Nothing
R/plot_inshore_vs_offshore_anavmass.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
plot_inshore_vs_offshore_anavmass
#
# plot_inshore_vs_offshore_anavmass.R
#
#' Plots of annual average inshore and offshore mass densities generated a StrathE2E simulation.
#'
#' Create a plot showing the distribution of annual average inshore and offshore mass densities over the final year of a simulation generated by the e2e_run() function.
#'
#' The format of the output is a single panel with rows symbols. Each row represents a different
#' state variable in the model (bacteria and detritus, phytoplankton etc etc). Each row consists of two symbols, one (red) for the offshore
#' zone and the other (blue) for the inshore zone. The data represented are values of the mass densities (mMn/m2) of each variable, averaged
#' over the final year of a model run.
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param use.saved Logical. If TRUE use data from a prior user-defined run held as csv files data in the current results folder, (default=FALSE).
#' @param results R-list object of baseline model output generated by the e2e_run(), (default=NULL).
#'
#' @return Graphical display in a new graphics window
#'
#' @importFrom graphics text
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_inshore_vs_offshore_anavmass <- function(model, use.saved=FALSE, results=NULL) {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
if(use.saved==FALSE & is.list(results)==FALSE){
stop("no source of data has been specified ! \n")
}
if(use.saved==TRUE & is.list(results)==TRUE){
stop("use.saved is TRUE but a results list object has also been specified ! \n")
}
if(use.saved==FALSE & is.list(results)==TRUE){
O_rawresults <- elt(results, "final.year.outputs", "mass_results_offshore")
I_rawresults <- elt(results, "final.year.outputs", "mass_results_inshore")
}
if(use.saved==TRUE & is.list(results)==FALSE){
resultsdir <- elt(model, "setup", "resultsdir")
model.ident <- elt(model, "setup", "model.ident")
# model.name <- elt(model, "setup", "model.name")
# model.variant <- elt(model, "setup", "model.variant")
datafile_o <- csvname(resultsdir, "OFFSHORE_model_anav_biomass", model.ident)
datafile_i <- csvname(resultsdir, "INSHORE_model_anav_biomass", model.ident)
message("Reading data from '", datafile_o, "'")
message("Reading data from '", datafile_i, "'")
O_rawresults<-readcsv(datafile_o)
I_rawresults<-readcsv(datafile_i)
}
shallowprop <- O_rawresults[which(O_rawresults$Description == "Area_proportion_of_inshore_zone"),1]
#Set up two dataframes to hold the area density data
O_results<-data.frame("total_labile_detritus_bd"=rep(NA,6),
"kelp_bd"=rep(NA,6),
"phyt_bd"=rep(NA,6),
"benth_susp_bd"=rep(NA,6),
"omni_bd"=rep(NA,6),
"benth_carn_bd"=rep(NA,6),
"carn_bd"=rep(NA,6),
"plankfish_bd"=rep(NA,6),
"migfish_bd"=rep(NA,6),
"demfish_bd"=rep(NA,6),
"bird_bd"=rep(NA,6),
"seal_bd"=rep(NA,6),
"ceta_bd"=rep(NA,6))
I_results<-O_results
# Rows in the raw input data....
#1 Surface_layer_detritus
#2 Deep_layer_detritus
#3 Sediment_labile_plus_refractory_detritus
#4 Sediment_refractory_detritus
#5 Fishery_discards
#6 Corpses
#7 Macrophyte_debris
#8 Surface_layer_ammonia
#9 Deep_layer_ammonia
#10 Sediment_porewater_ammonia
#11 Surface_layer_nitrate
#12 Deep_layer_nitrate
#13 Sediment_porewater_nitrate
#14 Macrophyte_nitrogen
#15 Surface_layer_phytoplankton
#16 Deep_layer_phytoplankton
#17 Omnivorous_zooplankton
#18 Carnivorous_zooplankton
#19 Benthos_susp/dep_feeders_larvae
#20 Benthos_susp/dep_feeders
#21 Benthos_carn/scav_feeders_larvae
#22 Benthos_carn/scav_feeders
#23 Planktivorous_fish_larvae
#24 Planktivorous_fish
#25 Migratory_fish
#26 Demersal_fish_larvae
#27 Demersal_fish
#28 Birds
#29 Pinnipeds
#30 Cetaceans
xRdetritus_i <- I_rawresults[which(I_rawresults$Description=="Sediment_refractory_detritus"),1]
xRdetritus_o <- O_rawresults[which(O_rawresults$Description=="Sediment_refractory_detritus"),1]
xLdetritus_i <- I_rawresults[which(I_rawresults$Description== "Sediment_labile_plus_refractory_detritus"),1]-xRdetritus_i
xLdetritus_o <- O_rawresults[which(O_rawresults$Description== "Sediment_labile_plus_refractory_detritus"),1]-xRdetritus_o
total_labile_detritus_i <- xLdetritus_i + I_rawresults[which(I_rawresults$Description=="Surface_layer_detritus"),1] +
I_rawresults[which(I_rawresults$Description=="Fishery_discards"),1] +
I_rawresults[which(I_rawresults$Description=="Corpses"),1] +
I_rawresults[which(I_rawresults$Description=="Macrophyte_debris"),1]
total_labile_detritus_o <- xLdetritus_o + O_rawresults[which(O_rawresults$Description=="Surface_layer_detritus"),1] +
+ O_rawresults[which(O_rawresults$Description=="Fishery_discards"),1] +
+ O_rawresults[which(O_rawresults$Description=="Corpses"),1] +
+ O_rawresults[which(O_rawresults$Description=="Deep_layer_detritus"),1]
I_results$total_labile_detritus_bd <- total_labile_detritus_i/(shallowprop)
O_results$total_labile_detritus_bd <- total_labile_detritus_o/(1-shallowprop)
I_results$kelp_bd <- (I_rawresults[which(I_rawresults$Description=="Macrophyte_nitrogen"),1])/shallowprop
I_results$phyt_bd <- (I_rawresults[which(I_rawresults$Description=="Surface_layer_phytoplankton"),1])/shallowprop
O_results$phyt_bd <- ( (O_rawresults[which(O_rawresults$Description=="Surface_layer_phytoplankton"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Deep_layer_phytoplankton"),1]) ) /(1-shallowprop)
I_results$benth_susp_bd <- ( (I_rawresults[which(I_rawresults$Description=="Benthos_susp/dep_feeders"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Benthos_susp/dep_feeders_larvae"),1]) ) /shallowprop
O_results$benth_susp_bd <- ( (O_rawresults[which(O_rawresults$Description=="Benthos_susp/dep_feeders"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Benthos_susp/dep_feeders_larvae"),1]) ) /(1-shallowprop)
I_results$benth_carn_bd <- ( (I_rawresults[which(I_rawresults$Description=="Benthos_carn/scav_feeders"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Benthos_carn/scav_feeders_larvae"),1]) ) /shallowprop
O_results$benth_carn_bd <- ( (O_rawresults[which(O_rawresults$Description=="Benthos_carn/scav_feeders"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Benthos_carn/scav_feeders_larvae"),1]) ) /(1-shallowprop)
I_results$plankfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Planktivorous_fish"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Planktivorous_fish_larvae"),1]) ) /shallowprop
O_results$plankfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Planktivorous_fish"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Planktivorous_fish_larvae"),1]) ) /(1-shallowprop)
I_results$demfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Demersal_fish"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Demersal_fish_larvae"),1]) ) /shallowprop
O_results$demfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Demersal_fish"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Demersal_fish_larvae"),1]) ) /(1-shallowprop)
I_results$migfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Migratory_fish"),1]) ) /shallowprop
O_results$migfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Migratory_fish"),1]) ) /(1-shallowprop)
I_results$omni_bd <- ( (I_rawresults[which(I_rawresults$Description=="Omnivorous_zooplankton"),1]) ) /shallowprop
O_results$omni_bd <- ( (O_rawresults[which(O_rawresults$Description=="Omnivorous_zooplankton"),1]) ) /(1-shallowprop)
I_results$carn_bd <- ( (I_rawresults[which(I_rawresults$Description=="Carnivorous_zooplankton"),1]) ) /shallowprop
O_results$carn_bd <- ( (O_rawresults[which(O_rawresults$Description=="Carnivorous_zooplankton"),1]) ) /(1-shallowprop)
I_results$bird_bd <- ( (I_rawresults[which(I_rawresults$Description=="Birds"),1]) ) /shallowprop
O_results$bird_bd <- ( (O_rawresults[which(O_rawresults$Description=="Birds"),1]) ) /(1-shallowprop)
I_results$seal_bd <- ( (I_rawresults[which(I_rawresults$Description=="Pinnipeds"),1]) ) /shallowprop
O_results$seal_bd <- ( (O_rawresults[which(O_rawresults$Description=="Pinnipeds"),1]) ) /(1-shallowprop)
I_results$ceta_bd <- ( (I_rawresults[which(I_rawresults$Description=="Cetaceans"),1]) ) /shallowprop
O_results$ceta_bd <- ( (O_rawresults[which(O_rawresults$Description=="Cetaceans"),1]) ) /(1-shallowprop)
Nind<-13
#Plot the inshore and offshore results
#plotlabels<-c("bact.&.detritus","phyt","s/d.benth","omniv.zoo","c/s.benth","carn.zoo","plankt.fish","mig.fish","dem.fish","bird.&.mam")
plotlabels<-c("Bact.&.detritus","Macrophytes","Phytoplankton","S/d.benthos","Omniv.zoo","C/s.benthos","Carn.zoo","Plankt.fish","Mig.fish","Dem.fish","Birds","Pinnipeds","Cetaceans")
modeldata2plot<-log10(O_results[2:6,1])
for(jj in 2:Nind) { modeldata2plot<-c(modeldata2plot,log10(O_results[2:6,jj]))}
array2plot<- array(dim=c(5,Nind),modeldata2plot)
colnames(array2plot)<-plotlabels
bxpdata_O<-list(stats=array2plot,n=rep(100,Nind),conf=NULL,out=numeric(length=0),names=plotlabels)
modeldata2plot<-log10(I_results[2:6,1])
for(jj in 2:Nind) { modeldata2plot<-c(modeldata2plot,log10(I_results[2:6,jj]))}
array2plot<- array(dim=c(5,Nind),modeldata2plot)
colnames(array2plot)<-plotlabels
bxpdata_I<-list(stats=array2plot,n=rep(100,Nind),conf=NULL,out=numeric(length=0),names=plotlabels)
combdata<-rbind(bxpdata_O$stats,bxpdata_I$stats)
combdata[1:5,2]<-NA # reset offshore macrophytes to NA instead of -Inf
ulm<-max(combdata[c(5,10),],na.rm=TRUE)
llm<-min(combdata[c(2,7),],na.rm=TRUE)
ymin<-floor(llm)
ymax<-ceiling(ulm)
par(mfrow=c(1,1))
par(mar=c(5,8,1,1))
bxp(bxpdata_O,boxwex=0.35,at=seq(1,Nind),ylim=c(ymin,ymax),cex.axis=1.2,show.names=TRUE,horizontal=TRUE,las=1,boxcol="red",whiskcol="red",whisklty="solid",medcol="red",staplecol="red")
#axis(side=1,las=1,cex.axis=1.2)
#axis(side=1,las=1,cex.axis=1.2,at=c(-1,0,-1,2))
# mtext("Log(annual average biomass density)",cex=1.2,side=1,line=3)
mtext(bquote("Annual average biomass log"[10] ~ "mMN.m"^-2),cex=1.2,side=1,line=3)
bxp(bxpdata_I,add=TRUE,boxwex=0.35,at=seq(1,Nind)+0.35,yaxt="n",xaxt="n",horizontal=TRUE,boxcol="blue",whiskcol="blue",whisklty="solid",medcol="blue",staplecol="blue")
legend("bottomleft",box.lty=0,bg="transparent",c("Inshore","Offshore"),col=c("blue","red"),lty=c(1,1),lwd=c(2,2),pt.cex=c(1,1),cex=c(0.9,0.9))
abline(h=1.7,lty="dashed")
abline(h=2.7,lty="dashed")
abline(h=3.7,lty="dashed")
abline(h=4.7,lty="dashed")
abline(h=5.7,lty="dashed")
abline(h=6.7,lty="dashed")
abline(h=7.7,lty="dashed")
abline(h=8.7,lty="dashed")
abline(h=9.7,lty="dashed")
abline(h=10.7,lty="dashed")
abline(h=11.7,lty="dashed")
abline(h=12.7,lty="dashed")
}
Try the StrathE2E2 package in your browser
Any scripts or data that you put into this service are public.
StrathE2E2 documentation built on Jan. 23, 2021, 1:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions plot_inshore_vs_offshore_anavmass
#
# plot_inshore_vs_offshore_anavmass.R
#
#' Plots of annual average inshore and offshore mass densities generated a StrathE2E simulation.
#'
#' Create a plot showing the distribution of annual average inshore and offshore mass densities over the final year of a simulation generated by the e2e_run() function.
#'
#' The format of the output is a single panel with rows symbols. Each row represents a different
#' state variable in the model (bacteria and detritus, phytoplankton etc etc). Each row consists of two symbols, one (red) for the offshore
#' zone and the other (blue) for the inshore zone. The data represented are values of the mass densities (mMn/m2) of each variable, averaged
#' over the final year of a model run.
#'
#' @param model R-list object defining the model configuration compiled by the e2e_read() function
#' @param use.saved Logical. If TRUE use data from a prior user-defined run held as csv files data in the current results folder, (default=FALSE).
#' @param results R-list object of baseline model output generated by the e2e_run(), (default=NULL).
#'
#' @return Graphical display in a new graphics window
#'
#' @importFrom graphics text
#'
#' @noRd
#
# ------------------------------------------------------------------------------
plot_inshore_vs_offshore_anavmass <- function(model, use.saved=FALSE, results=NULL) {
start_par = par()$mfrow
on.exit(par(mfrow = start_par))
if(use.saved==FALSE & is.list(results)==FALSE){
stop("no source of data has been specified ! \n")
}
if(use.saved==TRUE & is.list(results)==TRUE){
stop("use.saved is TRUE but a results list object has also been specified ! \n")
}
if(use.saved==FALSE & is.list(results)==TRUE){
O_rawresults <- elt(results, "final.year.outputs", "mass_results_offshore")
I_rawresults <- elt(results, "final.year.outputs", "mass_results_inshore")
}
if(use.saved==TRUE & is.list(results)==FALSE){
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")
datafile_o <- csvname(resultsdir, "OFFSHORE_model_anav_biomass", model.ident)
datafile_i <- csvname(resultsdir, "INSHORE_model_anav_biomass", model.ident)
message("Reading data from '", datafile_o, "'")
message("Reading data from '", datafile_i, "'")
O_rawresults<-readcsv(datafile_o)
I_rawresults<-readcsv(datafile_i)
}
shallowprop <- O_rawresults[which(O_rawresults$Description == "Area_proportion_of_inshore_zone"),1]
#Set up two dataframes to hold the area density data
O_results<-data.frame("total_labile_detritus_bd"=rep(NA,6),
"kelp_bd"=rep(NA,6),
"phyt_bd"=rep(NA,6),
"benth_susp_bd"=rep(NA,6),
"omni_bd"=rep(NA,6),
"benth_carn_bd"=rep(NA,6),
"carn_bd"=rep(NA,6),
"plankfish_bd"=rep(NA,6),
"migfish_bd"=rep(NA,6),
"demfish_bd"=rep(NA,6),
"bird_bd"=rep(NA,6),
"seal_bd"=rep(NA,6),
"ceta_bd"=rep(NA,6))
I_results<-O_results
# Rows in the raw input data....
#1 Surface_layer_detritus
#2 Deep_layer_detritus
#3 Sediment_labile_plus_refractory_detritus
#4 Sediment_refractory_detritus
#5 Fishery_discards
#6 Corpses
#7 Macrophyte_debris
#8 Surface_layer_ammonia
#9 Deep_layer_ammonia
#10 Sediment_porewater_ammonia
#11 Surface_layer_nitrate
#12 Deep_layer_nitrate
#13 Sediment_porewater_nitrate
#14 Macrophyte_nitrogen
#15 Surface_layer_phytoplankton
#16 Deep_layer_phytoplankton
#17 Omnivorous_zooplankton
#18 Carnivorous_zooplankton
#19 Benthos_susp/dep_feeders_larvae
#20 Benthos_susp/dep_feeders
#21 Benthos_carn/scav_feeders_larvae
#22 Benthos_carn/scav_feeders
#23 Planktivorous_fish_larvae
#24 Planktivorous_fish
#25 Migratory_fish
#26 Demersal_fish_larvae
#27 Demersal_fish
#28 Birds
#29 Pinnipeds
#30 Cetaceans
xRdetritus_i <- I_rawresults[which(I_rawresults$Description=="Sediment_refractory_detritus"),1]
xRdetritus_o <- O_rawresults[which(O_rawresults$Description=="Sediment_refractory_detritus"),1]
xLdetritus_i <- I_rawresults[which(I_rawresults$Description== "Sediment_labile_plus_refractory_detritus"),1]-xRdetritus_i
xLdetritus_o <- O_rawresults[which(O_rawresults$Description== "Sediment_labile_plus_refractory_detritus"),1]-xRdetritus_o
total_labile_detritus_i <- xLdetritus_i + I_rawresults[which(I_rawresults$Description=="Surface_layer_detritus"),1] +
I_rawresults[which(I_rawresults$Description=="Fishery_discards"),1] +
I_rawresults[which(I_rawresults$Description=="Corpses"),1] +
I_rawresults[which(I_rawresults$Description=="Macrophyte_debris"),1]
total_labile_detritus_o <- xLdetritus_o + O_rawresults[which(O_rawresults$Description=="Surface_layer_detritus"),1] +
+ O_rawresults[which(O_rawresults$Description=="Fishery_discards"),1] +
+ O_rawresults[which(O_rawresults$Description=="Corpses"),1] +
+ O_rawresults[which(O_rawresults$Description=="Deep_layer_detritus"),1]
I_results$total_labile_detritus_bd <- total_labile_detritus_i/(shallowprop)
O_results$total_labile_detritus_bd <- total_labile_detritus_o/(1-shallowprop)
I_results$kelp_bd <- (I_rawresults[which(I_rawresults$Description=="Macrophyte_nitrogen"),1])/shallowprop
I_results$phyt_bd <- (I_rawresults[which(I_rawresults$Description=="Surface_layer_phytoplankton"),1])/shallowprop
O_results$phyt_bd <- ( (O_rawresults[which(O_rawresults$Description=="Surface_layer_phytoplankton"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Deep_layer_phytoplankton"),1]) ) /(1-shallowprop)
I_results$benth_susp_bd <- ( (I_rawresults[which(I_rawresults$Description=="Benthos_susp/dep_feeders"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Benthos_susp/dep_feeders_larvae"),1]) ) /shallowprop
O_results$benth_susp_bd <- ( (O_rawresults[which(O_rawresults$Description=="Benthos_susp/dep_feeders"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Benthos_susp/dep_feeders_larvae"),1]) ) /(1-shallowprop)
I_results$benth_carn_bd <- ( (I_rawresults[which(I_rawresults$Description=="Benthos_carn/scav_feeders"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Benthos_carn/scav_feeders_larvae"),1]) ) /shallowprop
O_results$benth_carn_bd <- ( (O_rawresults[which(O_rawresults$Description=="Benthos_carn/scav_feeders"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Benthos_carn/scav_feeders_larvae"),1]) ) /(1-shallowprop)
I_results$plankfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Planktivorous_fish"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Planktivorous_fish_larvae"),1]) ) /shallowprop
O_results$plankfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Planktivorous_fish"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Planktivorous_fish_larvae"),1]) ) /(1-shallowprop)
I_results$demfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Demersal_fish"),1]) +
+ (I_rawresults[which(I_rawresults$Description=="Demersal_fish_larvae"),1]) ) /shallowprop
O_results$demfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Demersal_fish"),1]) +
+ (O_rawresults[which(O_rawresults$Description=="Demersal_fish_larvae"),1]) ) /(1-shallowprop)
I_results$migfish_bd <- ( (I_rawresults[which(I_rawresults$Description=="Migratory_fish"),1]) ) /shallowprop
O_results$migfish_bd <- ( (O_rawresults[which(O_rawresults$Description=="Migratory_fish"),1]) ) /(1-shallowprop)
I_results$omni_bd <- ( (I_rawresults[which(I_rawresults$Description=="Omnivorous_zooplankton"),1]) ) /shallowprop
O_results$omni_bd <- ( (O_rawresults[which(O_rawresults$Description=="Omnivorous_zooplankton"),1]) ) /(1-shallowprop)
I_results$carn_bd <- ( (I_rawresults[which(I_rawresults$Description=="Carnivorous_zooplankton"),1]) ) /shallowprop
O_results$carn_bd <- ( (O_rawresults[which(O_rawresults$Description=="Carnivorous_zooplankton"),1]) ) /(1-shallowprop)
I_results$bird_bd <- ( (I_rawresults[which(I_rawresults$Description=="Birds"),1]) ) /shallowprop
O_results$bird_bd <- ( (O_rawresults[which(O_rawresults$Description=="Birds"),1]) ) /(1-shallowprop)
I_results$seal_bd <- ( (I_rawresults[which(I_rawresults$Description=="Pinnipeds"),1]) ) /shallowprop
O_results$seal_bd <- ( (O_rawresults[which(O_rawresults$Description=="Pinnipeds"),1]) ) /(1-shallowprop)
I_results$ceta_bd <- ( (I_rawresults[which(I_rawresults$Description=="Cetaceans"),1]) ) /shallowprop
O_results$ceta_bd <- ( (O_rawresults[which(O_rawresults$Description=="Cetaceans"),1]) ) /(1-shallowprop)
Nind<-13
#Plot the inshore and offshore results
#plotlabels<-c("bact.&.detritus","phyt","s/d.benth","omniv.zoo","c/s.benth","carn.zoo","plankt.fish","mig.fish","dem.fish","bird.&.mam")
plotlabels<-c("Bact.&.detritus","Macrophytes","Phytoplankton","S/d.benthos","Omniv.zoo","C/s.benthos","Carn.zoo","Plankt.fish","Mig.fish","Dem.fish","Birds","Pinnipeds","Cetaceans")
modeldata2plot<-log10(O_results[2:6,1])
for(jj in 2:Nind) { modeldata2plot<-c(modeldata2plot,log10(O_results[2:6,jj]))}
array2plot<- array(dim=c(5,Nind),modeldata2plot)
colnames(array2plot)<-plotlabels
bxpdata_O<-list(stats=array2plot,n=rep(100,Nind),conf=NULL,out=numeric(length=0),names=plotlabels)
modeldata2plot<-log10(I_results[2:6,1])
for(jj in 2:Nind) { modeldata2plot<-c(modeldata2plot,log10(I_results[2:6,jj]))}
array2plot<- array(dim=c(5,Nind),modeldata2plot)
colnames(array2plot)<-plotlabels
bxpdata_I<-list(stats=array2plot,n=rep(100,Nind),conf=NULL,out=numeric(length=0),names=plotlabels)
combdata<-rbind(bxpdata_O$stats,bxpdata_I$stats)
combdata[1:5,2]<-NA # reset offshore macrophytes to NA instead of -Inf
ulm<-max(combdata[c(5,10),],na.rm=TRUE)
llm<-min(combdata[c(2,7),],na.rm=TRUE)
ymin<-floor(llm)
ymax<-ceiling(ulm)
par(mfrow=c(1,1))
par(mar=c(5,8,1,1))
bxp(bxpdata_O,boxwex=0.35,at=seq(1,Nind),ylim=c(ymin,ymax),cex.axis=1.2,show.names=TRUE,horizontal=TRUE,las=1,boxcol="red",whiskcol="red",whisklty="solid",medcol="red",staplecol="red")
#axis(side=1,las=1,cex.axis=1.2)
#axis(side=1,las=1,cex.axis=1.2,at=c(-1,0,-1,2))
# mtext("Log(annual average biomass density)",cex=1.2,side=1,line=3)
mtext(bquote("Annual average biomass log"[10] ~ "mMN.m"^-2),cex=1.2,side=1,line=3)
bxp(bxpdata_I,add=TRUE,boxwex=0.35,at=seq(1,Nind)+0.35,yaxt="n",xaxt="n",horizontal=TRUE,boxcol="blue",whiskcol="blue",whisklty="solid",medcol="blue",staplecol="blue")
legend("bottomleft",box.lty=0,bg="transparent",c("Inshore","Offshore"),col=c("blue","red"),lty=c(1,1),lwd=c(2,2),pt.cex=c(1,1),cex=c(0.9,0.9))
abline(h=1.7,lty="dashed")
abline(h=2.7,lty="dashed")
abline(h=3.7,lty="dashed")
abline(h=4.7,lty="dashed")
abline(h=5.7,lty="dashed")
abline(h=6.7,lty="dashed")
abline(h=7.7,lty="dashed")
abline(h=8.7,lty="dashed")
abline(h=9.7,lty="dashed")
abline(h=10.7,lty="dashed")
abline(h=11.7,lty="dashed")
abline(h=12.7,lty="dashed")
}
Try the StrathE2E2 package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.