porewater_nitrate_offshore_mud_id <-grep("Porewater_nitrate_offshore_mud",row.names(Result_data_store))
Porewater_nitrate_offshore_sand_id <-grep("Porewater_nitrate_offshore_sand",row.names(Result_data_store))
Porewater_nitrate_inshore_mud_id <-grep("Porewater_nitrate_inshore_mud",row.names(Result_data_store))
Porewater_nitrate_inshore_sand_id <-grep("Porewater_nitrate_inshore_sand",row.names(Result_data_store))
Porewater_ammonia_offshore_mud_id <-grep("Porewater_ammonia_offshore_mud",row.names(Result_data_store))
Porewater_ammonia_offshore_sand_id <-grep("Porewater_ammonia_offshore_sand",row.names(Result_data_store))
Porewater_ammonia_inshore_mud_id <-grep("Porewater_ammonia_inshore_mud",row.names(Result_data_store))
Porewater_ammonia_inshore_sand_id <-grep("Porewater_ammonia_inshore_sand",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Sediment_detritus_N_by_weight_offshore_mud_id,
Sediment_detritus_N_by_weight_offshore_sand_id,
Sediment_detritus_N_by_weight_inshore_mud_id,
Sediment_detritus_N_by_weight_inshore_sand_id))
C2max<-1.2*findyaxmax(c(Porewater_nitrate_offshore_mud_id,
Porewater_nitrate_offshore_sand_id,
Porewater_nitrate_inshore_mud_id,
Porewater_nitrate_inshore_sand_id))
C3max<-1.2*findyaxmax(c(Porewater_ammonia_offshore_mud_id,
Porewater_ammonia_offshore_sand_id,
Porewater_ammonia_inshore_mud_id,
Porewater_ammonia_inshore_sand_id))
unitsize<-0.55
unitline<-0.35
unitadj<- -0.25
par(mfrow=c(4,3))
VtoGet<-Sediment_detritus_N_by_weight_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_offshore_mud_id
tspmain<-"Offshore mud"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_offshore_sand_id
tspmain<-"Offshore sand"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_inshore_mud_id
tspmain<-"Inshore mud"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Sediment_detritus_N_by_weight_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Sediment bact. & detritus"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("gN.gDW"^-1),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_nitrate_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Porewater nitrate"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Porewater_ammonia_inshore_sand_id
tspmain<-"Inshore sand"
axtitle<-"Porewater ammonia"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-3),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "ZOOPLANKTON") {
#ZOOPLANKTON
Omnivorous_zooplankton_offshore_id <-grep("Omnivorous_zooplankton_offshore",row.names(Result_data_store))
Omnivorous_zooplankton_inshore_id <-grep("Omnivorous_zooplankton_inshore",row.names(Result_data_store))
Carnivorous_zooplankton_offshore_id <-grep("Carnivorous_zooplankton_offshore",row.names(Result_data_store))
Carnivorous_zooplankton_inshore_id <-grep("Carnivorous_zooplankton_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Omnivorous_zooplankton_offshore_id,
Omnivorous_zooplankton_inshore_id))
C2max<-1.2*findyaxmax(c(Carnivorous_zooplankton_offshore_id,
Carnivorous_zooplankton_inshore_id))
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Omnivorous_zooplankton_offshore_id
tspmain<-"Offshore zone "
axtitle<-"Omnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivorous_zooplankton_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Omnivorous_zooplankton_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Omnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivorous_zooplankton_inshore_id
tspmain<-"Inshore zone "
axtitle<-"Carnivorous zooplankton"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "FISH") {
#FISH AND FISH LARVAE
Planktivorous_fish_offshore_id <-grep("Planktivorous_fish_offshore",row.names(Result_data_store))
Planktivorous_fish_larvae_offshore_id <-grep("Planktivorous_fish_larvae_offshore",row.names(Result_data_store))
Demersal_fish_offshore_id <-grep("Demersal_fish_offshore",row.names(Result_data_store))
Demersal_fish_larvae_offshore_id <-grep("Demersal_fish_larvae_offshore",row.names(Result_data_store))
Planktivorous_fish_inshore_id <-grep("Planktivorous_fish_inshore",row.names(Result_data_store))
Planktivorous_fish_larvae_inshore_id <-grep("Planktivorous_fish_larvae_inshore",row.names(Result_data_store))
Demersal_fish_inshore_id <-grep("Demersal_fish_inshore",row.names(Result_data_store))
Demersal_fish_larvae_inshore_id <-grep("Demersal_fish_larvae_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Planktivorous_fish_offshore_id,
Planktivorous_fish_inshore_id))
C2max<-1.2*findyaxmax(c(Planktivorous_fish_larvae_offshore_id,
Planktivorous_fish_larvae_inshore_id))
C3max<-1.2*findyaxmax(c(Demersal_fish_offshore_id,
Demersal_fish_inshore_id))
C4max<-1.2*findyaxmax(c(Demersal_fish_larvae_offshore_id,
Demersal_fish_larvae_inshore_id))
unitsize<-0.55
unitline<- -0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Planktivorous_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Planktivorous fish"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Planktivorous fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Demersal fish"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Demersal fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Planktivorous fish"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Planktivorous_fish_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Planktivorous fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Demersal fish"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Demersal_fish_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Demersal fish larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "BENTHOS") {
#BENTHOS AND BENTHOS LARVAE
Suspension_deposit_benthos_offshore_id <-grep("Suspension_deposit_benthos_offshore",row.names(Result_data_store))
Suspension_deposit_benthos_larvae_offshore_id <-grep("Suspension_deposit_benthos_larvae_offshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_offshore_id <-grep("Carnivore_scavenge_benthos_offshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_larvae_offshore_id <-grep("Carnivore_scavenge_benthos_larvae_offshore",row.names(Result_data_store))
Suspension_deposit_benthos_inshore_id <-grep("Suspension_deposit_benthos_inshore",row.names(Result_data_store))
Suspension_deposit_benthos_larvae_inshore_id <-grep("Suspension_deposit_benthos_larvae_inshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_inshore_id <-grep("Carnivore_scavenge_benthos_inshore",row.names(Result_data_store))
Carnivore_scavenge_benthos_larvae_inshore_id <-grep("Carnivore_scavenge_benthos_larvae_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Suspension_deposit_benthos_offshore_id,
Suspension_deposit_benthos_inshore_id))
C2max<-1.2*findyaxmax(c(Suspension_deposit_benthos_larvae_offshore_id,
Suspension_deposit_benthos_larvae_inshore_id))
C3max<-1.2*findyaxmax(c(Carnivore_scavenge_benthos_offshore_id,
Carnivore_scavenge_benthos_inshore_id))
C4max<-1.2*findyaxmax(c(Carnivore_scavenge_benthos_larvae_offshore_id,
Carnivore_scavenge_benthos_larvae_inshore_id))
unitsize<-0.55
unitline<- - 0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Suspension_deposit_benthos_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Susp./dep. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Susp./dep. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carn./scav. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_larvae_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Carn./scav. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Susp./dep. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Suspension_deposit_benthos_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Susp./dep. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Carn./scav. benthos"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Carnivore_scavenge_benthos_larvae_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Carn./scav. benthos larvae"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "PREDATORS") {
#BIRDS/MAMMALS, MIGRATORY FISH
Birds_offshore_id <-grep("Birds_offshore",row.names(Result_data_store))
Seals_offshore_id <-grep("Pinnipeds_offshore",row.names(Result_data_store))
Cetaceans_offshore_id <-grep("Cetaceans_offshore",row.names(Result_data_store))
Migratory_fish_inshore_id <-grep("Migratory_fish_inshore",row.names(Result_data_store))
Birds_inshore_id <-grep("Birds_inshore",row.names(Result_data_store))
Seals_inshore_id <-grep("Pinnipeds_inshore",row.names(Result_data_store))
Cetaceans_inshore_id <-grep("Cetaceans_inshore",row.names(Result_data_store))
Migratory_fish_offshore_id <-grep("Migratory_fish_offshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Birds_offshore_id,
Birds_inshore_id))
C2max<-1.2*findyaxmax(c(Seals_offshore_id,
Seals_inshore_id))
C3max<-1.2*findyaxmax(c(Cetaceans_offshore_id,
Cetaceans_inshore_id))
C4max<-1.2*findyaxmax(c(Migratory_fish_inshore_id,
Migratory_fish_offshore_id))
unitsize<-0.55
unitline<- - 0.15
unitadj<- -0.9
par(mfrow=c(2,4))
VtoGet<-Birds_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Birds"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Seals_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Pinnipeds"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Cetaceans_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Cetaceans"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Migratory_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Migratory fish"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Birds_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Birds"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Seals_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Pinnipeds"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Cetaceans_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Cetaceans"
tsplotCI(tspmain,axtitle,VtoGet,C3max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Migratory_fish_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Migratory fish"
tsplotCI(tspmain,axtitle,VtoGet,C4max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "CORP_DISC") {
#CORPSES and DISCARDS
Corpses_offshore_id <-grep("Corpses_offshore",row.names(Result_data_store))
Discards_offshore_id <-grep("Discards_offshore",row.names(Result_data_store))
Corpses_inshore_id <-grep("Corpses_inshore",row.names(Result_data_store))
Discards_inshore_id <-grep("Discards_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(c(Corpses_offshore_id,
Corpses_inshore_id))
C2max<-1.2*findyaxmax(c(Discards_offshore_id,
Discards_inshore_id))
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Corpses_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Seabed corpses"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Discards_offshore_id
tspmain<-"Offshore zone"
axtitle<-"Fishery discards"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Corpses_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Seabed corpses"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Discards_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Fishery discards"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else if (selection == "MACROPHYTE") {
#KELP and KELP DEBRIS
Kelp_inshore_id <-grep("Macrophytes_inshore",row.names(Result_data_store))
Kelp_debris_inshore_id <-grep("Macrophyte_debris_inshore",row.names(Result_data_store))
C1max<-1.2*findyaxmax(Kelp_inshore_id)
C2max<-1.2*findyaxmax(Kelp_debris_inshore_id)
unitsize<-0.65
unitline<-0.35
unitadj<- -0.2
par(mfrow=c(2,2))
VtoGet<-Kelp_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Macrophytes"
tsplotCI(tspmain,axtitle,VtoGet,C1max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
VtoGet<-Kelp_debris_inshore_id
tspmain<-"Inshore zone"
axtitle<-"Macrophyte debris"
tsplotCI(tspmain,axtitle,VtoGet,C2max)
# mtext(bquote("mMN.m"^-2),cex=unitsize,side=3,line=unitline,adj=unitadj)
# ---------------------------------------------------------------------------------
} else {
stop("Error: unknown plot selection '", selection, "' !\n")
}
}
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