# Function to create rough estimates of parameters based on data
createEst <- function(dataDir){
rdat <- read.csv(file=paste(dataDir,"together.csv",sep=""),stringsAsFactors=FALSE)
hdat <- read.csv(file=paste(dataDir,"habitatData.csv",sep=""),stringsAsFactors=FALSE)
habDat1 <- hdat$poolPer10k
names(habDat1) <- hdat$population
habDat <- habDat1[rdat$population]
pops <-hdat$population
parr <- (rdat$spring_survToLGR*rdat$spr_mig + rdat$fall_survToLGR*rdat$fall_mig)/
rdat$summer_survToLGR
pOut <- rdat$fall_mig/parr
winterSurv <- pmin(0.999,rdat$spr_mig / (parr*(1-pOut)))
moveSurvRes <- rdat$spring_survToLGR
moveSurvMig <- pmin(0.999,rdat$fall_survToLGR*rdat$fall_mig / (parr * pOut * winterSurv))
# we have two different ways of estimating winter survival (what we did above, and dividing the observed winter parr to dam survival by moveSurvRes)
winterSurv2 <- rdat$winter_survToLGR/rdat$spring_survToLGR
survMax <- max(c(winterSurv,winterSurv2),na.rm=T)
# from Tom's stuff
Spr_LGR <- rdat$spring_survToLGR*rdat$spr_mig
win_parr <- Spr_LGR/rdat$winter_survToLGR
pseudoparr <- win_parr + rdat$fall_mig
srDat <- data.frame(
S=rdat$spawners45*rdat$Agewt/habDat,
parr=parr/habDat,
ws=winterSurv,
ws2=winterSurv2,
ws3=win_parr/parr,
win_parr=win_parr,
pseudoparr=pseudoparr,
pop=rdat$population)
plotVars <- function(srDat,x,y,xLab=NULL,yLab=NULL,xLim=NULL,yLim=NUll){
if(is.null(xLim)) xLim <- range(srDat[,x],na.rm=TRUE)
if(is.null(yLim)) yLim <- range(srDat[,y],na.rm=TRUE)
if(is.null(xLab)) xLab <- x
if(is.null(yLab)) yLab <- y
windows(10,10)
par(mfrow=c(2,2))
pops <- unique(srDat$pop)
for(pop in pops){
pDat <- srDat[srDat$pop==pop,]
plot(pDat[,x],pDat[,y],xlab=xLab,ylab=yLab,bty="l",main=pop,
pch=16,col=rgb(0,0,0,0.5),xlim=xLim,ylim=yLim)
}
}
plotVars(srDat,"S","parr",xLab="Spawner/PEU",yLab="Parr/PEU",xLim=c(0,100),yLim=c(0,20000))
plotVars(srDat,"parr","ws",xLab="Parr/PEU",yLab="Winter Survival",xLim=NULL,yLim=c(0,1))
# plotVars(srDat,"parr","ws2",xLab="Parr/PEU",yLab="Winter Survival 2",xLim=NULL,yLim=c(0,1))
# plotVars(srDat,"parr","ws3",xLab="Parr/PEU",yLab="Winter Survival 3",xLim=NULL,yLim=c(0,1))
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.