R/plotTCSAM2013I.R
In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.
#'
#' @title Plot TCSAM2013 model results.
#'
#' @description Function to plot model results from TCSAM2013.
#'
#' @param obj.rep - report file list object
#' @param obj.std - dataframe object with parameter std info
#' @param obj.prs - dataframe object w/ parameters info
#' @param obj.wts - TCSAM_WTS-type list object
#' @param base.dir - path to base folder
#' @param mdl - model name (optional if R report file is read)
#' @param styr - model start year
#' @param endyr - assessment year
#' @param obsyr - first year for survey observations
#' @param pltyr - first year for some plots
#' @param F35 - F35 value for control rule plot
#' @param B35 - B35 value for control rule plot
#'
#' @return nothing.
#'
#' @details Uses \code{wtsPlots::plotErrorBars.V()},
#' \code{wtsUtilities::formatZeros} and \code{wtsUtilities::parseNum}.
#'
#' @export
#'
#----------------------------------
# Set model variables for plots
plotTCSAM2013I<-function(obj.rep=NULL,
obj.std=NULL,
obj.prs=NULL,
obj.wts=NULL,
base.dir='./',
mdl='tcsam2013alta',#executable model name
endyr=NULL, #assessment year
styr=NULL, #model start year
obsyr=NULL, #first year of survey observations
pltyr=1965, #first year for plots
F35=0.73, #F35 value
B35=33.54){ #B35 value
if (is.null(obj.rep)){
cat("obj.rep file is NULL.\n")
cat("Aborting...\n");
return(NULL);
}
#------------
if (is.null(endyr)){
if (is.null(obj.rep$endyr)){
cat("'endyr' missing from rep file and not specified as an input.\n")
cat("Must set 'endyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
endyr<-obj.rep$endyr;
}
}
if (is.null(styr)){
if (is.null(obj.rep$styr)){
cat("'styr' missing from rep file and not specified as an input.\n")
cat("Must set 'styr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
styr<-obj.rep$styr;
}
}
if (is.null(obsyr)){
if (is.null(obj.rep$obsyr)){
cat("'obsyr' missing from rep file and not specified as an input.\n")
cat("Must set 'obsyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
obsyr<-obj.rep$obsyr;
}
}
if (is.null(pltyr)){
if (is.null(obj.rep$pltyr)){
cat("'pltyr' missing from rep file and not specified as an input.\n")
cat("Must set 'pltyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
pltyr<-obj.rep$pltyr;
}
}
#set some constants
isGmacs <- (obj.rep$optFM==1)
THOUSAND <-1000;
years <-seq(styr,endyr);
years.m1 <-seq(styr,endyr-1);
obsyears <-seq(obsyr,endyr);
plotyears<-seq(pltyr,endyr);
length.bins<-obj.rep$length.bins;
if (is.null(length.bins)) length.bins<- seq(27,182,length=32);
#----------------------------------
# Set filename for pdf output
filen=paste(mdl,"oldstyle.pdf",sep='.');
pdf(file=file.path(base.dir,filen),width=8.5,height=11);
#----------------------------------
#----------------------------------
# Plot parameter values w/ limits and std's
if (!is.null(obj.prs)) checkParams(obj.prs,obj.std);
#----------------------------------
#----------------------------------
# Pull out data
#----------------------------------
recruitsd<-NULL;
if (!is.null(obj.std)) recruitsd=rbind(obj.std[obj.std[,2]=="rec_early_sd",],obj.std[obj.std[,2]=="recm_sd",])
tanner.cv= cbind(obsyears,obj.rep$Observed.survey.female.spawning.biomass.cv,obj.rep$Observed.survey.male.spawning.biomass.cv)
#----------------------------------
#----------------------------------
# plot observed and predicted mature biomass by sex
#----------------------------------
idx<-(1:length(years))[years==min(obsyears)]:length(years)
#observed spawning biomass
spB.f.obs <-obj.rep$"Observed.survey.female.spawning.biomass"
spB.m.obs <-obj.rep$"Observed.survey.male.spawning.biomass"
cv.f<-tanner.cv[,2];
cv.m<-tanner.cv[,3];
spB.f.prd <-obj.rep$"Predicted.Female.survey.mature.Biomass"
spB.m.prd <-obj.rep$"Predicted.Male.survey.mature.Biomass"
par(oma=c(0.5,1,1,0.5),mar=c(2,5,1,1)+0.2,mfrow=c(3,1))
#mature survey biomass by sex
#--females
lower= (spB.f.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.f^2)))-1);#lower error bar
upper= (spB.f.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.f^2)))-1);#upper error bar
plot(c(0,1),c(0,1),type="n",
ylim=c(0,300),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lines(years,spB.f.prd,lty=1,lwd=2,col='black')
wtsPlots::plotErrorBars.V(obsyears,spB.f.obs[idx],upper=upper,lower=lower,col='green');
points(obsyears,spB.f.obs[idx],pch=21,col='green',bg='green');
mtext("Mature female survey biomass", side=3, adj=0.05,cex=0.9)
legend("topright",
c("observed", "predicted"),
pch=c(21,NA),col=c('green','black'),pt.bg=c('green',NA),
lty=c(NA,1))
#--males
lower= (spB.m.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.m^2)))-1);#lower error bar
upper= (spB.m.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.m^2)))-1);#upper error bar
plot(c(0,1),c(0,1),type="n",
ylim=c(0,300),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lines(years,spB.m.prd,lty=1,lwd=2,col='black')
wtsPlots::plotErrorBars.V(obsyears,spB.m.obs[idx],upper=upper,lower=lower,col='blue');
points(obsyears,spB.m.obs[idx],pch=23,col='blue',bg='blue');
mtext("Mature male survey biomass", side=3, adj=0.05,cex=0.9)
legend("topright",
c("observed", "predicted"),
pch=c(21,NA),col=c('blue','black'),pt.bg=c('blue',NA),
lty=c(NA,1))
#----------------------------------
#----------------------------------
# total spawning biomass
#----------------------------------
spB.tm.obs<-spB.m.obs+spB.f.obs;#total observed survey MATURE biomass
spB.t.prd<-obj.rep$"Total.Spawning.Biomass";
plot(years,spB.t.prd,type="l",lty=2,lwd=1,
ylim=c(0,500),xlim=c(min(obsyears),max(obsyears)),
ylab="Mature Biomass (1000 t)",xlab="Year");
wtsPlots::plotErrorBars.V(obsyears,spB.tm.obs[idx],upper=upper,lower=lower);
points(obsyears,spB.tm.obs[idx],pch=21);
spB.m.prd<-obj.rep$"Predicted.Male.survey.mature.Biomass"
spB.f.prd<-obj.rep$"Predicted.Female.survey.mature.Biomass"
spB.t.prd<-spB.m.prd+spB.f.prd;
lines(years,spB.t.prd,type="l",lty=1,lwd=1)
mtext("Total mature biomass", side=3, adj=0.05)
legend("topright",
c("predicted in population","predicted in survey", "observed in survey"),
lty=c(2,1,NA),pch=c(NA,NA,21))
#----------------------------------
#------------------------------------
# Fits to retained & male discard mortalities
#------------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(2,5,1,1)+0.2,mfrow=c(3,1))
#total, retained, and total male mortality in TCF
obs.yd<-obj.rep$"observed.TCF.years.discard.catch"
obs.rd<-obj.rep$"observed.TCF.male.tot.biomass.mortality"; #total mortality for TCF
prd.rd<-obj.rep$"predicted.TCF.male.tot.biomass.mortality";#total mortality for TCF
obs.yr<-wtsUtilities::parseNum(obj.rep$"observed.TCF.years.retained.catch")
obs.r<-obj.rep$"observed.retained.catch.biomass";
prd.r<-obj.rep$"predicted.retained.catch.biomass";
prd.t<-obj.rep$"predicted.total.male.catch.biomass";#total over all fisheries
plot(years.m1, prd.t,lty=3,lwd=2,col="green",
type="l",xlab="Fishery Year",ylab="Catch (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.rd)));
lines(years.m1, prd.rd,lty=1,lwd=1)
points(obs.yd,obs.rd,pch=22)
lines(years.m1, prd.r, lty=2,lwd=1)
points(obs.yr,obs.r, pch=21)
mtext("Male catch mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted Total","Predicted Total: TCF","Observed Total: TCF","Predicted Retained","Observed Retained"),
lty=c( 3, 1,NA, 2,NA),
pch=c(NA,NA,22,NA,21),
col=c('green','black','black','black','black'),cex=1)
#retained catch only
plot(years.m1, prd.r,
type="l",xlab="Fishery Year",ylab="Retained Catch (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.r)))
points(obs.yr, obs.r)
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
mtext("Retained catch",side=3,adj=0.0,outer=FALSE);
#male discard mortality
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.r)))
points(yd,obs)
mtext("Directed fishery, male discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
# Directed fishery discards mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#male discard mortality (again)
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Directed fishery, male discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#female discard mortality
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Directed fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#Snow crab fishery discard mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#--male discard mortality
yd <-obj.rep$"observed.SCF.years.discard.catch"
obs<-obj.rep$"observed.SCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.SCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(1992:(endyr-1),obs)
mtext("Snow crab fishery, male discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#--female discard mortality
yd <-obj.rep$"observed.SCF.years.discard.catch"
obs<-obj.rep$"observed.SCF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.SCF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Snow crab fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#predicted red king crab fishery discard catch biomass
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#--male discard mortality
yd <-obj.rep$"observed.RKF.years.discard.catch"
obs<-obj.rep$"observed.RKF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.RKF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Red king crab fishery, male discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#--female discard mortality
yd <-obj.rep$"observed.RKF.years.discard.catch"
obs<-obj.rep$"observed.RKF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.RKF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Red king crab fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#groundfish trawl bycatch
#-------------------------------------------------
yd <-obj.rep$"observed.GTF.years.discard.catch"
prd<-obj.rep$"predicted.GTF.discard.mortality.biomass";
obs<-obj.rep$"observed.GTF.discard.mortality.biomass"
plot(years.m1,prd,type="l",
xlab="Fishery Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Groundfish discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#----------------------------------
#Z-scores
#----------------------------------
if (!is.null(obj.wts)){
plts.zscrs<-plotTCSAM_WTS.ZScores(obj.wts,
facet.scales='free_y',
showPlot=TRUE);
}
#--------------------------------------------
#Survey size comps: proportions at size
#--------------------------------------------
#--all females-----------
colnames(obj.rep$"Observed.Length.Prop.survey.all.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.all.females",
obj.rep$"Predicted.length.prop.survey.all.females", nr = 7, nc = 6,
nplot = length(obsyears),yearlb=obsyears,maxy=.12);
mtext("Survey proportions, females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.all.females",
datap=obj.rep$"Predicted.length.prop.survey.all.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.all.females.sampsize"[1:15]);
mtext("Survey proportions, females",side=3,adj=0.0);
#--all males-------------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.all.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.all.males",
obj.rep$"Predicted.length.prop.survey.all.males", nr = 7, nc = 6,
nplot = length(obsyears),yearlb=obsyears,maxy=.07);
mtext("Survey proportions, males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.all.males",
datap=obj.rep$"Predicted.length.prop.survey.all.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.all.males.sampsize");
mtext("Survey proportions, males",side=3,adj=0.0);
#--sum of survey length proportions: all males, all females
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
obs.comps<-obj.rep$"Observed.Length.Prop.survey.all.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.all.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.all.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.all.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean survey proportions, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#sum of survey length proportions: mature males, mature females
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
obs.comps<-obj.rep$"Observed.Length.Prop.survey.mature.new.females"+
obj.rep$"Observed.Length.Prop.survey.mature.old.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.mature.new.females"+
obj.rep$"Predicted.length.prop.survey.mature.old.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.mature.new.males"+
obj.rep$"Observed.Length.Prop.survey.mature.old.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.mature.new.males"+
obj.rep$"Predicted.length.prop.survey.mature.old.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean survey proportions, mature individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#sum of survey length proportions: immature males, immature females
obs.comps<-obj.rep$"Observed.Length.Prop.survey.immature.new.females"+
obj.rep$"Observed.Length.Prop.survey.immature.old.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.immature.new.females"+
obj.rep$"Predicted.length.prop.survey.immature.old.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.immature.new.males"+
obj.rep$"Observed.Length.Prop.survey.immature.old.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.immature.new.males"+
obj.rep$"Predicted.length.prop.survey.immature.old.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Summed survey proportions, immature individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#-------------------------------------------------
# Directed fishery
#-------------------------------------------------
#--Directed fishery: retained males
obs=obj.rep$"Observed.Prop.fishery.ret.new.males"+
obj.rep$"Observed.Prop.fishery.ret.old.males"
prd=obj.rep$"Predicted.length.prop.fishery.ret.new.males"+
obj.rep$"Predicted.length.prop.fishery.ret.old.males"
ss=obj.rep$"Observed.Prop.fishery.ret.new.males.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
obs[,1]=obj.rep$"Observed.Prop.fishery.ret.new.males"[,1]
prd[,1]=obj.rep$"Predicted.length.prop.fishery.ret.new.males"[,1]
years.ret=obs[,1];
#size comps
plotSizeCompsComparisons(obs, prd, nr = 6, nc = 4, nplot = length(years.ret), yearlb=years.ret)
mtext("directed fishery, all retained males",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd, nlen=32, sampsize=ss);
mtext("directed fishery, all retained males",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all retained males",side=3,adj=0.0);
legend("topleft",
c("observed males", "predicted males"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#--Directed fishery: all males
yrs.tcf<-obj.rep$"Observed.Prop.fishery.total.new.males"[,1];
obs=obj.rep$"Observed.Prop.fishery.total.new.males"+
obj.rep$"Observed.Prop.fishery.total.old.males"
prd=obj.rep$"Predicted.length.prop.fishery.total.new.males"+
obj.rep$"Predicted.length.prop.fishery.total.old.males"
ss=obj.rep$"Observed.Prop.fishery.total.new.males.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
obs[,1]=yrs.tcf
prd[,1]=yrs.tcf
#size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs,prd, nr = 6, nc = 4, nplot=nrow(obs), yearlb=obs[,1]);
mtext("directed fishery, all males",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd, nlen=32, sampsize=ss);
mtext("directed fishery, all males",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all males",side=3,adj=0.0);
legend("topleft",
c("observed males", "predicted males"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#--Directed fishery: all females
obs<-(obj.rep$"Observed.length.prop.fishery.discard.all.females")
prd=obj.rep$"Predicted.length.prop.fishery.discard.all.females"
ss=obj.rep$"Observed.Prop.fishery.discard.all.females.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
#size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs,prd,nr = 6,nc = 4, nplot = nrow(obs), yearlb=obs[,1])
mtext("directed fishery, all females",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd,
nlen=32,sampsize=ss);
mtext("directed fishery, all females",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all females",side=3,adj=0.0);
legend("topright",
c("observed females", "predicted females"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#----------------------------------
#----------------------------------------
# Snow crab fishery discards comps
#----------------------------------------
yrs.scf=obj.rep$"Observed.length.prop.snow.fishery.males"[,1]
obs.m=obj.rep$"Observed.length.prop.snow.fishery.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.snow.fishery.males"
colnames(prd.m)=c("year",as.character(length.bins))
obs.f=obj.rep$"Observed.length.prop.snow.fishery.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.snow.fishery.females"
colnames(prd.f)=c("year",as.character(length.bins))
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=6,nc=4,nplot=nrow(obs.m),yearlb=yrs.scf)
mtext("snow crab fishery discards, all males",side=3,adj=0.0,outer=TRUE);
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=6,nc=4,nplot=nrow(obs.f),yearlb=yrs.scf)
mtext("snow crab fishery discards, all females",side=3,adj=0.0,outer=TRUE);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the snow crab fishery, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#---------------------------------------------
# BBRKC fishery discard size comps
#---------------------------------------------
yrs.rkf=obj.rep$"Observed.length.prop.redk.fishery.females"[,1]
obs.f=obj.rep$"Observed.length.prop.redk.fishery.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.redk.fishery.females"
colnames(prd.f)=c("year",as.character(length.bins))
obs.m=obj.rep$"Observed.length.prop.redk.fishery.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.redk.fishery.males"
colnames(prd.m)=c("year",as.character(length.bins))
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=6,nc=4,nplot=nrow(obs.f),yearlb=yrs.rkf)
mtext("BBRKC fishery discards, all females",side=3,adj=0.0,outer=TRUE);
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=6,nc=4,nplot=nrow(obs.m),yearlb=yrs.rkf)
mtext("BBRKC fishery discards, all males",side=3,adj=0.0,outer=TRUE);
#summed size frequency plots
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the BBRKC fishery, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#--------------------------------
# groundfish fishery size comps
#--------------------------------
yrs.gtf<-obj.rep$"Observed.length.prop.trawl.females"[,1]
obs.f=obj.rep$"Observed.length.prop.trawl.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.trawl.females"
colnames(prd.f)=c("year",as.character(length.bins))
obs.m=obj.rep$"Observed.length.prop.trawl.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.trawl.males"
colnames(prd.m)=c("year",as.character(length.bins))
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=8,nc=6,nplot=nrow(obs.f),yearlb=yrs.gtf)
mtext("groundfish fishery: females",side=3,adj=0.0,outer=TRUE);
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=8,nc=6,nplot=nrow(obs.m),yearlb=yrs.gtf)
mtext("groundfish fishery: males",side=3,adj=0.0,outer=TRUE);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
cols<-2:33;
ymx<-max(colMeans(obs.f,na.rm=TRUE)[cols],
colMeans(prd.f,na.rm=TRUE)[cols],
colMeans(obs.m,na.rm=TRUE)[cols],
colMeans(prd.m,na.rm=TRUE)[cols]);
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions",ymx=1.1*ymx);
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the groundfish fisheries, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#----------------------------------
# natural mortality estimates
#----------------------------------
if (!is.null(obj.std)){
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
plotNatMort(obj.std,styr=styr,endyr=endyr,min.yr=1970);
}
#----------------------------------
#------------------------------------------
# growth estimates
#------------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins[1:24],
obj.rep$"Predicted.mean.postmolt.length.females"[1:24],type="l",
xlab="Pre-Molt Length",ylab="Post-Molt Length",ylim=c(35,185),xlim=c(25,200))
points(length.bins[1:24],exp(0.5656024)*length.bins[1:24]^0.913266,pch=1)
points(length.bins,exp(0.43794)*length.bins^0.948703,pch=3)
lines(length.bins, obj.rep$"Predicted.mean.postmolt.length.males",lty=1)
mtext("Growth",side=3,adj=0.0);
#----------------------------------
#---------------------------------------
# probability of maturing
#---------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins,
obj.rep$"Predicted.probability.of.maturing.females",
xlab="Carapace Width (mm)", ylab="Probability of Maturing",type="l",lty=2)
lines(length.bins,obj.rep$"Predicted.probability.of.maturing.males")
#maturity 2009 assessment
lines(length.bins, 1/(1+exp(-(0.07754*(length.bins-130.8540)))),lty=3)
mtext("Maturation",side=3,adj=0.0);
#----------------------------------
#---------------------------------------
# size distribution of recruits
#---------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins,
obj.rep$"distribution.of.recruits.to.length.bins",
type="b",xlab="Carapace Width (mm)",ylab="Proportion",lty=1,pch=21)
mtext("Assumed size distribution at recruitment",side=3,adj=0.0);
#----------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
#----------------------------------------------
# Survey selectivity
#----------------------------------------------
#tanner underbag selectivity parameters
pa=0.8743/(1+ 10.95*exp(-.0504*(seq(27.5,182.5,by=5))))
pb=1-(1/(1+185.9*exp(-.1742*(seq(27.5,182.5,by=5)))))
ubx.x<-seq(27.5,182.5,by=5)
ubx.y<-pa+(1-pa)*pb
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
pchs<-c(21,22,23,24)
ltys<-c( 1, 1, 2,NA)
#--males ??
plot(length.bins,
obj.rep$"selectivity.survey.males.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr",pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr",lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.males.1982.to.1987", pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.males.1982.to.1987", lty=ltys[2])
points(length.bins,obj.rep$"selectivity.survey.males.1974.to.1981", pch=pchs[3])
lines( length.bins,obj.rep$"selectivity.survey.males.1974.to.1981", lty=ltys[3])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(140,140),c(0,1.0)) #ref size males
mtext("Trawl survey selectivity, males",side=3,adj=0)
legend("topright",
c("males, 1988+","males, 1982-1987","males 1974-1981","Somerton underbag exp."),
lty=ltys,pch=pchs,cex=0.7)
#--females ??
plot(length.bins,
obj.rep$"selectivity.survey.females.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.females.1982.to.1987", pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.females.1982.to.1987", lty=ltys[2])
points(length.bins,obj.rep$"selectivity.survey.females.1974.to.1981", pch=pchs[3])
lines( length.bins,obj.rep$"selectivity.survey.females.1974.to.1981", lty=ltys[3])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(100,100),c(0,1.0)) #ref size females
mtext("Trawl survey selectivity, females",side=3,adj=0)
legend("topright",
c("females, 1988+","females, 1982-1987","females 1974-1981","Somerton underbag exp."),
lty=ltys,pch=pchs,cex=0.7)
#most recent period
plot(length.bins,
obj.rep$"selectivity.survey.males.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr", pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr", lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",lty=ltys[2])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(140,140),c(0,1.0),lty=2) #ref size males
lines(c(100,100),c(0,1.0),lty=3) #ref size females
mtext("Trawl survey selectivity, 1988+",side=3,adj=0)
legend("topright",
c("males","females","Somerton underbag exp."),
lty=ltys[c(1,2,4)],pch=pchs[c(1,2,4)],cex=0.7)
#----------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
#----------------------------------------------
# TCF retained selectivity for new shell males
#----------------------------------------------
sel<-obj.rep$"selectivity.fishery.ret.new.males"
plot(length.bins,sel[1,],
type="l",ylim=c(0,1.0),lwd=3,xlab="Carapace width (mm)",ylab="Retention")
rownames(sel)<-years.m1;
ctr<-0
for (i in as.character(yrs.tcf)) {
lines(length.bins,sel[i,],lty=2,lwd=2)
y<-0.75-ctr*0.5/length(yrs.tcf)
iz<-which.min((sel[i,]-y)^2)
text(length.bins[iz],y,labels=i,cex=0.9,col="dark blue")
ctr<-ctr+1
}
mtext("Directed fishery retention",side=3,adj=0,outer=FALSE)
#----------------------------------
#----------------------------------------------
# TCF total selectivity for males
#----------------------------------------------
sel<-obj.rep$"selectivity.fishery.total.new.males";
plot(length.bins,sel[1,],type="l",lwd=3,ylim=c(0,1.0),xlab="Carapace Width (mm)",ylab="Total Selectivity")
rownames(sel)<-years.m1;
ctr<-0
for (i in as.character(yrs.tcf)) {
lines(length.bins,sel[i,],lty=2,lwd=2)
y<-0.75-ctr*0.5/length(yrs.tcf)
iz<-which.min((sel[i,]-y)^2)
text(length.bins[iz],y,labels=i,cex=0.9,col="dark blue")
ctr<-ctr+1
}
mtext("Total directed fishery selectivity on males",side=3,adj=0.0);
#----------------------------------
#----------------------------------------------
# TCF total selectivity for females
#----------------------------------------------
sel<-obj.rep$"selectivity.discard.females";
plot(length.bins,sel,type="l",lwd=3,ylim=c(0,1.0),xlab="Carapace Width (mm)",ylab="Total Selectivity")
mtext("Total directed fishery selectivity on females",side=3,adj=0.0);
#----------------------------------
#--------------------------------
# snow crab fishery selectivity
#--------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
plot(length.bins,obj.rep$"selectivity.snow.females"[1,],
type="l",lty=2,lwd=2,ylim=c(0,1.1),
xlab="Carapace width(mm)",ylab="Selectivity")
lines(length.bins,obj.rep$"selectivity.snow.females"[2,],lty=2,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.snow.females"[3,],lty=2,lwd=2,col="blue")
lines(length.bins,obj.rep$"selectivity.snow.males"[1,],lty=1,lwd=2,col="black")
lines(length.bins,obj.rep$"selectivity.snow.males"[2,],lty=1,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.snow.males"[3,],lty=1,lwd=2,col="blue")
mtext("snow crab fishery",side=3,adj=0.0,outer=FALSE);
legend("bottomright",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#--------------------------------
# BBRKC fishery selectivity
#--------------------------------
plot(length.bins,
obj.rep$"selectivity.redk.females"[1,],
type="l",lty=2,lwd=2,ylim=c(0,1.1),
xlab="Carapace width(mm)",ylab="Selectivity Red King Fishery")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.females"[2,],lty=2,lwd=2,col="green")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.females"[3,],lty=2,lwd=2,col="blue")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[1,],lwd=2)
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[2,],lwd=2,col="green")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[3,],lwd=2,col="blue")
mtext("BBRKC fishery",side=3,adj=0.0,outer=FALSE);
legend("topleft",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#----------------------------------------------
# Groundfish fishery selectivity
#----------------------------------------------
plot(length.bins, obj.rep$"selectivity.trawl.females"[1,],
type="l",xlab="Carapace width(mm)",ylab="Selectivity",ylim=c(0,1.1),lty=2,lwd=2,col="black")
lines(length.bins,obj.rep$"selectivity.trawl.females"[2,],lty=2,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.trawl.females"[3,],lty=2,lwd=2,col="blue")
names(obj.rep$"selectivity.trawl.males")<-as.character(length.bins)
lines(length.bins, obj.rep$"selectivity.trawl.males"[1,],lty=1,lwd=2)
lines(length.bins, obj.rep$"selectivity.trawl.males"[2,],lty=1,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.trawl.males"[3,],lty=1,lwd=2,col="blue")
mtext("groundfish fishery",side=3,adj=0.0,outer=FALSE);
legend("bottomright",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#-------------------------------------------------
# Directed fishery capture rates/fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.TCF.male.new.shell.mortality.rate"
f.r<-obj.rep$"max.retained.mortality.rate"
f.c<-obj.rep$"max.TCFM.new.shell.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,f.r,na.rm=TRUE)))
lines(years.m1,f.r,lty=2,col='green',lwd=3)
if (isGmacs) lines(years.m1,f.c,lty=3,col='cyan',lwd=3)
mtext("Directed fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality","retained mortality"),pch=c(NA,NA,NA),
lty=c(3,1,2),lwd=c(3,3,3),col=c('cyan','blue','green'),cex=1)
f.m<-obj.rep$"mean.TCF.male.new.shell.mortality.rate"
f.r<-obj.rep$"mean.retained.mortality.rate"
f.c<-obj.rep$"mean.TCFM.new.shell.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,f.r,na.rm=TRUE)))
lines(years.m1,f.r,lty=1,col='green',lwd=3)
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality","retained mortality"),pch=c(NA,NA,NA),
lty=c(1,1,1),lwd=c(3,3,3),col=c('cyan','blue','green'),cex=1)
#--females
f.m<-obj.rep$"max.TCF.female.mortality.rate"
f.c<-obj.rep$"max.TCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Directed fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.TCF.female.mortality.rate"
f.c<-obj.rep$"mean.TCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Snow crab fishery capture rate/fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.SCF.male.mortality.rate"
f.c<-obj.rep$"max.SCF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Snow crab fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.SCF.male.mortality.rate"
f.c<-obj.rep$"mean.SCF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.SCF.female.mortality.rate"
f.c<-obj.rep$"max.SCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Snow crab fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.SCF.female.mortality.rate"
f.c<-obj.rep$"mean.SCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Red king crab fishery fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.RKF.male.mortality.rate"
f.c<-obj.rep$"max.RKF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("BBRKC fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.RKF.male.mortality.rate"
f.c<-obj.rep$"mean.RKF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.RKF.female.mortality.rate"
f.c<-obj.rep$"max.RKF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("BBRKC fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.RKF.female.mortality.rate"
f.c<-obj.rep$"mean.RKF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Groundfish fishery fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.GTF.male.mortality.rate"
f.c<-obj.rep$"max.GTF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Groundfish fisheries: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.GTF.male.mortality.rate"
f.c<-obj.rep$"mean.GTF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.GTF.female.mortality.rate"
f.c<-obj.rep$"max.GTF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Groundfish fisheries: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.GTF.female.mortality.rate"
f.c<-obj.rep$"mean.GTF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Total fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(2,4,1,1)+0.2,mfrow=c(2,1))
#--max mortality
fm.m<-obj.rep$"max.TOT.male.NS.mortality.rate"
fm.f<-obj.rep$"max.TOT.female.NS.mortality.rate"
plot(years.m1, fm.m, type="l",col='blue',lwd=3,
xlab="", ylab="Fishing Mortality Rate",
xlim=range(plotyears),ylim=c(0,max(fm.m,fm.f,na.rm=TRUE)))
lines(years.m1,fm.f,lty=1,col='green',lwd=3)
mtext("Max (fully-selected) fishing mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("males","females"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('blue','green'),cex=1)
#--mean mortality
fm.m<-obj.rep$"mean.TOT.male.NS.mortality.rate"
fm.f<-obj.rep$"mean.TOT.female.NS.mortality.rate"
plot(years.m1, fm.m, type="l",col='blue',lwd=3,
xlab="Year", ylab="Fishing Mortality Rate",
xlim=range(plotyears),ylim=c(0,max(fm.m,fm.f,na.rm=TRUE)))
lines(years.m1,fm.f,lty=1,col='green',lwd=3)
mtext("Mean fishing mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("males","females"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('blue','green'),cex=1)
#----------------------------------
if (!is.null(obj.std)){
par(oma=c(1,1,1,1),mar=c(4,3,2,1)+0.2,mfrow=c(3,1))
#-------------------------------------------------
# Mature male biomass at mating time
#-------------------------------------------------
sdf.mmb<-obj.std[obj.std[,2]=="sdrMMB",]
mmb.sd<-sdf.mmb[,4]
mmb.mn<-sdf.mmb[,3]
plot(years[1:(length(years)-1)],mmb.mn,type="l",lty=1,
xlab="Year",ylab="Biomass (1000's t)",
ylim=c(0,1.2*max(mmb.mn+mmb.sd,na.rm=TRUE)))
points(years[1:(length(years)-1)],mmb.mn,pch=1)
wtsPlots::plotErrorBars.V(years[1:(length(years)-1)],mmb.mn,
sigma=mmb.sd,CI=0.8)
mtext("MMB at Mating",side=3,adj=0.0);
#----------------------------------
#-------------------------------------------
# Recruitment
#-------------------------------------------
##-by model year
recLag<-obj.rep$recLag;
sdf.R<-obj.std[obj.std[,2]=="sdrLnRec",];#1st year is styr+recLag
R.mn<-2*exp(sdf.R[,3])/THOUSAND;#scale to total recruitment in millions
R.sd<-sqrt(exp(sdf.R[,4]^2)-1)*R.mn;
yrs.R<-(styr+recLag):endyr;
plot(yrs.R,R.mn,type="l",lty=1,
xlab="Year",ylab="numbers (millions)",
ylim=c(0,1.2*max(R.mn+R.sd,na.rm=TRUE)))
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr),lty=2,lwd=2,col='grey')
points(yrs.R,R.mn,pch=1)
wtsPlots::plotErrorBars.V(yrs.R,R.mn,sigma=R.sd,CI=0.8,lognormal=TRUE)
mtext("Total recruitment",side=3,adj=0.0);
mnR<-mean(R.mn[(1977-styr+1):length(R.mn)]);
lines(((1977+recLag):endyr),mnR+0*((1977+recLag):endyr),lty=2,lwd=2)
##-lagged to fertilization year
recLag<-obj.rep$recLag;
sdf.R<-obj.std[obj.std[,2]=="sdrLnRec",];#1st year is styr+recLag
R.mn<-2*exp(sdf.R[,3])/THOUSAND;#scale to total recruitment in millions
R.sd<-sqrt(exp(sdf.R[,4]^2)-1)*R.mn;
yrs.R<-styr:(endyr-recLag);
plot(yrs.R,R.mn,type="l",lty=1,
xlab="Fertilization Year",ylab="numbers (millions)",
ylim=c(0,1.2*max(R.mn+R.sd,na.rm=TRUE)))
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr)-recLag,lty=2,lwd=2,col='grey')
points(yrs.R,R.mn,pch=1)
wtsPlots::plotErrorBars.V(yrs.R,R.mn,sigma=R.sd,CI=0.8,lognormal=TRUE)
mtext("Total recruitment",side=3,adj=0.0);
mnR<-mean(R.mn[(1977-styr+1):length(R.mn)]);
lines(1977:(endyr-recLag),mnR+0*(1977:(endyr-recLag)),lty=2,lwd=2)
#----------------------------------
}## if obj.std not null
par(oma=c(1,1,1,1),mar=c(4,3,2,1)+0.2,mfrow=c(3,1))
#----------------------------------
# spawning biomass by sex
#----------------------------------
prd.MMB<-obj.rep$"Mating.time.Male.Spawning.Biomass";
prd.MFB<-obj.rep$"Mating.time.Female.Spawning.Biomass";
plot(years.m1,prd.MMB+prd.MFB,type="l",lty=2,lwd=1,
ylab="Mature Biomass (1000 t)",xlab="Year");
lines(years.m1,prd.MMB,lty=1,lwd=2,col='blue')
lines(years.m1,prd.MFB,lty=1,lwd=2,col='green')
mtext("Spawning biomass at mating time", side=3, adj=0.05)
legend("topright",
c("males (MMB)","females", "total"),
lty=c(1,1,2),col=c('blue','green','black'))
#----------------------------------
#-------------------------------------------
# Recruitment
#-------------------------------------------
##-by model year
recLag<-obj.rep$recLag
tsR<-2*(obj.rep$"estimated.number.of.recruits.female")/THOUSAND;
yrs.R<-years;##-gives model year
plot(yrs.R,tsR,type="l",lty=1,
xlab="Year",ylab="numbers (millions)",
xlim=range(years),
ylim=c(0,1.2*max(tsR,na.rm=TRUE)))
mnRec<-mean(tsR[(1977+recLag-styr+1):length(tsR)]);
lines((1977+recLag):endyr,mnRec+0*((1977+recLag):endyr),lty=2,lwd=2)
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr),lty=2,lwd=2,col='grey')
points(yrs.R,tsR,pch=1)
mtext("Total recruitment",side=3,adj=0.0);
##-by fertilization year
recLag<-obj.rep$recLag;##-will lag to fertilization year
tsR<-2*(obj.rep$"estimated.number.of.recruits.female")/THOUSAND;
yrs.R<-years-1-recLag;
plot(yrs.R,tsR,type="l",lty=1,
xlab="Fertilization Year",ylab="numbers (millions)",
xlim=range(years),
ylim=c(0,1.2*max(tsR,na.rm=TRUE)))
mnRec<-mean(tsR[(1983-1-recLag-styr+1):length(tsR)]);
lines(1977:(endyr-recLag),mnRec+0*(1977:(endyr-recLag)),lty=2,lwd=2)
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr)-recLag,lty=2,lwd=2,col='grey')
points(yrs.R,tsR,pch=1)
mtext("Total recruitment (by fertilization year)",side=3,adj=0.0);
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
#--------------------------------------------
#Legal males.
#--------------------------------------------
plot(obsyears, obj.rep$"observed.number.of.males.greater.than.101.mm"/THOUSAND,type="p",
xlab="Year",ylab="Number (millions)",ylim=c(0,200))
lines(obsyears,obj.rep$"estimated.survey.numbers.of.males.101"[(1:length(years))[years==min(obsyears)]:length(years)]/THOUSAND,
lty=1,lwd=1)
lines(obsyears,obj.rep$"pop.estimate.numbers.of.males.101"[(1:length(years))[years==min(obsyears)]:length(years)]/THOUSAND,
lty=2)
legend("topright",
c("predicted total numbers","predicted survey numbers", "observed survey numbers"),
lty=c(2,1,NA),pch=c(NA,NA,21))
mtext(paste("Legal males (>=",obj.rep$legalSize,"mm CW)"), side=3, adj=0.05)
#----------------------------------
#-------------------------------------------------
# Fraction of male discard mortality in directed fishery
#-------------------------------------------------
frc<-obj.rep$"predicted.TCF.male.discard.mortality.biomass"/obj.rep$"predicted.retained.catch.biomass";
plot(years.m1,frc,type='l',
xlab="Fishery Year",ylab="ratio",
xlim=range(years),ylim=c(0,2.0))
mtext("Directed fishery male discard mortality biomass relative to retained catch biomass",side=3,adj=0.0,outer=FALSE);
#----------------------------------
#-------------------------------------------------
# Exploitation rate
#-------------------------------------------------
xpl<-obj.rep$"estimated.total.catch.divided.by.male.spawning.biomass.at.fishtime";
plot(years.m1, xpl, type="l",
xlab="Year",ylab="Exploitation Rate",xlim=range(plotyears),ylim=c(0,1.0))
xpl<-obj.rep$"estimated.total.catch.of.legal.males.divided.by.legal.males.at.fishtime"
lines(years.m1,xpl,,lty=2)
legend("topright",legend=c("total catch","legal males"),
lty=c(1,2),pch=c(NA,NA),cex=1)
#------------------------------------------------------------
# Harvest control rule and fishing mortality
#------------------------------------------------------------
if (!is.na(F35)){
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
yrs<-styr:(endyr-1)
mmb<-obj.rep$"Mating.time.Male.Spawning.Biomass";
tfm<-obj.rep$"max.TOT.male.NS.mortality.rate";
idx<-(yrs>=1965)&(tfm>0);
yrs<-yrs[idx];
mmb<-mmb[idx];
tfm<-tfm[idx];
plot(mmb,tfm,type='n',
xlab=" MMB (1000 t)",ylab="Full Selection Fishing Mortality Rate",
xlim=c(0,1.1*max(mmb)),ylim=c(0,1.1*max(tfm)))
n<-length(yrs);
ctr<-1:(n-1);
text(mmb[ctr],tfm[ctr],as.character(yrs[ctr]),cex=0.7,adj=0)
text(mmb[n],tfm[n],as.character(yrs[n]),cex=1.1,col='red',adj=0)
alpha<-0.1
beta<-0.25
lines(rep(B35,length=20),seq(0,1.1*max(tfm),length=20),lty=4,col="blue")
lines(seq(0,1.1*max(mmb),length=20),rep(F35,length=20),lty=4,col="blue")
text(B35,1.1*max(tfm),expression(bold(B[35])),cex=0.8,adj=0.5,col="blue")
text(1.1*max(mmb),F35,expression(bold(F[35])),cex=0.8,adj=0.5,col="blue")
lines(rep(B35*beta,length=20),
seq(0,F35*((((B35*beta)/B35)-alpha)/(1.-alpha)),length=20),
type="l",lty=1,lwd=2)
lines(seq(B35*beta,B35,length=20),
F35*(((seq(B35*beta,B35,length=20)/B35)-alpha)/(1.-alpha)),
type="l",lty=1,lwd=2)
lines(seq(B35,max(mmb),length=20),
rep(F35,length=20),
lty=1,lwd=2)
}
##Stock-recruit relationship
cex<-par("cex")
par(cex=0.75)
recLag<-obj.rep$recLag;
yrs<-styr:(endyr-1)
tmp=length(unlist((obj.rep$"Mating.time.Male.Spawning.Biomass")));
x<-obj.rep$"Mating.time.Male.Spawning.Biomass";
y<-obj.rep$"estimated.number.of.recruits.female"/1000;
idx<-(obj.rep$mnYrRecCurr-1-recLag-styr+1):(endyr-1-recLag-styr+1);
plot(x[idx],y[idx+1+recLag],
xlim=c(0,1.1*max(x)),ylim=c(0,1.1*max(y)),
xlab="Male Spawning Biomass(1000 t) at Feb. 15",
ylab="Recruitment (millions)",type="n")
yrs.tmp<-(obj.rep$mnYrRecCurr-1-recLag):(endyr-1-recLag);
text(x,y,wtsUtilities::formatZeros(yrs.tmp%%100,width=2),adj=0,cex=1.0);
par(cex=cex)
#----------------------------------
# plot observed total and mature (spawning) biomass from survey
#----------------------------------
#observed spawning biomass
spB.m.obs <-obj.rep$"Observed.survey.male.spawning.biomass"
spB.f.obs <-obj.rep$"Observed.survey.female.spawning.biomass"
spB.t.obs <-obj.rep$"Observed.survey.biomass"
spB.tm.obs<-spB.m.obs+spB.f.obs;#total observed survey MATURE biomass
#cv's
idx<-(1:length(years))[years==min(obsyears)]:length(years)
cv.f<-tanner.cv[,2];
cv.m<-tanner.cv[,3];
cv.t=sqrt((spB.m.obs[idx]*cv.m)^2 + (spB.f.obs[idx]*cv.f)^2)/(spB.tm.obs[idx]);
par(oma=c(0.5,1,1,0.5),mar=c(2,5,2,1)+0.2,mfrow=c(2,1))
#total survey biomass
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
#CV's assumed same as for total SPAWNING biomass in survey
lower= (spB.t.obs)*(exp(-1.96*sqrt(log(1+cv.t^2)))-1);#lower error bar
upper= (spB.t.obs)*(exp( 1.96*sqrt(log(1+cv.t^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.t.obs,upper=upper,lower=lower);
points(obsyears,spB.t.obs,pch=21);
mtext("Observed total survey biomass", side=3, adj=0.05)
#total mature survey biomass
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lower= (spB.tm.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.t^2)))-1);#lower error bar
upper= (spB.tm.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.t^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.tm.obs[idx],upper=upper,lower=lower);
points(obsyears,spB.tm.obs[idx],pch=21);
mtext("Observed total mature survey biomass", side=3, adj=0.05)
par(oma=c(0.5,1,1,0.5),mar=c(2,5,2,1)+0.2,mfrow=c(2,1))
#mature survey biomass by sex
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lower= (spB.f.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.f^2)))-1);#lower error bar
upper= (spB.f.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.f^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.f.obs[idx],upper=upper,lower=lower,col='green');
points(obsyears,spB.f.obs[idx],pch=21,col='green');
lower= (spB.m.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.m^2)))-1);#lower error bar
upper= (spB.m.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.m^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears+0.2,spB.m.obs[idx],upper=upper,lower=lower,col='blue');
points(obsyears+0.2,spB.m.obs[idx],pch=23,col='blue');
mtext("Observed mature survey biomass", side=3, adj=0.05)
legend("topright",
c("females", "males"),
pch=c(21,23),col=c('green','blue'))
#----------------------------------
#----------------------------------
# Plot survey numbers
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
plot(years,obj.rep$"predicted.survey.numbers.female"/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years, obj.rep$"Observed.survey.numbers.female"/THOUSAND,pch=21);
mtext("Females",side=3,adj=0.1,cex=1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"predicted.survey.numbers.male"/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years, obj.rep$"Observed.survey.numbers.male"/THOUSAND);
mtext("Males",side=3,adj=0.1,cex=1)
#----------------------------------
#----------------------------------
# Plot mature new/old shell survey numbers (female)
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
plot(years,obj.rep$"Predicted.Female.survey.new.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.female.new.spawning.numbers"/THOUSAND);
mtext("Mature new shell female",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"Predicted.Female.survey.old.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.female.old.spawning.numbers"/THOUSAND);
mtext("Mature old shell female",side=3,adj=0.1)
tot.p.f<-obj.rep$"Predicted.Female.survey.new.mature.numbers"+
obj.rep$"Predicted.Female.survey.old.mature.numbers";
tot.o.f<-obj.rep$"Observed.survey.female.old.spawning.numbers"+
obj.rep$"Observed.survey.female.new.spawning.numbers";
plot(years,tot.p.f/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,tot.o.f/THOUSAND);
mtext("All mature female",side=3,adj=0.1)
#----------------------------------
#----------------------------------
# Plot mature new/old shell survey numbers (male)
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
plot(years,obj.rep$"Predicted.Male.survey.new.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.male.new.spawning.numbers"/THOUSAND);
mtext("Mature new shell male",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"Predicted.Male.survey.old.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.male.old.spawning.numbers"/THOUSAND);
mtext("Mature old shell male",side=3,adj=0.1)
tot.p.m<-obj.rep$"Predicted.Male.survey.new.mature.numbers"+
obj.rep$"Predicted.Male.survey.old.mature.numbers";
tot.o.m<-obj.rep$"Observed.survey.male.old.spawning.numbers"+
obj.rep$"Observed.survey.male.new.spawning.numbers";
plot(years,tot.p.m/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,tot.o.m/THOUSAND);
mtext("All mature male",side=3,adj=0.1)
#----------------------------------
#----------------------------------
# fraction mature by size
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
frac.p.f<-tot.p.f/obj.rep$"predicted.survey.numbers.female";
frac.o.f<-tot.o.f/obj.rep$"Observed.survey.numbers.female";
plot(years,frac.p.f,type="l",
ylim=c(0,1.0),xlim=range(obsyears),ylab="fraction mature",xlab="Year");
points(years,frac.o.f);
mtext("Female",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
frac.p.m<-tot.p.m/obj.rep$"predicted.survey.numbers.male";
frac.o.m<-tot.o.m/obj.rep$"Observed.survey.numbers.male";
plot(years,frac.p.m,type="l",
ylim=c(0,1.0),xlim=range(obsyears),ylab="fraction mature",xlab="Year");
points(years,frac.o.m);
mtext("Male",side=3,adj=0.1)
#----------------------------------
#--------------------------------------------
#Survey size comps: numbers at size
#--------------------------------------------
colnames(obj.rep$"Observed.Survey.Numbers.by.length.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Survey.Numbers.by.length.females",
obj.rep$"Predicted.Survey.Numbers.by.length.females",
nr = 8, nc = 6,nplot = length(obsyears));
mtext("Survey numbers, females",side=3,adj=0.0,outer=TRUE);
colnames(obj.rep$"Observed.Survey.Numbers.by.length.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Survey.Numbers.by.length.males",
obj.rep$"Predicted.Survey.Numbers.by.length.males",
nr = 8, nc = 6,nplot = length(obsyears));
mtext("Survey numbers, males",side=3,adj=0.0,outer=TRUE);
#----------------------------------
#----------------------------------
# plot fits to components of survey size comps
#----------------------------------
#--immature, new shell females-------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.immature.new.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.immature.new.females",
obj.rep$"Predicted.length.prop.survey.immature.new.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.19)
mtext("Survey proportions, immature new shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.immature.new.females",
datap=obj.rep$"Predicted.length.prop.survey.immature.new.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.immature.new.females.sampsize"[1:15]);
mtext("Survey proportions, immature new shell females",side=3,adj=0.0);
#--mature, new shell females---------
colnames(obj.rep$"Observed.Length.Prop.survey.mature.new.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.new.females",
obj.rep$"Predicted.length.prop.survey.mature.new.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.1)
mtext("Survey proportions, mature new shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.new.females",
datap=obj.rep$"Predicted.length.prop.survey.mature.new.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.females.sampsize"[1:15]);
mtext("Survey proportions, mature new shell females",side=3,adj=0.0);
#--mature, old shell females----------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.mature.old.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.old.females",
obj.rep$"Predicted.length.prop.survey.mature.old.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.19)
mtext("Survey proportions, mature old shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.old.females",
datap=obj.rep$"Predicted.length.prop.survey.mature.old.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.old.females.sampsize"[1:15]);
mtext("Survey proportions, mature old shell females",side=3,adj=0.0);
#--immature, new shell males-----------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.immature.new.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.immature.new.males",
obj.rep$"Predicted.length.prop.survey.immature.new.males", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.08)
mtext("Survey proportions, immature new shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.immature.new.males",
datap=obj.rep$"Predicted.length.prop.survey.immature.new.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.immature.new.males.sampsize");
mtext("Survey proportions, immature new shell males",side=3,adj=0.0);
#--mature, new shell males-----------------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.mature.new.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.new.males",
obj.rep$"Predicted.length.prop.survey.mature.new.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.025)
mtext("Survey proportions, mature new shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.new.males",
datap=obj.rep$"Predicted.length.prop.survey.mature.new.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.males.sampsize");
mtext("Survey proportions, mature new shell males",side=3,adj=0.0);
#--mature, old shell males----------------
colnames(obj.rep$"Observed.Length.Prop.survey.mature.old.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.old.males",
obj.rep$"Predicted.length.prop.survey.mature.old.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.025)
mtext("Survey proportions, mature old shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.old.males",
datap=obj.rep$"Predicted.length.prop.survey.mature.old.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.old.males.sampsize");
mtext("Survey proportions, mature old shell males",side=3,adj=0.0);
#--mature males---------------
tmpobs=obj.rep$"Observed.Length.Prop.survey.mature.new.males"+obj.rep$"Observed.Length.Prop.survey.mature.old.males"
colnames(tmpobs)=c("year",as.character(length.bins))
tmpobs[,1]=obj.rep$"Observed.Length.Prop.survey.mature.new.males"[,1]
plotSizeCompsComparisons(tmpobs,
obj.rep$"Predicted.length.prop.survey.mature.new.males"+obj.rep$"Predicted.length.prop.survey.mature.old.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.05)
mtext("Survey proportions, mature males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=tmpobs,
datap=(obj.rep$"Predicted.length.prop.survey.mature.old.males"+obj.rep$"Predicted.length.prop.survey.mature.new.males"),
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.males.sampsize");
mtext("Survey proportions, mature males",side=3,adj=0.0);
#----------------------
dev.off()
}
wStockhausen/rTCSAM2013 documentation built on May 3, 2019, 7:13 p.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.
#'
#' @title Plot TCSAM2013 model results.
#'
#' @description Function to plot model results from TCSAM2013.
#'
#' @param obj.rep - report file list object
#' @param obj.std - dataframe object with parameter std info
#' @param obj.prs - dataframe object w/ parameters info
#' @param obj.wts - TCSAM_WTS-type list object
#' @param base.dir - path to base folder
#' @param mdl - model name (optional if R report file is read)
#' @param styr - model start year
#' @param endyr - assessment year
#' @param obsyr - first year for survey observations
#' @param pltyr - first year for some plots
#' @param F35 - F35 value for control rule plot
#' @param B35 - B35 value for control rule plot
#'
#' @return nothing.
#'
#' @details Uses \code{wtsPlots::plotErrorBars.V()},
#' \code{wtsUtilities::formatZeros} and \code{wtsUtilities::parseNum}.
#'
#' @export
#'
#----------------------------------
# Set model variables for plots
plotTCSAM2013I<-function(obj.rep=NULL,
obj.std=NULL,
obj.prs=NULL,
obj.wts=NULL,
base.dir='./',
mdl='tcsam2013alta',#executable model name
endyr=NULL, #assessment year
styr=NULL, #model start year
obsyr=NULL, #first year of survey observations
pltyr=1965, #first year for plots
F35=0.73, #F35 value
B35=33.54){ #B35 value
if (is.null(obj.rep)){
cat("obj.rep file is NULL.\n")
cat("Aborting...\n");
return(NULL);
}
#------------
if (is.null(endyr)){
if (is.null(obj.rep$endyr)){
cat("'endyr' missing from rep file and not specified as an input.\n")
cat("Must set 'endyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
endyr<-obj.rep$endyr;
}
}
if (is.null(styr)){
if (is.null(obj.rep$styr)){
cat("'styr' missing from rep file and not specified as an input.\n")
cat("Must set 'styr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
styr<-obj.rep$styr;
}
}
if (is.null(obsyr)){
if (is.null(obj.rep$obsyr)){
cat("'obsyr' missing from rep file and not specified as an input.\n")
cat("Must set 'obsyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
obsyr<-obj.rep$obsyr;
}
}
if (is.null(pltyr)){
if (is.null(obj.rep$pltyr)){
cat("'pltyr' missing from rep file and not specified as an input.\n")
cat("Must set 'pltyr' to assessment year.\n",
"Aborting...\n");
return(NULL);
} else {
pltyr<-obj.rep$pltyr;
}
}
#set some constants
isGmacs <- (obj.rep$optFM==1)
THOUSAND <-1000;
years <-seq(styr,endyr);
years.m1 <-seq(styr,endyr-1);
obsyears <-seq(obsyr,endyr);
plotyears<-seq(pltyr,endyr);
length.bins<-obj.rep$length.bins;
if (is.null(length.bins)) length.bins<- seq(27,182,length=32);
#----------------------------------
# Set filename for pdf output
filen=paste(mdl,"oldstyle.pdf",sep='.');
pdf(file=file.path(base.dir,filen),width=8.5,height=11);
#----------------------------------
#----------------------------------
# Plot parameter values w/ limits and std's
if (!is.null(obj.prs)) checkParams(obj.prs,obj.std);
#----------------------------------
#----------------------------------
# Pull out data
#----------------------------------
recruitsd<-NULL;
if (!is.null(obj.std)) recruitsd=rbind(obj.std[obj.std[,2]=="rec_early_sd",],obj.std[obj.std[,2]=="recm_sd",])
tanner.cv= cbind(obsyears,obj.rep$Observed.survey.female.spawning.biomass.cv,obj.rep$Observed.survey.male.spawning.biomass.cv)
#----------------------------------
#----------------------------------
# plot observed and predicted mature biomass by sex
#----------------------------------
idx<-(1:length(years))[years==min(obsyears)]:length(years)
#observed spawning biomass
spB.f.obs <-obj.rep$"Observed.survey.female.spawning.biomass"
spB.m.obs <-obj.rep$"Observed.survey.male.spawning.biomass"
cv.f<-tanner.cv[,2];
cv.m<-tanner.cv[,3];
spB.f.prd <-obj.rep$"Predicted.Female.survey.mature.Biomass"
spB.m.prd <-obj.rep$"Predicted.Male.survey.mature.Biomass"
par(oma=c(0.5,1,1,0.5),mar=c(2,5,1,1)+0.2,mfrow=c(3,1))
#mature survey biomass by sex
#--females
lower= (spB.f.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.f^2)))-1);#lower error bar
upper= (spB.f.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.f^2)))-1);#upper error bar
plot(c(0,1),c(0,1),type="n",
ylim=c(0,300),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lines(years,spB.f.prd,lty=1,lwd=2,col='black')
wtsPlots::plotErrorBars.V(obsyears,spB.f.obs[idx],upper=upper,lower=lower,col='green');
points(obsyears,spB.f.obs[idx],pch=21,col='green',bg='green');
mtext("Mature female survey biomass", side=3, adj=0.05,cex=0.9)
legend("topright",
c("observed", "predicted"),
pch=c(21,NA),col=c('green','black'),pt.bg=c('green',NA),
lty=c(NA,1))
#--males
lower= (spB.m.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.m^2)))-1);#lower error bar
upper= (spB.m.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.m^2)))-1);#upper error bar
plot(c(0,1),c(0,1),type="n",
ylim=c(0,300),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lines(years,spB.m.prd,lty=1,lwd=2,col='black')
wtsPlots::plotErrorBars.V(obsyears,spB.m.obs[idx],upper=upper,lower=lower,col='blue');
points(obsyears,spB.m.obs[idx],pch=23,col='blue',bg='blue');
mtext("Mature male survey biomass", side=3, adj=0.05,cex=0.9)
legend("topright",
c("observed", "predicted"),
pch=c(21,NA),col=c('blue','black'),pt.bg=c('blue',NA),
lty=c(NA,1))
#----------------------------------
#----------------------------------
# total spawning biomass
#----------------------------------
spB.tm.obs<-spB.m.obs+spB.f.obs;#total observed survey MATURE biomass
spB.t.prd<-obj.rep$"Total.Spawning.Biomass";
plot(years,spB.t.prd,type="l",lty=2,lwd=1,
ylim=c(0,500),xlim=c(min(obsyears),max(obsyears)),
ylab="Mature Biomass (1000 t)",xlab="Year");
wtsPlots::plotErrorBars.V(obsyears,spB.tm.obs[idx],upper=upper,lower=lower);
points(obsyears,spB.tm.obs[idx],pch=21);
spB.m.prd<-obj.rep$"Predicted.Male.survey.mature.Biomass"
spB.f.prd<-obj.rep$"Predicted.Female.survey.mature.Biomass"
spB.t.prd<-spB.m.prd+spB.f.prd;
lines(years,spB.t.prd,type="l",lty=1,lwd=1)
mtext("Total mature biomass", side=3, adj=0.05)
legend("topright",
c("predicted in population","predicted in survey", "observed in survey"),
lty=c(2,1,NA),pch=c(NA,NA,21))
#----------------------------------
#------------------------------------
# Fits to retained & male discard mortalities
#------------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(2,5,1,1)+0.2,mfrow=c(3,1))
#total, retained, and total male mortality in TCF
obs.yd<-obj.rep$"observed.TCF.years.discard.catch"
obs.rd<-obj.rep$"observed.TCF.male.tot.biomass.mortality"; #total mortality for TCF
prd.rd<-obj.rep$"predicted.TCF.male.tot.biomass.mortality";#total mortality for TCF
obs.yr<-wtsUtilities::parseNum(obj.rep$"observed.TCF.years.retained.catch")
obs.r<-obj.rep$"observed.retained.catch.biomass";
prd.r<-obj.rep$"predicted.retained.catch.biomass";
prd.t<-obj.rep$"predicted.total.male.catch.biomass";#total over all fisheries
plot(years.m1, prd.t,lty=3,lwd=2,col="green",
type="l",xlab="Fishery Year",ylab="Catch (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.rd)));
lines(years.m1, prd.rd,lty=1,lwd=1)
points(obs.yd,obs.rd,pch=22)
lines(years.m1, prd.r, lty=2,lwd=1)
points(obs.yr,obs.r, pch=21)
mtext("Male catch mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted Total","Predicted Total: TCF","Observed Total: TCF","Predicted Retained","Observed Retained"),
lty=c( 3, 1,NA, 2,NA),
pch=c(NA,NA,22,NA,21),
col=c('green','black','black','black','black'),cex=1)
#retained catch only
plot(years.m1, prd.r,
type="l",xlab="Fishery Year",ylab="Retained Catch (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.r)))
points(obs.yr, obs.r)
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
mtext("Retained catch",side=3,adj=0.0,outer=FALSE);
#male discard mortality
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(pretty(1965:endyr,h=2,n=(endyr-1965)/5)),
ylim=c(0,max(prd.r)))
points(yd,obs)
mtext("Directed fishery, male discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
# Directed fishery discards mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#male discard mortality (again)
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Directed fishery, male discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#female discard mortality
yd <-obj.rep$"observed.TCF.years.discard.catch"
obs<-obj.rep$"observed.TCF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.TCF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Directed fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#Snow crab fishery discard mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#--male discard mortality
yd <-obj.rep$"observed.SCF.years.discard.catch"
obs<-obj.rep$"observed.SCF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.SCF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(1992:(endyr-1),obs)
mtext("Snow crab fishery, male discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#--female discard mortality
yd <-obj.rep$"observed.SCF.years.discard.catch"
obs<-obj.rep$"observed.SCF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.SCF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Snow crab fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#predicted red king crab fishery discard catch biomass
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
#--male discard mortality
yd <-obj.rep$"observed.RKF.years.discard.catch"
obs<-obj.rep$"observed.RKF.male.discard.mortality.biomass"
prd<-obj.rep$"predicted.RKF.male.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Red king crab fishery, male discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#--female discard mortality
yd <-obj.rep$"observed.RKF.years.discard.catch"
obs<-obj.rep$"observed.RKF.female.discard.mortality.biomass"
prd<-obj.rep$"predicted.RKF.female.discard.mortality.biomass";
plot(years.m1,prd,type="l",
xlab="Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Red king crab fishery, female discards",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#-------------------------------------------------
#groundfish trawl bycatch
#-------------------------------------------------
yd <-obj.rep$"observed.GTF.years.discard.catch"
prd<-obj.rep$"predicted.GTF.discard.mortality.biomass";
obs<-obj.rep$"observed.GTF.discard.mortality.biomass"
plot(years.m1,prd,type="l",
xlab="Fishery Year",ylab="Discard Mortality (1000 t)",
xlim=range(years),ylim=c(0,max(prd,obs,na.rm=TRUE)))
points(yd,obs)
mtext("Groundfish discard mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("Predicted","Observed"),
lty=c(1,NA),pch=c(NA,1),cex=1)
#----------------------------------
#----------------------------------
#Z-scores
#----------------------------------
if (!is.null(obj.wts)){
plts.zscrs<-plotTCSAM_WTS.ZScores(obj.wts,
facet.scales='free_y',
showPlot=TRUE);
}
#--------------------------------------------
#Survey size comps: proportions at size
#--------------------------------------------
#--all females-----------
colnames(obj.rep$"Observed.Length.Prop.survey.all.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.all.females",
obj.rep$"Predicted.length.prop.survey.all.females", nr = 7, nc = 6,
nplot = length(obsyears),yearlb=obsyears,maxy=.12);
mtext("Survey proportions, females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.all.females",
datap=obj.rep$"Predicted.length.prop.survey.all.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.all.females.sampsize"[1:15]);
mtext("Survey proportions, females",side=3,adj=0.0);
#--all males-------------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.all.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.all.males",
obj.rep$"Predicted.length.prop.survey.all.males", nr = 7, nc = 6,
nplot = length(obsyears),yearlb=obsyears,maxy=.07);
mtext("Survey proportions, males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.all.males",
datap=obj.rep$"Predicted.length.prop.survey.all.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.all.males.sampsize");
mtext("Survey proportions, males",side=3,adj=0.0);
#--sum of survey length proportions: all males, all females
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
obs.comps<-obj.rep$"Observed.Length.Prop.survey.all.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.all.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.all.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.all.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean survey proportions, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#sum of survey length proportions: mature males, mature females
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
obs.comps<-obj.rep$"Observed.Length.Prop.survey.mature.new.females"+
obj.rep$"Observed.Length.Prop.survey.mature.old.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.mature.new.females"+
obj.rep$"Predicted.length.prop.survey.mature.old.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.mature.new.males"+
obj.rep$"Observed.Length.Prop.survey.mature.old.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.mature.new.males"+
obj.rep$"Predicted.length.prop.survey.mature.old.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean survey proportions, mature individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#sum of survey length proportions: immature males, immature females
obs.comps<-obj.rep$"Observed.Length.Prop.survey.immature.new.females"+
obj.rep$"Observed.Length.Prop.survey.immature.old.females";
prd.comps<-obj.rep$"Predicted.length.prop.survey.immature.new.females"+
obj.rep$"Predicted.length.prop.survey.immature.old.females";
plotMeanSizeComps(length.bins,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
obs.comps<-obj.rep$"Observed.Length.Prop.survey.immature.new.males"+
obj.rep$"Observed.Length.Prop.survey.immature.old.males";
prd.comps<-obj.rep$"Predicted.length.prop.survey.immature.new.males"+
obj.rep$"Predicted.length.prop.survey.immature.old.males";
plotMeanSizeComps(length.bins+1,obs.comps,prd.comps,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Summed survey proportions, immature individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#-------------------------------------------------
# Directed fishery
#-------------------------------------------------
#--Directed fishery: retained males
obs=obj.rep$"Observed.Prop.fishery.ret.new.males"+
obj.rep$"Observed.Prop.fishery.ret.old.males"
prd=obj.rep$"Predicted.length.prop.fishery.ret.new.males"+
obj.rep$"Predicted.length.prop.fishery.ret.old.males"
ss=obj.rep$"Observed.Prop.fishery.ret.new.males.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
obs[,1]=obj.rep$"Observed.Prop.fishery.ret.new.males"[,1]
prd[,1]=obj.rep$"Predicted.length.prop.fishery.ret.new.males"[,1]
years.ret=obs[,1];
#size comps
plotSizeCompsComparisons(obs, prd, nr = 6, nc = 4, nplot = length(years.ret), yearlb=years.ret)
mtext("directed fishery, all retained males",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd, nlen=32, sampsize=ss);
mtext("directed fishery, all retained males",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all retained males",side=3,adj=0.0);
legend("topleft",
c("observed males", "predicted males"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#--Directed fishery: all males
yrs.tcf<-obj.rep$"Observed.Prop.fishery.total.new.males"[,1];
obs=obj.rep$"Observed.Prop.fishery.total.new.males"+
obj.rep$"Observed.Prop.fishery.total.old.males"
prd=obj.rep$"Predicted.length.prop.fishery.total.new.males"+
obj.rep$"Predicted.length.prop.fishery.total.old.males"
ss=obj.rep$"Observed.Prop.fishery.total.new.males.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
obs[,1]=yrs.tcf
prd[,1]=yrs.tcf
#size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs,prd, nr = 6, nc = 4, nplot=nrow(obs), yearlb=obs[,1]);
mtext("directed fishery, all males",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd, nlen=32, sampsize=ss);
mtext("directed fishery, all males",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all males",side=3,adj=0.0);
legend("topleft",
c("observed males", "predicted males"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#--Directed fishery: all females
obs<-(obj.rep$"Observed.length.prop.fishery.discard.all.females")
prd=obj.rep$"Predicted.length.prop.fishery.discard.all.females"
ss=obj.rep$"Observed.Prop.fishery.discard.all.females.sampsize"
colnames(obs)=c("year",as.character(length.bins))
colnames(prd)=c("year",as.character(length.bins))
#size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs,prd,nr = 6,nc = 4, nplot = nrow(obs), yearlb=obs[,1])
mtext("directed fishery, all females",side=3,adj=0.0,outer=TRUE);
#bubble plot
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obs, datap=prd,
nlen=32,sampsize=ss);
mtext("directed fishery, all females",side=3,adj=0.0);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs,prd,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
mtext("directed fishery, all females",side=3,adj=0.0);
legend("topright",
c("observed females", "predicted females"),
lty=c(NA,1),pch=c(21,NA),col=c('black','black'))
#----------------------------------
#----------------------------------------
# Snow crab fishery discards comps
#----------------------------------------
yrs.scf=obj.rep$"Observed.length.prop.snow.fishery.males"[,1]
obs.m=obj.rep$"Observed.length.prop.snow.fishery.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.snow.fishery.males"
colnames(prd.m)=c("year",as.character(length.bins))
obs.f=obj.rep$"Observed.length.prop.snow.fishery.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.snow.fishery.females"
colnames(prd.f)=c("year",as.character(length.bins))
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=6,nc=4,nplot=nrow(obs.m),yearlb=yrs.scf)
mtext("snow crab fishery discards, all males",side=3,adj=0.0,outer=TRUE);
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=6,nc=4,nplot=nrow(obs.f),yearlb=yrs.scf)
mtext("snow crab fishery discards, all females",side=3,adj=0.0,outer=TRUE);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the snow crab fishery, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#---------------------------------------------
# BBRKC fishery discard size comps
#---------------------------------------------
yrs.rkf=obj.rep$"Observed.length.prop.redk.fishery.females"[,1]
obs.f=obj.rep$"Observed.length.prop.redk.fishery.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.redk.fishery.females"
colnames(prd.f)=c("year",as.character(length.bins))
obs.m=obj.rep$"Observed.length.prop.redk.fishery.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.redk.fishery.males"
colnames(prd.m)=c("year",as.character(length.bins))
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=6,nc=4,nplot=nrow(obs.f),yearlb=yrs.rkf)
mtext("BBRKC fishery discards, all females",side=3,adj=0.0,outer=TRUE);
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=6,nc=4,nplot=nrow(obs.m),yearlb=yrs.rkf)
mtext("BBRKC fishery discards, all males",side=3,adj=0.0,outer=TRUE);
#summed size frequency plots
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions")
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the BBRKC fishery, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#--------------------------------
# groundfish fishery size comps
#--------------------------------
yrs.gtf<-obj.rep$"Observed.length.prop.trawl.females"[,1]
obs.f=obj.rep$"Observed.length.prop.trawl.females"
colnames(obs.f)=c("year",as.character(length.bins))
prd.f=obj.rep$"Predicted.length.prop.trawl.females"
colnames(prd.f)=c("year",as.character(length.bins))
obs.m=obj.rep$"Observed.length.prop.trawl.males"
colnames(obs.m)=c("year",as.character(length.bins))
prd.m=obj.rep$"Predicted.length.prop.trawl.males"
colnames(prd.m)=c("year",as.character(length.bins))
#female size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.f,prd.f,nr=8,nc=6,nplot=nrow(obs.f),yearlb=yrs.gtf)
mtext("groundfish fishery: females",side=3,adj=0.0,outer=TRUE);
#male size comps
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(1,1))
plotSizeCompsComparisons(obs.m,prd.m,nr=8,nc=6,nplot=nrow(obs.m),yearlb=yrs.gtf)
mtext("groundfish fishery: males",side=3,adj=0.0,outer=TRUE);
#summed proportions
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
cols<-2:33;
ymx<-max(colMeans(obs.f,na.rm=TRUE)[cols],
colMeans(prd.f,na.rm=TRUE)[cols],
colMeans(obs.m,na.rm=TRUE)[cols],
colMeans(prd.m,na.rm=TRUE)[cols]);
plotMeanSizeComps(length.bins,obs.f,prd.f,cols=2:33,CI=0.95,addToPlot=FALSE,pch=21,lty=1,clr='black',
xlab="Carapace Width(mm)",ylab="Mean of Size Proportions",ymx=1.1*ymx);
plotMeanSizeComps(length.bins+1,obs.m,prd.m,cols=2:33,CI=0.95,addToPlot=TRUE,pch=22,lty=2,clr='blue')
mtext("Mean proportions in the groundfish fisheries, all individuals",side=3,adj=0.0);
legend("topright",
c("observed females","predicted females","observed males", "predicted males"),
lty=c(NA,1,NA,2),pch=c(21,NA,22,NA),col=c('black','black','blue','blue'))
#----------------------------------
#----------------------------------
# natural mortality estimates
#----------------------------------
if (!is.null(obj.std)){
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
plotNatMort(obj.std,styr=styr,endyr=endyr,min.yr=1970);
}
#----------------------------------
#------------------------------------------
# growth estimates
#------------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins[1:24],
obj.rep$"Predicted.mean.postmolt.length.females"[1:24],type="l",
xlab="Pre-Molt Length",ylab="Post-Molt Length",ylim=c(35,185),xlim=c(25,200))
points(length.bins[1:24],exp(0.5656024)*length.bins[1:24]^0.913266,pch=1)
points(length.bins,exp(0.43794)*length.bins^0.948703,pch=3)
lines(length.bins, obj.rep$"Predicted.mean.postmolt.length.males",lty=1)
mtext("Growth",side=3,adj=0.0);
#----------------------------------
#---------------------------------------
# probability of maturing
#---------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins,
obj.rep$"Predicted.probability.of.maturing.females",
xlab="Carapace Width (mm)", ylab="Probability of Maturing",type="l",lty=2)
lines(length.bins,obj.rep$"Predicted.probability.of.maturing.males")
#maturity 2009 assessment
lines(length.bins, 1/(1+exp(-(0.07754*(length.bins-130.8540)))),lty=3)
mtext("Maturation",side=3,adj=0.0);
#----------------------------------
#---------------------------------------
# size distribution of recruits
#---------------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
plot(length.bins,
obj.rep$"distribution.of.recruits.to.length.bins",
type="b",xlab="Carapace Width (mm)",ylab="Proportion",lty=1,pch=21)
mtext("Assumed size distribution at recruitment",side=3,adj=0.0);
#----------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
#----------------------------------------------
# Survey selectivity
#----------------------------------------------
#tanner underbag selectivity parameters
pa=0.8743/(1+ 10.95*exp(-.0504*(seq(27.5,182.5,by=5))))
pb=1-(1/(1+185.9*exp(-.1742*(seq(27.5,182.5,by=5)))))
ubx.x<-seq(27.5,182.5,by=5)
ubx.y<-pa+(1-pa)*pb
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
pchs<-c(21,22,23,24)
ltys<-c( 1, 1, 2,NA)
#--males ??
plot(length.bins,
obj.rep$"selectivity.survey.males.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr",pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr",lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.males.1982.to.1987", pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.males.1982.to.1987", lty=ltys[2])
points(length.bins,obj.rep$"selectivity.survey.males.1974.to.1981", pch=pchs[3])
lines( length.bins,obj.rep$"selectivity.survey.males.1974.to.1981", lty=ltys[3])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(140,140),c(0,1.0)) #ref size males
mtext("Trawl survey selectivity, males",side=3,adj=0)
legend("topright",
c("males, 1988+","males, 1982-1987","males 1974-1981","Somerton underbag exp."),
lty=ltys,pch=pchs,cex=0.7)
#--females ??
plot(length.bins,
obj.rep$"selectivity.survey.females.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.females.1982.to.1987", pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.females.1982.to.1987", lty=ltys[2])
points(length.bins,obj.rep$"selectivity.survey.females.1974.to.1981", pch=pchs[3])
lines( length.bins,obj.rep$"selectivity.survey.females.1974.to.1981", lty=ltys[3])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(100,100),c(0,1.0)) #ref size females
mtext("Trawl survey selectivity, females",side=3,adj=0)
legend("topright",
c("females, 1988+","females, 1982-1987","females 1974-1981","Somerton underbag exp."),
lty=ltys,pch=pchs,cex=0.7)
#most recent period
plot(length.bins,
obj.rep$"selectivity.survey.males.1988.to.endyr",
type="n",xlab="Carapace Width(mm)",ylab="Selectivity",ylim=c(0,1.5))
points(length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr", pch=pchs[1])
lines( length.bins,obj.rep$"selectivity.survey.males.1988.to.endyr", lty=ltys[1])
points(length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",pch=pchs[2])
lines( length.bins,obj.rep$"selectivity.survey.females.1988.to.endyr",lty=ltys[2])
points(ubx.x,ubx.y,pch=pchs[4]) #underbag exp.
#lines( ubx.x,ubx.y,lty=ltys[4]) #underbag exp.
lines(c(140,140),c(0,1.0),lty=2) #ref size males
lines(c(100,100),c(0,1.0),lty=3) #ref size females
mtext("Trawl survey selectivity, 1988+",side=3,adj=0)
legend("topright",
c("males","females","Somerton underbag exp."),
lty=ltys[c(1,2,4)],pch=pchs[c(1,2,4)],cex=0.7)
#----------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
#----------------------------------------------
# TCF retained selectivity for new shell males
#----------------------------------------------
sel<-obj.rep$"selectivity.fishery.ret.new.males"
plot(length.bins,sel[1,],
type="l",ylim=c(0,1.0),lwd=3,xlab="Carapace width (mm)",ylab="Retention")
rownames(sel)<-years.m1;
ctr<-0
for (i in as.character(yrs.tcf)) {
lines(length.bins,sel[i,],lty=2,lwd=2)
y<-0.75-ctr*0.5/length(yrs.tcf)
iz<-which.min((sel[i,]-y)^2)
text(length.bins[iz],y,labels=i,cex=0.9,col="dark blue")
ctr<-ctr+1
}
mtext("Directed fishery retention",side=3,adj=0,outer=FALSE)
#----------------------------------
#----------------------------------------------
# TCF total selectivity for males
#----------------------------------------------
sel<-obj.rep$"selectivity.fishery.total.new.males";
plot(length.bins,sel[1,],type="l",lwd=3,ylim=c(0,1.0),xlab="Carapace Width (mm)",ylab="Total Selectivity")
rownames(sel)<-years.m1;
ctr<-0
for (i in as.character(yrs.tcf)) {
lines(length.bins,sel[i,],lty=2,lwd=2)
y<-0.75-ctr*0.5/length(yrs.tcf)
iz<-which.min((sel[i,]-y)^2)
text(length.bins[iz],y,labels=i,cex=0.9,col="dark blue")
ctr<-ctr+1
}
mtext("Total directed fishery selectivity on males",side=3,adj=0.0);
#----------------------------------
#----------------------------------------------
# TCF total selectivity for females
#----------------------------------------------
sel<-obj.rep$"selectivity.discard.females";
plot(length.bins,sel,type="l",lwd=3,ylim=c(0,1.0),xlab="Carapace Width (mm)",ylab="Total Selectivity")
mtext("Total directed fishery selectivity on females",side=3,adj=0.0);
#----------------------------------
#--------------------------------
# snow crab fishery selectivity
#--------------------------------
par(oma=c(2,2,2,2),mar=c(4,4,2,1)+0.2,mfrow=c(3,1))
plot(length.bins,obj.rep$"selectivity.snow.females"[1,],
type="l",lty=2,lwd=2,ylim=c(0,1.1),
xlab="Carapace width(mm)",ylab="Selectivity")
lines(length.bins,obj.rep$"selectivity.snow.females"[2,],lty=2,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.snow.females"[3,],lty=2,lwd=2,col="blue")
lines(length.bins,obj.rep$"selectivity.snow.males"[1,],lty=1,lwd=2,col="black")
lines(length.bins,obj.rep$"selectivity.snow.males"[2,],lty=1,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.snow.males"[3,],lty=1,lwd=2,col="blue")
mtext("snow crab fishery",side=3,adj=0.0,outer=FALSE);
legend("bottomright",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#--------------------------------
# BBRKC fishery selectivity
#--------------------------------
plot(length.bins,
obj.rep$"selectivity.redk.females"[1,],
type="l",lty=2,lwd=2,ylim=c(0,1.1),
xlab="Carapace width(mm)",ylab="Selectivity Red King Fishery")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.females"[2,],lty=2,lwd=2,col="green")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.females"[3,],lty=2,lwd=2,col="blue")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[1,],lwd=2)
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[2,],lwd=2,col="green")
lines(as.numeric(length.bins),obj.rep$"selectivity.redk.males"[3,],lwd=2,col="blue")
mtext("BBRKC fishery",side=3,adj=0.0,outer=FALSE);
legend("topleft",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#----------------------------------------------
# Groundfish fishery selectivity
#----------------------------------------------
plot(length.bins, obj.rep$"selectivity.trawl.females"[1,],
type="l",xlab="Carapace width(mm)",ylab="Selectivity",ylim=c(0,1.1),lty=2,lwd=2,col="black")
lines(length.bins,obj.rep$"selectivity.trawl.females"[2,],lty=2,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.trawl.females"[3,],lty=2,lwd=2,col="blue")
names(obj.rep$"selectivity.trawl.males")<-as.character(length.bins)
lines(length.bins, obj.rep$"selectivity.trawl.males"[1,],lty=1,lwd=2)
lines(length.bins, obj.rep$"selectivity.trawl.males"[2,],lty=1,lwd=2,col="green")
lines(length.bins,obj.rep$"selectivity.trawl.males"[3,],lty=1,lwd=2,col="blue")
mtext("groundfish fishery",side=3,adj=0.0,outer=FALSE);
legend("bottomright",
c("females, era 1","females, era 2","females, era 3","males, era 1","males, era 2","males, era 3"),
lty=c(2,2,2,1,1,1),col=rep(c("black","green","blue"),times=2),lwd=2,cex=0.7)
#----------------------------------
#-------------------------------------------------
# Directed fishery capture rates/fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.TCF.male.new.shell.mortality.rate"
f.r<-obj.rep$"max.retained.mortality.rate"
f.c<-obj.rep$"max.TCFM.new.shell.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,f.r,na.rm=TRUE)))
lines(years.m1,f.r,lty=2,col='green',lwd=3)
if (isGmacs) lines(years.m1,f.c,lty=3,col='cyan',lwd=3)
mtext("Directed fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality","retained mortality"),pch=c(NA,NA,NA),
lty=c(3,1,2),lwd=c(3,3,3),col=c('cyan','blue','green'),cex=1)
f.m<-obj.rep$"mean.TCF.male.new.shell.mortality.rate"
f.r<-obj.rep$"mean.retained.mortality.rate"
f.c<-obj.rep$"mean.TCFM.new.shell.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,f.r,na.rm=TRUE)))
lines(years.m1,f.r,lty=1,col='green',lwd=3)
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality","retained mortality"),pch=c(NA,NA,NA),
lty=c(1,1,1),lwd=c(3,3,3),col=c('cyan','blue','green'),cex=1)
#--females
f.m<-obj.rep$"max.TCF.female.mortality.rate"
f.c<-obj.rep$"max.TCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Directed fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.TCF.female.mortality.rate"
f.c<-obj.rep$"mean.TCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Snow crab fishery capture rate/fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.SCF.male.mortality.rate"
f.c<-obj.rep$"max.SCF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Snow crab fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.SCF.male.mortality.rate"
f.c<-obj.rep$"mean.SCF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.SCF.female.mortality.rate"
f.c<-obj.rep$"max.SCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Snow crab fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.SCF.female.mortality.rate"
f.c<-obj.rep$"mean.SCF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Red king crab fishery fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.RKF.male.mortality.rate"
f.c<-obj.rep$"max.RKF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("BBRKC fishery: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.RKF.male.mortality.rate"
f.c<-obj.rep$"mean.RKF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.RKF.female.mortality.rate"
f.c<-obj.rep$"max.RKF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("BBRKC fishery: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.RKF.female.mortality.rate"
f.c<-obj.rep$"mean.RKF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Groundfish fishery fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(1,4,1,1)+0.2,mfrow=c(2,1))
#--males
f.m<-obj.rep$"max.GTF.male.mortality.rate"
f.c<-obj.rep$"max.GTF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Groundfish fisheries: males",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.GTF.male.mortality.rate"
f.c<-obj.rep$"mean.GTF.male.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#--females
f.m<-obj.rep$"max.GTF.female.mortality.rate"
f.c<-obj.rep$"max.GTF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Full-selected Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
mtext("Groundfish fisheries: females",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
f.m<-obj.rep$"mean.GTF.female.mortality.rate"
f.c<-obj.rep$"mean.GTF.female.capture.rate"
plot(years.m1, f.m, type="l",lty=1,col='blue',lwd=3,
xlab="", ylab="Mean Fishery Rate",
xlim=range(plotyears),ylim=c(0,max(f.c,f.m,na.rm=TRUE)))
if (isGmacs) lines(years.m1,f.c,lty=1,col='cyan',lwd=3)
legend("topright",legend=c("capture rate","total mortality"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('cyan','blue'),cex=1)
#----------------------------------
#-------------------------------------------------
# Total fishing mortality
#-------------------------------------------------
par(oma=c(1,1,1,1),mar=c(2,4,1,1)+0.2,mfrow=c(2,1))
#--max mortality
fm.m<-obj.rep$"max.TOT.male.NS.mortality.rate"
fm.f<-obj.rep$"max.TOT.female.NS.mortality.rate"
plot(years.m1, fm.m, type="l",col='blue',lwd=3,
xlab="", ylab="Fishing Mortality Rate",
xlim=range(plotyears),ylim=c(0,max(fm.m,fm.f,na.rm=TRUE)))
lines(years.m1,fm.f,lty=1,col='green',lwd=3)
mtext("Max (fully-selected) fishing mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("males","females"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('blue','green'),cex=1)
#--mean mortality
fm.m<-obj.rep$"mean.TOT.male.NS.mortality.rate"
fm.f<-obj.rep$"mean.TOT.female.NS.mortality.rate"
plot(years.m1, fm.m, type="l",col='blue',lwd=3,
xlab="Year", ylab="Fishing Mortality Rate",
xlim=range(plotyears),ylim=c(0,max(fm.m,fm.f,na.rm=TRUE)))
lines(years.m1,fm.f,lty=1,col='green',lwd=3)
mtext("Mean fishing mortality",side=3,adj=0.0,outer=FALSE);
legend("topright",legend=c("males","females"),pch=c(NA,NA),
lty=c(1,1),lwd=c(3,3),col=c('blue','green'),cex=1)
#----------------------------------
if (!is.null(obj.std)){
par(oma=c(1,1,1,1),mar=c(4,3,2,1)+0.2,mfrow=c(3,1))
#-------------------------------------------------
# Mature male biomass at mating time
#-------------------------------------------------
sdf.mmb<-obj.std[obj.std[,2]=="sdrMMB",]
mmb.sd<-sdf.mmb[,4]
mmb.mn<-sdf.mmb[,3]
plot(years[1:(length(years)-1)],mmb.mn,type="l",lty=1,
xlab="Year",ylab="Biomass (1000's t)",
ylim=c(0,1.2*max(mmb.mn+mmb.sd,na.rm=TRUE)))
points(years[1:(length(years)-1)],mmb.mn,pch=1)
wtsPlots::plotErrorBars.V(years[1:(length(years)-1)],mmb.mn,
sigma=mmb.sd,CI=0.8)
mtext("MMB at Mating",side=3,adj=0.0);
#----------------------------------
#-------------------------------------------
# Recruitment
#-------------------------------------------
##-by model year
recLag<-obj.rep$recLag;
sdf.R<-obj.std[obj.std[,2]=="sdrLnRec",];#1st year is styr+recLag
R.mn<-2*exp(sdf.R[,3])/THOUSAND;#scale to total recruitment in millions
R.sd<-sqrt(exp(sdf.R[,4]^2)-1)*R.mn;
yrs.R<-(styr+recLag):endyr;
plot(yrs.R,R.mn,type="l",lty=1,
xlab="Year",ylab="numbers (millions)",
ylim=c(0,1.2*max(R.mn+R.sd,na.rm=TRUE)))
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr),lty=2,lwd=2,col='grey')
points(yrs.R,R.mn,pch=1)
wtsPlots::plotErrorBars.V(yrs.R,R.mn,sigma=R.sd,CI=0.8,lognormal=TRUE)
mtext("Total recruitment",side=3,adj=0.0);
mnR<-mean(R.mn[(1977-styr+1):length(R.mn)]);
lines(((1977+recLag):endyr),mnR+0*((1977+recLag):endyr),lty=2,lwd=2)
##-lagged to fertilization year
recLag<-obj.rep$recLag;
sdf.R<-obj.std[obj.std[,2]=="sdrLnRec",];#1st year is styr+recLag
R.mn<-2*exp(sdf.R[,3])/THOUSAND;#scale to total recruitment in millions
R.sd<-sqrt(exp(sdf.R[,4]^2)-1)*R.mn;
yrs.R<-styr:(endyr-recLag);
plot(yrs.R,R.mn,type="l",lty=1,
xlab="Fertilization Year",ylab="numbers (millions)",
ylim=c(0,1.2*max(R.mn+R.sd,na.rm=TRUE)))
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr)-recLag,lty=2,lwd=2,col='grey')
points(yrs.R,R.mn,pch=1)
wtsPlots::plotErrorBars.V(yrs.R,R.mn,sigma=R.sd,CI=0.8,lognormal=TRUE)
mtext("Total recruitment",side=3,adj=0.0);
mnR<-mean(R.mn[(1977-styr+1):length(R.mn)]);
lines(1977:(endyr-recLag),mnR+0*(1977:(endyr-recLag)),lty=2,lwd=2)
#----------------------------------
}## if obj.std not null
par(oma=c(1,1,1,1),mar=c(4,3,2,1)+0.2,mfrow=c(3,1))
#----------------------------------
# spawning biomass by sex
#----------------------------------
prd.MMB<-obj.rep$"Mating.time.Male.Spawning.Biomass";
prd.MFB<-obj.rep$"Mating.time.Female.Spawning.Biomass";
plot(years.m1,prd.MMB+prd.MFB,type="l",lty=2,lwd=1,
ylab="Mature Biomass (1000 t)",xlab="Year");
lines(years.m1,prd.MMB,lty=1,lwd=2,col='blue')
lines(years.m1,prd.MFB,lty=1,lwd=2,col='green')
mtext("Spawning biomass at mating time", side=3, adj=0.05)
legend("topright",
c("males (MMB)","females", "total"),
lty=c(1,1,2),col=c('blue','green','black'))
#----------------------------------
#-------------------------------------------
# Recruitment
#-------------------------------------------
##-by model year
recLag<-obj.rep$recLag
tsR<-2*(obj.rep$"estimated.number.of.recruits.female")/THOUSAND;
yrs.R<-years;##-gives model year
plot(yrs.R,tsR,type="l",lty=1,
xlab="Year",ylab="numbers (millions)",
xlim=range(years),
ylim=c(0,1.2*max(tsR,na.rm=TRUE)))
mnRec<-mean(tsR[(1977+recLag-styr+1):length(tsR)]);
lines((1977+recLag):endyr,mnRec+0*((1977+recLag):endyr),lty=2,lwd=2)
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr),lty=2,lwd=2,col='grey')
points(yrs.R,tsR,pch=1)
mtext("Total recruitment",side=3,adj=0.0);
##-by fertilization year
recLag<-obj.rep$recLag;##-will lag to fertilization year
tsR<-2*(obj.rep$"estimated.number.of.recruits.female")/THOUSAND;
yrs.R<-years-1-recLag;
plot(yrs.R,tsR,type="l",lty=1,
xlab="Fertilization Year",ylab="numbers (millions)",
xlim=range(years),
ylim=c(0,1.2*max(tsR,na.rm=TRUE)))
mnRec<-mean(tsR[(1983-1-recLag-styr+1):length(tsR)]);
lines(1977:(endyr-recLag),mnRec+0*(1977:(endyr-recLag)),lty=2,lwd=2)
abline(v=c(obj.rep$mnYrRecDevsHist,obj.rep$mnYrRecCurr)-recLag,lty=2,lwd=2,col='grey')
points(yrs.R,tsR,pch=1)
mtext("Total recruitment (by fertilization year)",side=3,adj=0.0);
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
#--------------------------------------------
#Legal males.
#--------------------------------------------
plot(obsyears, obj.rep$"observed.number.of.males.greater.than.101.mm"/THOUSAND,type="p",
xlab="Year",ylab="Number (millions)",ylim=c(0,200))
lines(obsyears,obj.rep$"estimated.survey.numbers.of.males.101"[(1:length(years))[years==min(obsyears)]:length(years)]/THOUSAND,
lty=1,lwd=1)
lines(obsyears,obj.rep$"pop.estimate.numbers.of.males.101"[(1:length(years))[years==min(obsyears)]:length(years)]/THOUSAND,
lty=2)
legend("topright",
c("predicted total numbers","predicted survey numbers", "observed survey numbers"),
lty=c(2,1,NA),pch=c(NA,NA,21))
mtext(paste("Legal males (>=",obj.rep$legalSize,"mm CW)"), side=3, adj=0.05)
#----------------------------------
#-------------------------------------------------
# Fraction of male discard mortality in directed fishery
#-------------------------------------------------
frc<-obj.rep$"predicted.TCF.male.discard.mortality.biomass"/obj.rep$"predicted.retained.catch.biomass";
plot(years.m1,frc,type='l',
xlab="Fishery Year",ylab="ratio",
xlim=range(years),ylim=c(0,2.0))
mtext("Directed fishery male discard mortality biomass relative to retained catch biomass",side=3,adj=0.0,outer=FALSE);
#----------------------------------
#-------------------------------------------------
# Exploitation rate
#-------------------------------------------------
xpl<-obj.rep$"estimated.total.catch.divided.by.male.spawning.biomass.at.fishtime";
plot(years.m1, xpl, type="l",
xlab="Year",ylab="Exploitation Rate",xlim=range(plotyears),ylim=c(0,1.0))
xpl<-obj.rep$"estimated.total.catch.of.legal.males.divided.by.legal.males.at.fishtime"
lines(years.m1,xpl,,lty=2)
legend("topright",legend=c("total catch","legal males"),
lty=c(1,2),pch=c(NA,NA),cex=1)
#------------------------------------------------------------
# Harvest control rule and fishing mortality
#------------------------------------------------------------
if (!is.na(F35)){
par(oma=c(1,1,1,1),mar=c(4,4,2,1)+0.2,mfrow=c(2,1))
yrs<-styr:(endyr-1)
mmb<-obj.rep$"Mating.time.Male.Spawning.Biomass";
tfm<-obj.rep$"max.TOT.male.NS.mortality.rate";
idx<-(yrs>=1965)&(tfm>0);
yrs<-yrs[idx];
mmb<-mmb[idx];
tfm<-tfm[idx];
plot(mmb,tfm,type='n',
xlab=" MMB (1000 t)",ylab="Full Selection Fishing Mortality Rate",
xlim=c(0,1.1*max(mmb)),ylim=c(0,1.1*max(tfm)))
n<-length(yrs);
ctr<-1:(n-1);
text(mmb[ctr],tfm[ctr],as.character(yrs[ctr]),cex=0.7,adj=0)
text(mmb[n],tfm[n],as.character(yrs[n]),cex=1.1,col='red',adj=0)
alpha<-0.1
beta<-0.25
lines(rep(B35,length=20),seq(0,1.1*max(tfm),length=20),lty=4,col="blue")
lines(seq(0,1.1*max(mmb),length=20),rep(F35,length=20),lty=4,col="blue")
text(B35,1.1*max(tfm),expression(bold(B[35])),cex=0.8,adj=0.5,col="blue")
text(1.1*max(mmb),F35,expression(bold(F[35])),cex=0.8,adj=0.5,col="blue")
lines(rep(B35*beta,length=20),
seq(0,F35*((((B35*beta)/B35)-alpha)/(1.-alpha)),length=20),
type="l",lty=1,lwd=2)
lines(seq(B35*beta,B35,length=20),
F35*(((seq(B35*beta,B35,length=20)/B35)-alpha)/(1.-alpha)),
type="l",lty=1,lwd=2)
lines(seq(B35,max(mmb),length=20),
rep(F35,length=20),
lty=1,lwd=2)
}
##Stock-recruit relationship
cex<-par("cex")
par(cex=0.75)
recLag<-obj.rep$recLag;
yrs<-styr:(endyr-1)
tmp=length(unlist((obj.rep$"Mating.time.Male.Spawning.Biomass")));
x<-obj.rep$"Mating.time.Male.Spawning.Biomass";
y<-obj.rep$"estimated.number.of.recruits.female"/1000;
idx<-(obj.rep$mnYrRecCurr-1-recLag-styr+1):(endyr-1-recLag-styr+1);
plot(x[idx],y[idx+1+recLag],
xlim=c(0,1.1*max(x)),ylim=c(0,1.1*max(y)),
xlab="Male Spawning Biomass(1000 t) at Feb. 15",
ylab="Recruitment (millions)",type="n")
yrs.tmp<-(obj.rep$mnYrRecCurr-1-recLag):(endyr-1-recLag);
text(x,y,wtsUtilities::formatZeros(yrs.tmp%%100,width=2),adj=0,cex=1.0);
par(cex=cex)
#----------------------------------
# plot observed total and mature (spawning) biomass from survey
#----------------------------------
#observed spawning biomass
spB.m.obs <-obj.rep$"Observed.survey.male.spawning.biomass"
spB.f.obs <-obj.rep$"Observed.survey.female.spawning.biomass"
spB.t.obs <-obj.rep$"Observed.survey.biomass"
spB.tm.obs<-spB.m.obs+spB.f.obs;#total observed survey MATURE biomass
#cv's
idx<-(1:length(years))[years==min(obsyears)]:length(years)
cv.f<-tanner.cv[,2];
cv.m<-tanner.cv[,3];
cv.t=sqrt((spB.m.obs[idx]*cv.m)^2 + (spB.f.obs[idx]*cv.f)^2)/(spB.tm.obs[idx]);
par(oma=c(0.5,1,1,0.5),mar=c(2,5,2,1)+0.2,mfrow=c(2,1))
#total survey biomass
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
#CV's assumed same as for total SPAWNING biomass in survey
lower= (spB.t.obs)*(exp(-1.96*sqrt(log(1+cv.t^2)))-1);#lower error bar
upper= (spB.t.obs)*(exp( 1.96*sqrt(log(1+cv.t^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.t.obs,upper=upper,lower=lower);
points(obsyears,spB.t.obs,pch=21);
mtext("Observed total survey biomass", side=3, adj=0.05)
#total mature survey biomass
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lower= (spB.tm.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.t^2)))-1);#lower error bar
upper= (spB.tm.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.t^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.tm.obs[idx],upper=upper,lower=lower);
points(obsyears,spB.tm.obs[idx],pch=21);
mtext("Observed total mature survey biomass", side=3, adj=0.05)
par(oma=c(0.5,1,1,0.5),mar=c(2,5,2,1)+0.2,mfrow=c(2,1))
#mature survey biomass by sex
plot(c(0,1),c(0,1),type="l",lty=2,
ylim=c(0,400),xlim=c(min(obsyears),max(obsyears)),ylab="Biomass (1000's t)",xlab='');
lower= (spB.f.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.f^2)))-1);#lower error bar
upper= (spB.f.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.f^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears,spB.f.obs[idx],upper=upper,lower=lower,col='green');
points(obsyears,spB.f.obs[idx],pch=21,col='green');
lower= (spB.m.obs)[idx]*(exp(-1.96*sqrt(log(1+cv.m^2)))-1);#lower error bar
upper= (spB.m.obs)[idx]*(exp( 1.96*sqrt(log(1+cv.m^2)))-1);#upper error bar
wtsPlots::plotErrorBars.V(obsyears+0.2,spB.m.obs[idx],upper=upper,lower=lower,col='blue');
points(obsyears+0.2,spB.m.obs[idx],pch=23,col='blue');
mtext("Observed mature survey biomass", side=3, adj=0.05)
legend("topright",
c("females", "males"),
pch=c(21,23),col=c('green','blue'))
#----------------------------------
#----------------------------------
# Plot survey numbers
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
plot(years,obj.rep$"predicted.survey.numbers.female"/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years, obj.rep$"Observed.survey.numbers.female"/THOUSAND,pch=21);
mtext("Females",side=3,adj=0.1,cex=1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"predicted.survey.numbers.male"/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years, obj.rep$"Observed.survey.numbers.male"/THOUSAND);
mtext("Males",side=3,adj=0.1,cex=1)
#----------------------------------
#----------------------------------
# Plot mature new/old shell survey numbers (female)
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
plot(years,obj.rep$"Predicted.Female.survey.new.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.female.new.spawning.numbers"/THOUSAND);
mtext("Mature new shell female",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"Predicted.Female.survey.old.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.female.old.spawning.numbers"/THOUSAND);
mtext("Mature old shell female",side=3,adj=0.1)
tot.p.f<-obj.rep$"Predicted.Female.survey.new.mature.numbers"+
obj.rep$"Predicted.Female.survey.old.mature.numbers";
tot.o.f<-obj.rep$"Observed.survey.female.old.spawning.numbers"+
obj.rep$"Observed.survey.female.new.spawning.numbers";
plot(years,tot.p.f/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,tot.o.f/THOUSAND);
mtext("All mature female",side=3,adj=0.1)
#----------------------------------
#----------------------------------
# Plot mature new/old shell survey numbers (male)
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(3,1))
plot(years,obj.rep$"Predicted.Male.survey.new.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.male.new.spawning.numbers"/THOUSAND);
mtext("Mature new shell male",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
plot(years,obj.rep$"Predicted.Male.survey.old.mature.numbers"/THOUSAND,type="l",
ylim=c(0,500),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,obj.rep$"Observed.survey.male.old.spawning.numbers"/THOUSAND);
mtext("Mature old shell male",side=3,adj=0.1)
tot.p.m<-obj.rep$"Predicted.Male.survey.new.mature.numbers"+
obj.rep$"Predicted.Male.survey.old.mature.numbers";
tot.o.m<-obj.rep$"Observed.survey.male.old.spawning.numbers"+
obj.rep$"Observed.survey.male.new.spawning.numbers";
plot(years,tot.p.m/THOUSAND,type="l",
ylim=c(0,1000),xlim=range(obsyears),ylab="Survey Numbers (millions)",xlab="Year");
points(years,tot.o.m/THOUSAND);
mtext("All mature male",side=3,adj=0.1)
#----------------------------------
#----------------------------------
# fraction mature by size
#----------------------------------
par(oma=c(0.5,1,1,0.5),mar=c(4,5,2,1)+0.2,mfrow=c(2,1))
frac.p.f<-tot.p.f/obj.rep$"predicted.survey.numbers.female";
frac.o.f<-tot.o.f/obj.rep$"Observed.survey.numbers.female";
plot(years,frac.p.f,type="l",
ylim=c(0,1.0),xlim=range(obsyears),ylab="fraction mature",xlab="Year");
points(years,frac.o.f);
mtext("Female",side=3,adj=0.1)
legend("topright",
c("predicted","observed"),
lty=c(1,NA),pch=c(NA,21))
frac.p.m<-tot.p.m/obj.rep$"predicted.survey.numbers.male";
frac.o.m<-tot.o.m/obj.rep$"Observed.survey.numbers.male";
plot(years,frac.p.m,type="l",
ylim=c(0,1.0),xlim=range(obsyears),ylab="fraction mature",xlab="Year");
points(years,frac.o.m);
mtext("Male",side=3,adj=0.1)
#----------------------------------
#--------------------------------------------
#Survey size comps: numbers at size
#--------------------------------------------
colnames(obj.rep$"Observed.Survey.Numbers.by.length.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Survey.Numbers.by.length.females",
obj.rep$"Predicted.Survey.Numbers.by.length.females",
nr = 8, nc = 6,nplot = length(obsyears));
mtext("Survey numbers, females",side=3,adj=0.0,outer=TRUE);
colnames(obj.rep$"Observed.Survey.Numbers.by.length.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Survey.Numbers.by.length.males",
obj.rep$"Predicted.Survey.Numbers.by.length.males",
nr = 8, nc = 6,nplot = length(obsyears));
mtext("Survey numbers, males",side=3,adj=0.0,outer=TRUE);
#----------------------------------
#----------------------------------
# plot fits to components of survey size comps
#----------------------------------
#--immature, new shell females-------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.immature.new.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.immature.new.females",
obj.rep$"Predicted.length.prop.survey.immature.new.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.19)
mtext("Survey proportions, immature new shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.immature.new.females",
datap=obj.rep$"Predicted.length.prop.survey.immature.new.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.immature.new.females.sampsize"[1:15]);
mtext("Survey proportions, immature new shell females",side=3,adj=0.0);
#--mature, new shell females---------
colnames(obj.rep$"Observed.Length.Prop.survey.mature.new.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.new.females",
obj.rep$"Predicted.length.prop.survey.mature.new.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.1)
mtext("Survey proportions, mature new shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.new.females",
datap=obj.rep$"Predicted.length.prop.survey.mature.new.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.females.sampsize"[1:15]);
mtext("Survey proportions, mature new shell females",side=3,adj=0.0);
#--mature, old shell females----------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.mature.old.females")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.old.females",
obj.rep$"Predicted.length.prop.survey.mature.old.females", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.19)
mtext("Survey proportions, mature old shell females",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.old.females",
datap=obj.rep$"Predicted.length.prop.survey.mature.old.females",
nlen=15,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.old.females.sampsize"[1:15]);
mtext("Survey proportions, mature old shell females",side=3,adj=0.0);
#--immature, new shell males-----------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.immature.new.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.immature.new.males",
obj.rep$"Predicted.length.prop.survey.immature.new.males", nr = 7, nc = 6,
nplot = length(obsyears),maxy=.08)
mtext("Survey proportions, immature new shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.immature.new.males",
datap=obj.rep$"Predicted.length.prop.survey.immature.new.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.immature.new.males.sampsize");
mtext("Survey proportions, immature new shell males",side=3,adj=0.0);
#--mature, new shell males-----------------
par(col=1);
colnames(obj.rep$"Observed.Length.Prop.survey.mature.new.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.new.males",
obj.rep$"Predicted.length.prop.survey.mature.new.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.025)
mtext("Survey proportions, mature new shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.new.males",
datap=obj.rep$"Predicted.length.prop.survey.mature.new.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.males.sampsize");
mtext("Survey proportions, mature new shell males",side=3,adj=0.0);
#--mature, old shell males----------------
colnames(obj.rep$"Observed.Length.Prop.survey.mature.old.males")<-c("year",as.character(length.bins))
plotSizeCompsComparisons(obj.rep$"Observed.Length.Prop.survey.mature.old.males",
obj.rep$"Predicted.length.prop.survey.mature.old.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.025)
mtext("Survey proportions, mature old shell males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=obj.rep$"Observed.Length.Prop.survey.mature.old.males",
datap=obj.rep$"Predicted.length.prop.survey.mature.old.males",
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.old.males.sampsize");
mtext("Survey proportions, mature old shell males",side=3,adj=0.0);
#--mature males---------------
tmpobs=obj.rep$"Observed.Length.Prop.survey.mature.new.males"+obj.rep$"Observed.Length.Prop.survey.mature.old.males"
colnames(tmpobs)=c("year",as.character(length.bins))
tmpobs[,1]=obj.rep$"Observed.Length.Prop.survey.mature.new.males"[,1]
plotSizeCompsComparisons(tmpobs,
obj.rep$"Predicted.length.prop.survey.mature.new.males"+obj.rep$"Predicted.length.prop.survey.mature.old.males",
nr = 7, nc = 6,
nplot = length(obsyears),maxy=.05)
mtext("Survey proportions, mature males",side=3,adj=0.0,outer=TRUE);
par(oma=c(2,2,2,2),mar=c(7,4,2,1)+0.2,mfrow=c(1,1))
plotBubbles(datao=tmpobs,
datap=(obj.rep$"Predicted.length.prop.survey.mature.old.males"+obj.rep$"Predicted.length.prop.survey.mature.new.males"),
nlen=32,sampsize=obj.rep$"Observed.Length.Prop.survey.mature.new.males.sampsize");
mtext("Survey proportions, mature males",side=3,adj=0.0);
#----------------------
dev.off()
}
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.