inst/Frameworks/LFA2733Framework/2.PlotsofIndicators.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
require(bio.lobster)
require(bio.utilities)
require(PBSmapping)
la()
#whether subset weeks is true or fales from CohortAnalysis (ByWeeks)
sset = T
sset = F
#from cohort analysis
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryatSeaIndicatorsDataLFA27-33.rdata')) #at Sea
if(sset) load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SubsetWksSummaryatSeaIndicatorsDataLFA27-33.rdata')) #at Sea
aS = outS
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryfsrsCommercialSamplesLanded33.rdata')) #fsrs
fS = outS
fS$LFA=33
load(file.path(project.datadirectory('bio.lobster'),'outputs','portSummaryLFA27-33.rdata'))
if(sset) load(file.path(project.datadirectory('bio.lobster'),'outputs','subsetweeksportSummaryLFA27-33.rdata'))
pS = outS
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryfsrsrecruitmentSamplesLanded27-33.rdata'))
fR = outS
mls = read.csv(file=file.path(project.datadirectory('bio.lobster'),'data','inputs','MLS.Changes.all.LFA.csv'))
if(!sset) IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Proportion.Landings', out.dir='bio.lobster',mls=mls)
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Median.Size', out.dir='bio.lobster',mls=mls,subset=sset)
require(data.table)
aa = as.data.frame(rbindlist(list(aS,pS,fR),fill=T))
write.csv(aa,file=file.path(fd,'Figs21-70.csv'))
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Median Size',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMedianSize.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Median.Size',ylim=c(70,115),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMedianSizeByLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMedianSizeByLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Median.Size',ylim=c(70,115),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMedianSizeByLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMedianSizeByLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Maximum.Size', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
#ik = which(y$ID=='fsrs' & y$LFA %in% c(28,29,30,'31A'))
#y = y[-ik,]
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Maximum Size',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMaxSize.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Maximum.Size',ylim=c(90,160),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMaxSizeByLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMaxSizeByLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Maximum.Size',ylim=c(90,160),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMaxSizeByLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMaxSizeByLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = NULL, indicator = 'New.Recruits', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion New Recruits',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodNewRec.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,4,5,7,8,10,11)
if(sset) ats = c(1,2,4,5,7,8)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion New Recruits',ylim=c(0,1),notch=F,border=c('black','black','black'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropRecruitsLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropRecruitsLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','blue','red')
boxplot(Indi~ID+LFA,data=db2,at=ats,col=cc,xaxt='n',ylab='Proportion New Recruits',ylim=c(0,1),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropRecruitsLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropRecruitsLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Sex.Ratio', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Sex Ratio',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodSexRat.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Sex Ratio',ylim=c(0.2,.8),notch=F,border=c('black','black','black'))
abline(h=0.5,lty=3)
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropFemaleLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropFemaleLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Sex Ratio',ylim=c(0.2,0.8),notch=F,border=c('black','black','black','black'))
abline(h=0.5,lty=3)
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropFemaleLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropFemaleLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Proportion.Berried', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion Berried',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodBerr.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','orange')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion.Berried',ylim=c(00,.6),notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,11.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropBerriedLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropBerriedLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','blue')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Proportion.Berried',ylim=c(0,0.6),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropberriedLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropberriedLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, indicator = 'Proportion.Mature', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion Mature',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMated.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
if(sset) ats = c(1,2,4,5,7,8)
if(!sset) ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion Mature',ylim=c(0.1,1),notch=F,border=c('black','black'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropMatedLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropMatedLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Proportion Mature',ylim=c(0,1),notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropMatedLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropMatedLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, indicator = 'Reproductive.Potential', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Reproductive Potential',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodRepPo.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
if(sset) ats = c(1,2,4,5,7,8)
if(!sset) ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Reproductive.Potential',notch=F,border=c('black','black'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedReproductivePotLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedReproductivePotLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Reproductive.Potential',notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedReproductivePotLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedReproductivePotLFA31A-33.png'),type='png')
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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require(bio.lobster)
require(bio.utilities)
require(PBSmapping)
la()
#whether subset weeks is true or fales from CohortAnalysis (ByWeeks)
sset = T
sset = F
#from cohort analysis
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryatSeaIndicatorsDataLFA27-33.rdata')) #at Sea
if(sset) load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SubsetWksSummaryatSeaIndicatorsDataLFA27-33.rdata')) #at Sea
aS = outS
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryfsrsCommercialSamplesLanded33.rdata')) #fsrs
fS = outS
fS$LFA=33
load(file.path(project.datadirectory('bio.lobster'),'outputs','portSummaryLFA27-33.rdata'))
if(sset) load(file.path(project.datadirectory('bio.lobster'),'outputs','subsetweeksportSummaryLFA27-33.rdata'))
pS = outS
load(file = file.path(project.datadirectory('bio.lobster'),'outputs','SummaryfsrsrecruitmentSamplesLanded27-33.rdata'))
fR = outS
mls = read.csv(file=file.path(project.datadirectory('bio.lobster'),'data','inputs','MLS.Changes.all.LFA.csv'))
if(!sset) IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Proportion.Landings', out.dir='bio.lobster',mls=mls)
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Median.Size', out.dir='bio.lobster',mls=mls,subset=sset)
require(data.table)
aa = as.data.frame(rbindlist(list(aS,pS,fR),fill=T))
write.csv(aa,file=file.path(fd,'Figs21-70.csv'))
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Median Size',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMedianSize.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Median.Size',ylim=c(70,115),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMedianSizeByLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMedianSizeByLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Median.Size',ylim=c(70,115),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMedianSizeByLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMedianSizeByLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Maximum.Size', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
#ik = which(y$ID=='fsrs' & y$LFA %in% c(28,29,30,'31A'))
#y = y[-ik,]
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Maximum Size',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMaxSize.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Maximum.Size',ylim=c(90,160),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMaxSizeByLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMaxSizeByLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Maximum.Size',ylim=c(90,160),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedMaxSizeByLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedMaxSizeByLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = NULL, indicator = 'New.Recruits', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion New Recruits',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodNewRec.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,4,5,7,8,10,11)
if(sset) ats = c(1,2,4,5,7,8)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion New Recruits',ylim=c(0,1),notch=F,border=c('black','black','black'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropRecruitsLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropRecruitsLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','blue','red')
boxplot(Indi~ID+LFA,data=db2,at=ats,col=cc,xaxt='n',ylab='Proportion New Recruits',ylim=c(0,1),notch=F,border=c('black','black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropRecruitsLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropRecruitsLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Sex.Ratio', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Sex Ratio',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodSexRat.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Sex Ratio',ylim=c(0.2,.8),notch=F,border=c('black','black','black'))
abline(h=0.5,lty=3)
axis(side=1,at=c(2,6,10,14),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropFemaleLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropFemaleLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,4,6,7,8,9,11,12,13,14,16,17,18,19)
cc = c('grey','orange','blue','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Sex Ratio',ylim=c(0.2,0.8),notch=F,border=c('black','black','black','black'))
abline(h=0.5,lty=3)
axis(side=1,at=c(2.5,7.5,12.5,17.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropFemaleLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropFemaleLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, fsrs=fS,fsrs.rec = fR, indicator = 'Proportion.Berried', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('fsrs','port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion Berried',col= c('grey','orange','red'),notch=F,border=c('black','black','black'))
axis(side=1,at=c(1,2,3),labels=c('At-Sea','FSRS Rec','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodBerr.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','orange')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion.Berried',ylim=c(00,.6),notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,11.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','FSRSRec'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropBerriedLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropBerriedLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,3,5,6,7,9,10,11,13,14,15)
cc = c('grey','orange','blue')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Proportion.Berried',ylim=c(0,0.6),notch=F,border=c('black','black','black'))
axis(side=1,at=c(2,6,10,14),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','FSRSRec','FSRSComm'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropberriedLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropberriedLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, indicator = 'Proportion.Mature', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Proportion Mature',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodMated.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
if(sset) ats = c(1,2,4,5,7,8)
if(!sset) ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Proportion Mature',ylim=c(0.1,1),notch=F,border=c('black','black'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropMatedLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropMatedLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Proportion Mature',ylim=c(0,1),notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedPropMatedLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedPropMatedLFA31A-33.png'),type='png')
x = IndicatorplotsMultDataSets(atSea=aS, port=pS, indicator = 'Reproductive.Potential', out.dir='bio.lobster',mls=mls,subset=sset)
y = as.data.frame(do.call(rbind,x))
w = subset(y,ID %in% c('port','atSea'))
boxplot(Indi~ID,data=w,xaxt='n',ylab='Reproductive Potential',col= c('grey','red'),notch=F,border=c('black','black'))
axis(side=1,at=c(1,2),labels=c('At-Sea','Port'))
savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','MethodRepPo.png'),type='png')
db1 = subset(y,LFA %in% c(27,28,29,30))
if(sset) ats = c(1,2,4,5,7,8)
if(!sset) ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=db1,at=ats,col=cc,xaxt='n',ylab='Reproductive.Potential',notch=F,border=c('black','black'))
if(sset) axis(side=1,at=c(1.5,4.5,7.5),labels=c('LFA27','LFA29','LFA30'))
if(!sset) axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA27','LFA28','LFA29','LFA30'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedReproductivePotLFA27-30.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedReproductivePotLFA27-30.png'),type='png')
db2 = subset(y,LFA %in% c('31A','31B','32','33'))
ats = c(1,2,4,5,7,8,10,11)
cc = c('grey','red')
boxplot(Indi~ID+LFA,data=na.omit(db2),at=ats,col=cc,xaxt='n',ylab='Reproductive.Potential',notch=F,border=c('black','black'))
axis(side=1,at=c(1.5,4.5,7.5,10.5),labels=c('LFA31A','LFA31B','LFA32','LFA33'))
legend('topright',legend=c('AtSea','Port'),pch=15,col=cc,cex=0.8,pt.cex=1.3,bty='n')
if(sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','subsetCombinedReproductivePotLFA31A-33.png'),type='png')
if(!sset) savePlot(file.path(project.figuredirectory('bio.lobster'),'AtSeaIndictors','CombinedReproductivePotLFA31A-33.png'),type='png')
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