require(bio.survey)
require(bio.groundfish)
require(bio.utilities)
load_all('~/git/bio.groundfish')
load_all('~/git/bio.survey')
fp = file.path(project.datadirectory('bio.groundfish'),"analysis")
p=list()
p$strat=c(440:483) #unit III - subtract 457 for unit 3
p$series =c('summer')# p$series =c('4vswcod');p$series =c('georges')
p$years.to.estimate = c(1970:2016)
p$species = 14
p$vessel.correction = T
p$vessel.correction.fixed = 1.2
p$functional.groups = F
p$strata.efficiencies = F
p$vessel.correction = T
p$vessel.correction.fixed = 1.2
p$length.based = F
p$by.sex = F
p$sex = 1# male female berried c(1,2,3)
p$strata.efficiencies=F
#out = groundfish.db(DS='gsdet.spec.redo',p=p)
p$alpha = 0.05
#out = groundfish.analysis(DS='ab.redo',p=p)
#MPA functional groups
p$functional.groups = F
p$bootstrapped.ci = F
#
p$clusters = c( rep( "localhost", 7) )
p = make.list(list(v=p$species, yrs=p$years.to.estimate),Y=p)
p$runs = p$runs[order(p$runs$v),]
p$strata.files.return=F
#parallel.run(groundfish.analysis,DS='stratified.estimates.redo',p=p,specific.allocation.to.clusters=T) #silly error arisingexit
#not finished
#all sizes
aout= groundfish.analysis(DS='stratified.estimates.redo',p=p,out.dir='silverhake')
write.table(aout, pipe("xclip -i", "w"))
gc()
#recruitment
p$length.based =T
p$size.class = c(10,18)
aout= groundfish.analysis(DS='stratified.estimates.redo',p=p,out.dir='silverhake')
write.table(aout, pipe("xclip -i", "w"))
gc()
#commercial
p$length.based =T
p$size.class = c(19,100)
aout= groundfish.analysis(DS='stratified.estimates.redo',p=p,out.dir='silverhake')
write.table(aout, pipe("xclip -i", "w"))
gc()
#weight at length
if(redo.mean.wt.at.length) {
sc = c(17,22)
sc2 = c(21,28)
p$by.sex = T
p$sex = 2 #male; 2=female
o = NULL
for(i in 1:length(sc)) {
p$size.class = c(sc[i],sc2[i])
a = groundfish.analysis(DS='mean.wt.at.length',p=p,out.dir= 'silverhake')
a$length = paste(sc[i],sc2[i],sep="-")
o = rbind(o,a)
}
save(o,file= file.path(project.datadirectory('silverhake'),'analysis','male.mean.wt.at.length.r'))
write.csv(o,pipe("xclip -i", "w"))
gc()
plot(1,1,xlab='Year',xlim=c(min(o$yr,na.rm=T),max(o$yr,na.rm=T)),ylim=c(min(o$meanWt,na.rm=T),350),ylab='Mean Weight at Length (g)',type='n')
with(o[which(o$length==sc[1]),],lines(yr,meanWt,col='red',lty=2,pch=16,type='b'))
a =with(o[which(o$length==sc[1]),],summary(lm(meanWt~yr)))
abline(a=coef(a)[1],b=coef(a)[2],col='red',lwd=2)
with(o[which(o$length==sc[2]),],lines(yr,meanWt,col='blue',lty=2,pch=16,type='b'))
a1 =with(o[which(o$length==sc[2]),],summary(lm(meanWt~yr)))
abline(a=coef(a1)[1],b=coef(a1)[2],col='blue',lwd=2)
with(o[which(o$length==sc[3]),],lines(yr,meanWt,col='black',lty=2,pch=16,type='b'))
a2 =with(o[which(o$length==sc[3]),],summary(lm(meanWt~yr)))
abline(a=coef(a2)[1],b=coef(a2)[2],col='black',lwd=2)
legend('top',c('20 cm', '23 cm','26 cm'),lty=c(2,2,2),pch=16,col=c('red','blue','black'),bty='n',ncol=3)
savePlot(file.path(project.datadirectory('redfish'),'figures','weight.at.length.png'),type='png')
}
#numbers at size
len = 1:75
oo = NULL
p$length.based=T
p$bootstrapped.ci = F
for(l in len) {
p$size.class = c(l,l)
aout= groundfish.analysis(DS='stratified.estimates.redo',p=p,out.dir= 'silverhake')
aout$len.group = l
oo = rbind(oo,aout)
}
save(oo,file = file.path(project.datadirectory('silverhake'),'analysis','stratified.at.length.silverhake.rdata'))
if(redo.survey.bubbles) {
load(file.path(project.datadirectory('silverhake'),'analysis','stratified.at.length.silverhake.rdata')) #This matches PComeau's #s
out = reshape(oo[,c('yr','len.group','n.yst')], timevar= 'len.group',idvar='yr',direction='wide')
pdf(file.path(project.datadirectory('silverhake'),'figures','silverhakesurveybubbles.pdf'))
matrixBubbles(t(out[,2:60]),xr=1:47,yr=1:59,maxinch=0.1,xlab='Year',ylab='Length',yc.colors=T,ttl='Silver Hake')
dev.off()
}
#habitat associations
p$strata.files.return =T
p$plot.name = 'silverhake.habitat.associations.pdf'
aout= groundfish.analysis(DS='stratified.estimates.redo',p=p)
figure.habitat.associations(aout,p=p,f.name=p$plot.name,out.dir='silverhake')
p$length.based=T
p$bootstrapped.ci = F
if(redo.mean.wt.at.length) {
sc = c(18,21,25)
o = NULL
for(i in 1:length(sc)) {
p$size.class = c(sc[i],sc[i])
a = groundfish.analysis(DS='mean.wt.at.length',p=p,out.dir= 'silverhake')
a$length = sc[i]
o = rbind(o,a)
}
save(o,file= file.path(project.datadirectory('redfish'),'analysis','mean.wt.at.length.r'))
plot(1,1,xlab='Year',xlim=c(min(o$yr,na.rm=T),max(o$yr,na.rm=T)),ylim=c(min(o$meanWt,na.rm=T),350),ylab='Mean Weight at Length (g)',type='n')
with(o[which(o$length==sc[1]),],lines(yr,meanWt,col='red',lty=2,pch=16,type='b'))
a =with(o[which(o$length==sc[1]),],summary(lm(meanWt~yr)))
abline(a=coef(a)[1],b=coef(a)[2],col='red',lwd=2)
with(o[which(o$length==sc[2]),],lines(yr,meanWt,col='blue',lty=2,pch=16,type='b'))
a1 =with(o[which(o$length==sc[2]),],summary(lm(meanWt~yr)))
abline(a=coef(a1)[1],b=coef(a1)[2],col='blue',lwd=2)
with(o[which(o$length==sc[3]),],lines(yr,meanWt,col='black',lty=2,pch=16,type='b'))
a2 =with(o[which(o$length==sc[3]),],summary(lm(meanWt~yr)))
abline(a=coef(a2)[1],b=coef(a2)[2],col='black',lwd=2)
legend('top',c('20 cm', '23 cm','26 cm'),lty=c(2,2,2),pch=16,col=c('red','blue','black'),bty='n',ncol=3)
savePlot(file.path(project.datadirectory('redfish'),'figures','weight.at.length.png'),type='png')
}
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