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R/plot_final_year_time_series_data.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
plot_final_year_time_series_data
#
# plot_final_year_time_series_data.R
#
#' Plots of inshore and offshore low trophic level state variables for the final year of a model run
#'
#' Multi-panel time series plots of inshore and offshore low trophic level state variables for the final year of a model run generated by the e2e_run() function
#'
#' The function plots a multi-panel page of time series plots of daily values of nutrients, detritus, macrophyte, phytoplankton, zooplankton and suspension/deposit feeding benthos (including larvae) for the inshore zone and upper and lower levels of the offshore zone, for the final year of a model run.
#'
#' Units of the plotted varaiables are mass concentrations, scaled to seas surface area or layer volume, ie. mMN/m2 or mMN/m3
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param results R-list object containing model results generated by the e2e_run() 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.
#'
#' @return Graphical display in a new graphics window
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_final_year_time_series_data <- function(model, results, selection="NUT_PHYT") {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
build <- elt(results, "build")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
data <- elt(model, "data")
physical.parameters <- elt(data, "physical.parameters")
si_depth <- elt(physical.parameters, "si_depth")
so_depth <- elt(physical.parameters, "so_depth")
d_depth <- elt(physical.parameters, "d_depth")
x_shallowprop <- elt(physical.parameters, "x_shallowprop")
x_poros_s1 <- elt(physical.parameters, "x_poros_s1")
x_poros_s2 <- elt(physical.parameters, "x_poros_s2")
x_poros_s3 <- elt(physical.parameters, "x_poros_s3")
x_area_s1 <- elt(physical.parameters, "x_area_s1")
x_area_s2 <- elt(physical.parameters, "x_area_s2")
x_area_s3 <- elt(physical.parameters, "x_area_s3")
x_depth_s1 <- elt(physical.parameters, "x_depth_s1")
x_depth_s2 <- elt(physical.parameters, "x_depth_s2")
x_depth_s3 <- elt(physical.parameters, "x_depth_s3")
x_poros_d1 <- elt(physical.parameters, "x_poros_d1")
x_poros_d2 <- elt(physical.parameters, "x_poros_d2")
x_poros_d3 <- elt(physical.parameters, "x_poros_d3")
x_area_d1 <- elt(physical.parameters, "x_area_d1")
x_area_d2 <- elt(physical.parameters, "x_area_d2")
x_area_d3 <- elt(physical.parameters, "x_area_d3")
x_depth_d1 <- elt(physical.parameters, "x_depth_d1")
x_depth_d2 <- elt(physical.parameters, "x_depth_d2")
x_depth_d3 <- elt(physical.parameters, "x_depth_d3")
output <- elt(results, "output")
corpse_d1 <- elt(output, "corpse_d1")
corpse_d2 <- elt(output, "corpse_d2")
corpse_d3 <- elt(output, "corpse_d3")
corpse_s1 <- elt(output, "corpse_s1")
corpse_s2 <- elt(output, "corpse_s2")
corpse_s3 <- elt(output, "corpse_s3")
kelpdebris <- elt(output, "kelpdebris")
detritus_so <- elt(output, "detritus_so")
detritus_si <- elt(output, "detritus_si")
detritus_d <- elt(output, "detritus_d")
nitrate_so <- elt(output, "nitrate_so")
nitrate_si <- elt(output, "nitrate_si")
nitrate_d <- elt(output, "nitrate_d")
ammonia_so <- elt(output, "ammonia_so")
ammonia_si <- elt(output, "ammonia_si")
ammonia_d <- elt(output, "ammonia_d")
phyt_so <- elt(output, "phyt_so")
phyt_si <- elt(output, "phyt_si")
phyt_d <- elt(output, "phyt_d")
omni_o <- elt(output, "omni_o")
omni_i <- elt(output, "omni_i")
carn_o <- elt(output, "carn_o")
carn_i <- elt(output, "carn_i")
benths_o <- elt(output, "benths_o")
benths_i <- elt(output, "benths_i")
kelpN <- elt(output, "kelpN")
benthslar_o <- elt(output, "benthslar_o")
benthslar_i <- elt(output, "benthslar_i")
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")
discard_o <- elt(output, "discard_o")
discard_i <- elt(output, "discard_i")
x_ammonia_s1 <- elt(output, "x_ammonia_s1")
x_ammonia_s2 <- elt(output, "x_ammonia_s2")
x_ammonia_s3 <- elt(output, "x_ammonia_s3")
x_ammonia_d1 <- elt(output, "x_ammonia_d1")
x_ammonia_d2 <- elt(output, "x_ammonia_d2")
x_ammonia_d3 <- elt(output, "x_ammonia_d3")
x_nitrate_s1 <- elt(output, "x_nitrate_s1")
x_nitrate_s2 <- elt(output, "x_nitrate_s2")
x_nitrate_s3 <- elt(output, "x_nitrate_s3")
x_nitrate_d1 <- elt(output, "x_nitrate_d1")
x_nitrate_d2 <- elt(output, "x_nitrate_d2")
x_nitrate_d3 <- elt(output, "x_nitrate_d3")
x_detritus_s1 <- elt(output, "x_detritus_s1")
xR_detritus_s1 <- elt(output, "xR_detritus_s1")
x_detritus_s2 <- elt(output, "x_detritus_s2")
xR_detritus_s2 <- elt(output, "xR_detritus_s2")
x_detritus_s3 <- elt(output, "x_detritus_s3")
xR_detritus_s3 <- elt(output, "xR_detritus_s3")
x_detritus_d1 <- elt(output, "x_detritus_d1")
xR_detritus_d1 <- elt(output, "xR_detritus_d1")
x_detritus_d2 <- elt(output, "x_detritus_d2")
xR_detritus_d2 <- elt(output, "xR_detritus_d2")
x_detritus_d3 <- elt(output, "x_detritus_d3")
xR_detritus_d3 <- elt(output, "xR_detritus_d3")
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)
# ...................................................................
if(selection=="NUT_PHYT"){
#Plots the final year of output for water column detritus, nutrients and phytoplankton
# par(mfrow=c(3,4))
par(mfrow=c(2,2))
l1<-detritus_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-detritus_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-detritus_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Suspended bact. & detritus","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-ammonia_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-ammonia_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-ammonia_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Ammonia","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-nitrate_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-nitrate_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-nitrate_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Nitrate","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-phyt_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-phyt_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-phyt_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Phytoplankton","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="SEDIMENT"){
#Plot the final year of output for the sediment habitats separately
#Plots are:
# Shallow layer - wc ammonia, hab1 pw ammonia, hab2 pw ammonia, hab3 pw ammonia
# Deep layer - wc ammonia, hab1 pw ammonia, hab2 pw ammonia, hab3 pw ammonia
# Shallow layer - wc nitrate, hab1 pw nitrate, hab2 pw nitrate, hab3 pw nitrate
# Deep layer - wc nitrate, hab1 pw nitrate, hab2 pw nitrate, hab3 pw nitrate
# Shallow layer - wc detritus, hab1 detritus, hab2 detritus, hab3 pw detritus
# Deep layer - wc detritus, hab1 detritus, hab2 detritus, hab3 pw detritus
par(mfrow=c(4,2))
#Shallow sediment ammonia
#Converts the sediment ammonia into units of N /m3 in the pore water)
if(x_poros_s1>0 && x_area_s1>0){
l1<-x_ammonia_s1[((nyears-1)*360+1):ndays]/(x_area_s1*x_depth_s1*x_poros_s1)
} else {
l1<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2<-x_ammonia_s2[((nyears-1)*360+1):ndays]/(x_area_s2*x_depth_s2*x_poros_s2)
} else {
l2<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3<-x_ammonia_s3[((nyears-1)*360+1):ndays]/(x_area_s3*x_depth_s3*x_poros_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore ammonia","","Area_s1 porewater","Area_s2 porewater","Area_s3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment ammonia
#Converts the sediment ammonia into units of N /m3 in the pore water)
if(x_poros_d1>0 && x_area_d1>0){
l1<-x_ammonia_d1[((nyears-1)*360+1):ndays]/(x_area_d1*x_depth_d1*x_poros_d1)
} else {
l1<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2<-x_ammonia_d2[((nyears-1)*360+1):ndays]/(x_area_d2*x_depth_d2*x_poros_d2)
} else {
l2<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3<-x_ammonia_d3[((nyears-1)*360+1):ndays]/(x_area_d3*x_depth_d3*x_poros_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore ammonia","","Area_d1 porewater","Area_d2 porewater","Area_d3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment nitrate
#Converts the sediment nitrate into units of N /m3 in the pore water)
if(x_poros_s1>0 && x_area_s1>0){
l1<-x_nitrate_s1[((nyears-1)*360+1):ndays]/(x_area_s1*x_depth_s1*x_poros_s1)
} else {
l1<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2<-x_nitrate_s2[((nyears-1)*360+1):ndays]/(x_area_s2*x_depth_s2*x_poros_s2)
} else {
l3<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3<-x_nitrate_s3[((nyears-1)*360+1):ndays]/(x_area_s3*x_depth_s3*x_poros_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore nitrate","","Area_s1 porewater","Area_s2 porewater","Area_s3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment nitrate
#Converts the sediment nitrate into units of N /m3 in the pore water)
if(x_poros_d1>0 && x_area_d1>0){
l1<-x_nitrate_d1[((nyears-1)*360+1):ndays]/(x_area_d1*x_depth_d1*x_poros_d1)
} else {
l1<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2<-x_nitrate_d2[((nyears-1)*360+1):ndays]/(x_area_d2*x_depth_d2*x_poros_d2)
} else {
l2<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3<-x_nitrate_d3[((nyears-1)*360+1):ndays]/(x_area_d3*x_depth_d3*x_poros_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore nitrate","","Area_d1 porewater","Area_d2 porewater","Area_d3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment total detritus
#Converts the sediment detritus into units of %N by dry wt (100*gN/g-drysediment) (density of dry solid matter = 2.65g/cm3)
if(x_poros_s1>0 && x_area_s1>0){
l1a<-100*(((x_detritus_s1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s1*x_depth_s1*(((1-x_poros_s1)*(2650*1000))))
l1b<-100*(((xR_detritus_s1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s1*x_depth_s1*(((1-x_poros_s1)*(2650*1000))))
} else {
l1a<-rep(NA,361)
l1b<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2a<-100*(((x_detritus_s2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s2*x_depth_s2*(((1-x_poros_s2)*(2650*1000))))
l2b<-100*(((xR_detritus_s2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s2*x_depth_s2*(((1-x_poros_s2)*(2650*1000))))
} else {
l2a<-rep(NA,361)
l2b<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3a<-100*(((x_detritus_s3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s3*x_depth_s3*(((1-x_poros_s3)*(2650*1000))))
l3b<-100*(((xR_detritus_s3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s3*x_depth_s3*(((1-x_poros_s3)*(2650*1000))))
} else {
l3a<-rep(NA,361)
l3b<-rep(NA,361)
}
l1<-l1a+l1b
l2<-l2a+l2b
l3<-l3a+l3b
fyplot3_hab("Inshore detritus","","Area_s1 sediment","Area_s2 sediment","Area_s3 sediment",l1,l2,l3)
mtext(bquote("Nitrogen.DW"^-1 ~ " g.g"^-1),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment total detritus
#Converts the sediment detritus into units of %N by dry wt (100*gN/g-drysediment) (density of dry solid matter = 2.65g/cm3)
if(x_poros_d1>0 && x_area_d1>0){
l1a<-100*(((x_detritus_d1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d1*x_depth_d1*(((1-x_poros_d1)*(2650*1000))))
l1b<-100*(((xR_detritus_d1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d1*x_depth_d1*(((1-x_poros_d1)*(2650*1000))))
} else {
l1a<-rep(NA,361)
l1b<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2a<-100*(((x_detritus_d2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d2*x_depth_d2*(((1-x_poros_d2)*(2650*1000))))
l2b<-100*(((xR_detritus_d2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d2*x_depth_d2*(((1-x_poros_d2)*(2650*1000))))
} else {
l2a<-rep(NA,361)
l2b<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3a<-100*(((x_detritus_d3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d3*x_depth_d3*(((1-x_poros_d3)*(2650*1000))))
l3b<-100*(((xR_detritus_d3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d3*x_depth_d3*(((1-x_poros_d3)*(2650*1000))))
} else {
l3a<-rep(NA,361)
l3b<-rep(NA,361)
}
l1<-l1a+l1b
l2<-l2a+l2b
l3<-l3a+l3b
fyplot3_hab("Offshore detritus","","Area_d1 sediment","Area_d2 sediment","Area_d3 sediment",l1,l2,l3)
mtext(bquote("Nitrogen.DW"^-1 ~ " g.g"^-1),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment corpses
#Converts the sediment corpse mass into units of N /m2 of sediment surface)
if(x_area_s1>0){
l1<-corpse_s1[((nyears-1)*360+1):ndays]/(x_area_s1)
} else {
l1<-rep(NA,361)
}
if(x_area_s2>0){
l2<-corpse_s2[((nyears-1)*360+1):ndays]/(x_area_s2)
} else {
l2<-rep(NA,361)
}
if(x_area_s3>0){
l3<-corpse_s3[((nyears-1)*360+1):ndays]/(x_area_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore corpses","","Area_s1","Area_s2","Area_s3",l1,l2,l3)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment corpses
#Converts the sediment corpse mass into units of N /m2 of sediment surface)
if(x_area_d1>0){
l1<-corpse_d1[((nyears-1)*360+1):ndays]/(x_area_d1)
} else {
l1<-rep(NA,361)
}
if(x_area_d2>0){
l2<-corpse_d2[((nyears-1)*360+1):ndays]/(x_area_d2)
} else {
l2<-rep(NA,361)
}
if(x_area_d3>0){
l3<-corpse_d3[((nyears-1)*360+1):ndays]/(x_area_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore corpses","","Area_d1","Area_d2","Area_d3",l1,l2,l3)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="ZOOPLANKTON"){
par(mfrow=c(2,2))
l1<-omni_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-omni_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Omnivorous zooplankton","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-carn_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-carn_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Carnivorous zooplankton","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="FISH"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-fishp_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishp_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Planktivorous fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishplar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishplar_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Planktivorous fish larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishd_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishd_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Demersal fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishdlar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishdlar_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Demersal fish larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="BENTHOS"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-benths_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-benths_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Benthos susp/dep feeders","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthslar_o[((nyears-1)*360+1):ndays]/(xvolume_so+xd_volume)
l2<-benthslar_i[((nyears-1)*360+1):ndays]/xvolume_si
fyplot2("Benthos susp/dep feeders larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthc_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-benthc_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Benthos carn/scav feeders","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthclar_o[((nyears-1)*360+1):ndays]/(xvolume_so+xd_volume)
l2<-benthclar_i[((nyears-1)*360+1):ndays]/xvolume_si
fyplot2("Benthos carn/scav feeders larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="PREDATORS"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-bird_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-bird_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Birds","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-seal_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-seal_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Pinnipeds","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-ceta_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-ceta_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Cetaceans","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishm_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishm_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Migratory fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="CORP_DISC"){
par(mfrow=c(2,2))
l1<-(corpse_d1[((nyears-1)*360+1):ndays]+corpse_d2[((nyears-1)*360+1):ndays]+corpse_d3[((nyears-1)*360+1):ndays])/(1-x_shallowprop)
l2<-(corpse_s1[((nyears-1)*360+1):ndays]+corpse_s2[((nyears-1)*360+1):ndays]+corpse_s3[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot2("Corpses","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-(discard_o[((nyears-1)*360+1):ndays])/(1-x_shallowprop)
l2<-(discard_i[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot2("Discards","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="MACROPHYTE"){
par(mfrow=c(2,2))
l1<-kelpN[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
fyplot1("Inshore macrophytes","",l1)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-(kelpdebris[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot1("Inshore macrophyte debris","",l1)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else {
stop("Error: unknown selection '", selection, "' !\n")
}
#...........................................................
}
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Defines functions plot_final_year_time_series_data
#
# plot_final_year_time_series_data.R
#
#' Plots of inshore and offshore low trophic level state variables for the final year of a model run
#'
#' Multi-panel time series plots of inshore and offshore low trophic level state variables for the final year of a model run generated by the e2e_run() function
#'
#' The function plots a multi-panel page of time series plots of daily values of nutrients, detritus, macrophyte, phytoplankton, zooplankton and suspension/deposit feeding benthos (including larvae) for the inshore zone and upper and lower levels of the offshore zone, for the final year of a model run.
#'
#' Units of the plotted varaiables are mass concentrations, scaled to seas surface area or layer volume, ie. mMN/m2 or mMN/m3
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param results R-list object containing model results generated by the e2e_run() 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.
#'
#' @return Graphical display in a new graphics window
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_final_year_time_series_data <- function(model, results, selection="NUT_PHYT") {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
build <- elt(results, "build")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
data <- elt(model, "data")
physical.parameters <- elt(data, "physical.parameters")
si_depth <- elt(physical.parameters, "si_depth")
so_depth <- elt(physical.parameters, "so_depth")
d_depth <- elt(physical.parameters, "d_depth")
x_shallowprop <- elt(physical.parameters, "x_shallowprop")
x_poros_s1 <- elt(physical.parameters, "x_poros_s1")
x_poros_s2 <- elt(physical.parameters, "x_poros_s2")
x_poros_s3 <- elt(physical.parameters, "x_poros_s3")
x_area_s1 <- elt(physical.parameters, "x_area_s1")
x_area_s2 <- elt(physical.parameters, "x_area_s2")
x_area_s3 <- elt(physical.parameters, "x_area_s3")
x_depth_s1 <- elt(physical.parameters, "x_depth_s1")
x_depth_s2 <- elt(physical.parameters, "x_depth_s2")
x_depth_s3 <- elt(physical.parameters, "x_depth_s3")
x_poros_d1 <- elt(physical.parameters, "x_poros_d1")
x_poros_d2 <- elt(physical.parameters, "x_poros_d2")
x_poros_d3 <- elt(physical.parameters, "x_poros_d3")
x_area_d1 <- elt(physical.parameters, "x_area_d1")
x_area_d2 <- elt(physical.parameters, "x_area_d2")
x_area_d3 <- elt(physical.parameters, "x_area_d3")
x_depth_d1 <- elt(physical.parameters, "x_depth_d1")
x_depth_d2 <- elt(physical.parameters, "x_depth_d2")
x_depth_d3 <- elt(physical.parameters, "x_depth_d3")
output <- elt(results, "output")
corpse_d1 <- elt(output, "corpse_d1")
corpse_d2 <- elt(output, "corpse_d2")
corpse_d3 <- elt(output, "corpse_d3")
corpse_s1 <- elt(output, "corpse_s1")
corpse_s2 <- elt(output, "corpse_s2")
corpse_s3 <- elt(output, "corpse_s3")
kelpdebris <- elt(output, "kelpdebris")
detritus_so <- elt(output, "detritus_so")
detritus_si <- elt(output, "detritus_si")
detritus_d <- elt(output, "detritus_d")
nitrate_so <- elt(output, "nitrate_so")
nitrate_si <- elt(output, "nitrate_si")
nitrate_d <- elt(output, "nitrate_d")
ammonia_so <- elt(output, "ammonia_so")
ammonia_si <- elt(output, "ammonia_si")
ammonia_d <- elt(output, "ammonia_d")
phyt_so <- elt(output, "phyt_so")
phyt_si <- elt(output, "phyt_si")
phyt_d <- elt(output, "phyt_d")
omni_o <- elt(output, "omni_o")
omni_i <- elt(output, "omni_i")
carn_o <- elt(output, "carn_o")
carn_i <- elt(output, "carn_i")
benths_o <- elt(output, "benths_o")
benths_i <- elt(output, "benths_i")
kelpN <- elt(output, "kelpN")
benthslar_o <- elt(output, "benthslar_o")
benthslar_i <- elt(output, "benthslar_i")
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")
discard_o <- elt(output, "discard_o")
discard_i <- elt(output, "discard_i")
x_ammonia_s1 <- elt(output, "x_ammonia_s1")
x_ammonia_s2 <- elt(output, "x_ammonia_s2")
x_ammonia_s3 <- elt(output, "x_ammonia_s3")
x_ammonia_d1 <- elt(output, "x_ammonia_d1")
x_ammonia_d2 <- elt(output, "x_ammonia_d2")
x_ammonia_d3 <- elt(output, "x_ammonia_d3")
x_nitrate_s1 <- elt(output, "x_nitrate_s1")
x_nitrate_s2 <- elt(output, "x_nitrate_s2")
x_nitrate_s3 <- elt(output, "x_nitrate_s3")
x_nitrate_d1 <- elt(output, "x_nitrate_d1")
x_nitrate_d2 <- elt(output, "x_nitrate_d2")
x_nitrate_d3 <- elt(output, "x_nitrate_d3")
x_detritus_s1 <- elt(output, "x_detritus_s1")
xR_detritus_s1 <- elt(output, "xR_detritus_s1")
x_detritus_s2 <- elt(output, "x_detritus_s2")
xR_detritus_s2 <- elt(output, "xR_detritus_s2")
x_detritus_s3 <- elt(output, "x_detritus_s3")
xR_detritus_s3 <- elt(output, "xR_detritus_s3")
x_detritus_d1 <- elt(output, "x_detritus_d1")
xR_detritus_d1 <- elt(output, "xR_detritus_d1")
x_detritus_d2 <- elt(output, "x_detritus_d2")
xR_detritus_d2 <- elt(output, "xR_detritus_d2")
x_detritus_d3 <- elt(output, "x_detritus_d3")
xR_detritus_d3 <- elt(output, "xR_detritus_d3")
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)
# ...................................................................
if(selection=="NUT_PHYT"){
#Plots the final year of output for water column detritus, nutrients and phytoplankton
# par(mfrow=c(3,4))
par(mfrow=c(2,2))
l1<-detritus_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-detritus_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-detritus_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Suspended bact. & detritus","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-ammonia_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-ammonia_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-ammonia_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Ammonia","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-nitrate_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-nitrate_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-nitrate_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Nitrate","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
l1<-phyt_so[((nyears-1)*360+1):ndays]/xvolume_so
l2<-phyt_si[((nyears-1)*360+1):ndays]/xvolume_si
l3<-phyt_d[((nyears-1)*360+1):ndays]/xd_volume
fyplot3("Phytoplankton","","S-offshore","S-inshore","Deep",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="SEDIMENT"){
#Plot the final year of output for the sediment habitats separately
#Plots are:
# Shallow layer - wc ammonia, hab1 pw ammonia, hab2 pw ammonia, hab3 pw ammonia
# Deep layer - wc ammonia, hab1 pw ammonia, hab2 pw ammonia, hab3 pw ammonia
# Shallow layer - wc nitrate, hab1 pw nitrate, hab2 pw nitrate, hab3 pw nitrate
# Deep layer - wc nitrate, hab1 pw nitrate, hab2 pw nitrate, hab3 pw nitrate
# Shallow layer - wc detritus, hab1 detritus, hab2 detritus, hab3 pw detritus
# Deep layer - wc detritus, hab1 detritus, hab2 detritus, hab3 pw detritus
par(mfrow=c(4,2))
#Shallow sediment ammonia
#Converts the sediment ammonia into units of N /m3 in the pore water)
if(x_poros_s1>0 && x_area_s1>0){
l1<-x_ammonia_s1[((nyears-1)*360+1):ndays]/(x_area_s1*x_depth_s1*x_poros_s1)
} else {
l1<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2<-x_ammonia_s2[((nyears-1)*360+1):ndays]/(x_area_s2*x_depth_s2*x_poros_s2)
} else {
l2<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3<-x_ammonia_s3[((nyears-1)*360+1):ndays]/(x_area_s3*x_depth_s3*x_poros_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore ammonia","","Area_s1 porewater","Area_s2 porewater","Area_s3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment ammonia
#Converts the sediment ammonia into units of N /m3 in the pore water)
if(x_poros_d1>0 && x_area_d1>0){
l1<-x_ammonia_d1[((nyears-1)*360+1):ndays]/(x_area_d1*x_depth_d1*x_poros_d1)
} else {
l1<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2<-x_ammonia_d2[((nyears-1)*360+1):ndays]/(x_area_d2*x_depth_d2*x_poros_d2)
} else {
l2<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3<-x_ammonia_d3[((nyears-1)*360+1):ndays]/(x_area_d3*x_depth_d3*x_poros_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore ammonia","","Area_d1 porewater","Area_d2 porewater","Area_d3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment nitrate
#Converts the sediment nitrate into units of N /m3 in the pore water)
if(x_poros_s1>0 && x_area_s1>0){
l1<-x_nitrate_s1[((nyears-1)*360+1):ndays]/(x_area_s1*x_depth_s1*x_poros_s1)
} else {
l1<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2<-x_nitrate_s2[((nyears-1)*360+1):ndays]/(x_area_s2*x_depth_s2*x_poros_s2)
} else {
l3<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3<-x_nitrate_s3[((nyears-1)*360+1):ndays]/(x_area_s3*x_depth_s3*x_poros_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore nitrate","","Area_s1 porewater","Area_s2 porewater","Area_s3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment nitrate
#Converts the sediment nitrate into units of N /m3 in the pore water)
if(x_poros_d1>0 && x_area_d1>0){
l1<-x_nitrate_d1[((nyears-1)*360+1):ndays]/(x_area_d1*x_depth_d1*x_poros_d1)
} else {
l1<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2<-x_nitrate_d2[((nyears-1)*360+1):ndays]/(x_area_d2*x_depth_d2*x_poros_d2)
} else {
l2<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3<-x_nitrate_d3[((nyears-1)*360+1):ndays]/(x_area_d3*x_depth_d3*x_poros_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore nitrate","","Area_d1 porewater","Area_d2 porewater","Area_d3 porewater",l1,l2,l3)
mtext(bquote("Concentration mMN.m"^-3),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment total detritus
#Converts the sediment detritus into units of %N by dry wt (100*gN/g-drysediment) (density of dry solid matter = 2.65g/cm3)
if(x_poros_s1>0 && x_area_s1>0){
l1a<-100*(((x_detritus_s1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s1*x_depth_s1*(((1-x_poros_s1)*(2650*1000))))
l1b<-100*(((xR_detritus_s1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s1*x_depth_s1*(((1-x_poros_s1)*(2650*1000))))
} else {
l1a<-rep(NA,361)
l1b<-rep(NA,361)
}
if(x_poros_s2>0 && x_area_s2>0){
l2a<-100*(((x_detritus_s2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s2*x_depth_s2*(((1-x_poros_s2)*(2650*1000))))
l2b<-100*(((xR_detritus_s2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s2*x_depth_s2*(((1-x_poros_s2)*(2650*1000))))
} else {
l2a<-rep(NA,361)
l2b<-rep(NA,361)
}
if(x_poros_s3>0 && x_area_s3>0){
l3a<-100*(((x_detritus_s3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s3*x_depth_s3*(((1-x_poros_s3)*(2650*1000))))
l3b<-100*(((xR_detritus_s3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_s3*x_depth_s3*(((1-x_poros_s3)*(2650*1000))))
} else {
l3a<-rep(NA,361)
l3b<-rep(NA,361)
}
l1<-l1a+l1b
l2<-l2a+l2b
l3<-l3a+l3b
fyplot3_hab("Inshore detritus","","Area_s1 sediment","Area_s2 sediment","Area_s3 sediment",l1,l2,l3)
mtext(bquote("Nitrogen.DW"^-1 ~ " g.g"^-1),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment total detritus
#Converts the sediment detritus into units of %N by dry wt (100*gN/g-drysediment) (density of dry solid matter = 2.65g/cm3)
if(x_poros_d1>0 && x_area_d1>0){
l1a<-100*(((x_detritus_d1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d1*x_depth_d1*(((1-x_poros_d1)*(2650*1000))))
l1b<-100*(((xR_detritus_d1[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d1*x_depth_d1*(((1-x_poros_d1)*(2650*1000))))
} else {
l1a<-rep(NA,361)
l1b<-rep(NA,361)
}
if(x_poros_d2>0 && x_area_d2>0){
l2a<-100*(((x_detritus_d2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d2*x_depth_d2*(((1-x_poros_d2)*(2650*1000))))
l2b<-100*(((xR_detritus_d2[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d2*x_depth_d2*(((1-x_poros_d2)*(2650*1000))))
} else {
l2a<-rep(NA,361)
l2b<-rep(NA,361)
}
if(x_poros_d3>0 && x_area_d3>0){
l3a<-100*(((x_detritus_d3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d3*x_depth_d3*(((1-x_poros_d3)*(2650*1000))))
l3b<-100*(((xR_detritus_d3[((nyears-1)*360+1):ndays])*14)/1000)/(x_area_d3*x_depth_d3*(((1-x_poros_d3)*(2650*1000))))
} else {
l3a<-rep(NA,361)
l3b<-rep(NA,361)
}
l1<-l1a+l1b
l2<-l2a+l2b
l3<-l3a+l3b
fyplot3_hab("Offshore detritus","","Area_d1 sediment","Area_d2 sediment","Area_d3 sediment",l1,l2,l3)
mtext(bquote("Nitrogen.DW"^-1 ~ " g.g"^-1),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Shallow sediment corpses
#Converts the sediment corpse mass into units of N /m2 of sediment surface)
if(x_area_s1>0){
l1<-corpse_s1[((nyears-1)*360+1):ndays]/(x_area_s1)
} else {
l1<-rep(NA,361)
}
if(x_area_s2>0){
l2<-corpse_s2[((nyears-1)*360+1):ndays]/(x_area_s2)
} else {
l2<-rep(NA,361)
}
if(x_area_s3>0){
l3<-corpse_s3[((nyears-1)*360+1):ndays]/(x_area_s3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Inshore corpses","","Area_s1","Area_s2","Area_s3",l1,l2,l3)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Deep sediment corpses
#Converts the sediment corpse mass into units of N /m2 of sediment surface)
if(x_area_d1>0){
l1<-corpse_d1[((nyears-1)*360+1):ndays]/(x_area_d1)
} else {
l1<-rep(NA,361)
}
if(x_area_d2>0){
l2<-corpse_d2[((nyears-1)*360+1):ndays]/(x_area_d2)
} else {
l2<-rep(NA,361)
}
if(x_area_d3>0){
l3<-corpse_d3[((nyears-1)*360+1):ndays]/(x_area_d3)
} else {
l3<-rep(NA,361)
}
fyplot3_hab("Offshore corpses","","Area_d1","Area_d2","Area_d3",l1,l2,l3)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="ZOOPLANKTON"){
par(mfrow=c(2,2))
l1<-omni_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-omni_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Omnivorous zooplankton","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-carn_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-carn_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Carnivorous zooplankton","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="FISH"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-fishp_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishp_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Planktivorous fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishplar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishplar_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Planktivorous fish larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishd_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishd_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Demersal fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishdlar_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishdlar_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Demersal fish larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="BENTHOS"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-benths_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-benths_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Benthos susp/dep feeders","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthslar_o[((nyears-1)*360+1):ndays]/(xvolume_so+xd_volume)
l2<-benthslar_i[((nyears-1)*360+1):ndays]/xvolume_si
fyplot2("Benthos susp/dep feeders larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthc_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-benthc_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Benthos carn/scav feeders","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-benthclar_o[((nyears-1)*360+1):ndays]/(xvolume_so+xd_volume)
l2<-benthclar_i[((nyears-1)*360+1):ndays]/xvolume_si
fyplot2("Benthos carn/scav feeders larvae","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="PREDATORS"){
# par(mfrow=c(4,2))
par(mfrow=c(2,2))
l1<-bird_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-bird_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Birds","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-seal_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-seal_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Pinnipeds","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-ceta_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-ceta_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Cetaceans","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-fishm_o[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
l2<-fishm_i[((nyears-1)*360+1):ndays]/x_shallowprop
fyplot2("Migratory fish","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="CORP_DISC"){
par(mfrow=c(2,2))
l1<-(corpse_d1[((nyears-1)*360+1):ndays]+corpse_d2[((nyears-1)*360+1):ndays]+corpse_d3[((nyears-1)*360+1):ndays])/(1-x_shallowprop)
l2<-(corpse_s1[((nyears-1)*360+1):ndays]+corpse_s2[((nyears-1)*360+1):ndays]+corpse_s3[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot2("Corpses","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-(discard_o[((nyears-1)*360+1):ndays])/(1-x_shallowprop)
l2<-(discard_i[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot2("Discards","","Offshore","Inshore",l1,l2)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else if(selection=="MACROPHYTE"){
par(mfrow=c(2,2))
l1<-kelpN[((nyears-1)*360+1):ndays]/(1-x_shallowprop)
fyplot1("Inshore macrophytes","",l1)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
l1<-(kelpdebris[((nyears-1)*360+1):ndays])/x_shallowprop
fyplot1("Inshore macrophyte debris","",l1)
mtext(bquote("Area density mMN.m"^-2),cex=0.7,side=2,line=2.5)
#...........................................................
} else {
stop("Error: unknown selection '", selection, "' !\n")
}
#...........................................................
}
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