if (params$tabs) { cat('### Growth Parameters {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Growth Parameters') } dd <- params$Pars$M_ageArray %>% dim() nsim <- dd[1] maxage <- dd[2] nsamp <- length(params$its)
Histograms of r nsim
simulations of von Bertalanffy growth parameters Linf
, K
, and t0
, and inter-annual variability in Linf and K (Linfsd
and Ksd
), with vertical colored lines indicating r nsamp
randomly drawn values used in other plots:
par(mfrow=c(2,3)) hist2(Pars$Linf, main="Linf", col=params$plotPars$col, axes=params$plotPars$axes, breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main) abline(v=Pars$Linf[params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$Linfsd, main="Linfsd", col=params$plotPars$col, axes=params$plotPars$axes, breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main) abline(v=Pars$Linfsd[params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$K, main="K", col=params$plotPars$col, axes=params$plotPars$axes, breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main) abline(v=Pars$K[params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$Ksd, main="Ksd", col=params$plotPars$col, axes=params$plotPars$axes, breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main) abline(v=Pars$Ksd[params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$t0, main="t0", col=params$plotPars$col, axes=params$plotPars$axes, breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main) abline(v=Pars$t0[params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1)
The Linf and K parameters in each year for r nsamp
simulations. The vertical dashed line indicates the end of the historical period:
years <- c(seq(-nyears+1, 0, by=1), seq(1, proyears,1)) matplot(years, t(Pars$Linfarray[params$its,]), type="l", bty="l", main="", lwd=params$plotPars$lwd, lty=1, ylab="Linf", xlab="Year") abline(v=0, col="darkgray", lty=2) matplot(years, t(Pars$Karray[params$its,]), type="l", bty="l", main="", lwd=params$plotPars$lwd, lty=1, ylab="K", xlab="Year") abline(v=0, col="darkgray", lty=2)
Sampled length-at-age curves for r nsamp
simulations in the first historical year, the last historical year, and the last projection year.
par(mfrow=c(1,3), oma=c(2,3,1,1), mar=c(3,2,1,1)) fstYr <- Pars$Len_age[params$its,,1] curYr <- Pars$Len_age[params$its,,nyears] lstYr <- Pars$Len_age[params$its,,proyears+nyears] MaxL <- max(Pars$Len_age) matplot(t(fstYr), type="l", bty="l", main="First historical year", ylim=c(0, MaxL), xlab="Age", ylab="Length", cex.lab=2, lwd=params$plotPars$lwd, lty=1, xpd=NA) matplot(t(curYr), type="l", bty="l", main="Last historical year", ylim=c(0, MaxL), axes=params$plotPars$axes, xlab="Age", ylab="", cex.lab=2, lwd=params$plotPars$lwd, lty=1, xpd=NA) axis(side=1) axis(side=2, labels=FALSE) matplot(t(lstYr), type="l", bty="l", main="Last projected year", ylim=c(0, MaxL), axes=params$plotPars$axes, xlab="Age", ylab="", cex.lab=2, lwd=params$plotPars$lwd, lty=1, xpd=NA) axis(side=1) axis(side=2, labels=FALSE)
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