if (params$tabs) { cat('### Selectivity and Retention {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Selectivity and Retention') } dd <- params$Pars$M_ageArray %>% dim() nsim <- dd[1] maxage <- dd[2] nsamp <- length(params$its)
Histograms of r nsim
simulations of length at 5% selection (L5
), first length at full selection (LFS
), and vulnerability of animals at mean asymptotic length (Vmaxlen
) for the first historical year, the last historical year, and the last projection year, wtih vertical colored lines indicating r nsamp
randomly drawn values used in the other plots:
par(mfrow=c(3,3), oma=c(0,0,3,0), mar=c(2,1,3,1)) Yr <- 1 hist2(Pars$L5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="L5", breaks=params$plotPars$breaks) abline(v=Pars$L5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFS[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFS", breaks=params$plotPars$breaks) abline(v=Pars$LFS[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "First Historical Year", xpd=NA) hist2(Pars$Vmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Vmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Vmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) Yr <- nyears hist2(Pars$L5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="L5", breaks=params$plotPars$breaks) abline(v=Pars$L5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFS[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFS", breaks=params$plotPars$breaks) abline(v=Pars$LFS[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "Last Historical Year", xpd=NA) hist2(Pars$Vmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Vmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Vmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) Yr <- nyears + proyears hist2(Pars$L5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="L5", breaks=params$plotPars$breaks) abline(v=Pars$L5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFS[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFS", breaks=params$plotPars$breaks) abline(v=Pars$LFS[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "Last Projection Year", xpd=NA) hist2(Pars$Vmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Vmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Vmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1)
Histograms of r nsim
simulations of length at 5% retention (LR5
), first length at full retention (LFR
), and retention of animals at mean asymptotic length (Rmaxlen
) for the first historical year, the last historical year, and the last projection year, wtih vertical colored lines indicating r nsamp
randomly drawn values used in the other plots:
par(mfrow=c(3,3), oma=c(0,0,3,0), mar=c(2,1,3,1)) Yr <- 1 hist2(Pars$LR5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LR5", breaks=params$plotPars$breaks) abline(v=Pars$LR5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFR[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFR", breaks=params$plotPars$breaks) abline(v=Pars$LFR[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "First Historical Year", xpd=NA) hist2(Pars$Rmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Rmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Rmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) Yr <- nyears hist2(Pars$LR5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LR5", breaks=params$plotPars$breaks) abline(v=Pars$LR5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFR[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFR", breaks=params$plotPars$breaks) abline(v=Pars$LFR[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "Last Historical Year", xpd=NA) hist2(Pars$Rmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Rmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Rmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) Yr <- nyears + proyears hist2(Pars$LR5[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LR5", breaks=params$plotPars$breaks) abline(v=Pars$LR5[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) hist2(Pars$LFR[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="LFR", breaks=params$plotPars$breaks) abline(v=Pars$LFR[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1) mtext(side=3, "Last Projection Year", xpd=NA) hist2(Pars$Rmaxlen[1,], col=params$plotPars$col, axes=params$plotPars$axes, main="Rmaxlen", breaks=params$plotPars$breaks) abline(v=Pars$Rmaxlen[1,params$its], col=1:nsamp, lwd=params$plotPars$lwd) axis(side=1)
par(mfrow=c(3,3), oma=c(3,3,1,1), mar=c(1,1,1,1)) yr.vert <- c(1, nyears, nyears+proyears) YrText <- list() YrText[yr.vert[1]] <- "First Historical Year" YrText[yr.vert[2]] <- "Last Historical Year" YrText[yr.vert[3]] <- "Last Projection Year" cnt <- 0 for (sim in params$its) { cnt <- cnt + 1 for (yr in yr.vert) { # plot vulnerability & selection at length plot(Pars$CAL_binsmid, Pars$SLarray2[sim,, yr], type='l', ylim=c(0,1), lwd=params$plotPars$lwd, axes=FALSE, ylab="", xlab="") if (sim == params$its[1]) { mtext(side=3, YrText[[yr]]) } if (sim == params$its[length(params$its)]) { axis(side=1) } else { axis(side=1, labels = FALSE) } if (sim == params$its[nsamp]) mtext(side=1, "Length", line=2.5) if (yr == yr.vert[1] & sim ==params$its[1]) { mtext(side=2, "Vulnerability/Retention", las=3, outer=TRUE, line=2) } if (yr == yr.vert[1]) { text(Pars$CAL_binsmid[1], 1, "Simulation", xpd=NA, col=cnt, pos=4) axis(side=2) } if (yr != yr.vert[1]) axis(side=2, labels=FALSE) polygon(x=c(Pars$CAL_binsmid, rev(Pars$CAL_binsmid)), y=c(Pars$SLarray[sim,, yr], rev(Pars$retL[sim,, yr])), col="gray", border=FALSE) lines(Pars$CAL_binsmid, Pars$SLarray[sim,, yr], col=2, lwd=params$plotPars$lwd, lty=2, type='l') lines(Pars$CAL_binsmid, Pars$retL[sim,, yr], col=4, lwd=params$plotPars$lwd, lty=3, type='l') if (yr == max(yr.vert) & sim == params$its[1]) { minval <- min(c(Pars$V[sim,Pars$maxage, yr], Pars$retA[sim,Pars$maxage, yr])) if (minval >= 0.5) loc <- "bottomright" if (minval < 0.5) loc <- "topright" legend(loc, legend = c("Vulnerability", "Realized Selection", "Retention"), lwd=2, col=c(1, 2, 4), bty="n", lty=c(1,2,3)) } } }
par(mfrow=c(3,3), oma=c(3,3,1,1), mar=c(1,1,1,1)) yr.vert <- c(1, nyears, nyears+proyears) YrText <- list() YrText[yr.vert[1]] <- "First Historical Year" YrText[yr.vert[2]] <- "Last Historical Year" YrText[yr.vert[3]] <- "Last Projection Year" cnt <- 0 for (sim in params$its) { cnt <- cnt + 1 for (yr in yr.vert) { # plot vulnerability & selection at length plot(1:Pars$maxage, Pars$V2[sim,, yr], type='l', ylim=c(0,1), lwd=params$plotPars$lwd, axes=FALSE, ylab="", xlab="") if (sim == params$its[1]) { mtext(side=3, YrText[[yr]]) } if (sim == params$its[length(params$its)]) { axis(side=1) } else { axis(side=1, labels = FALSE) } if (sim == params$its[nsamp]) mtext(side=1, "Age", line=2.5) if (yr == yr.vert[1] & sim ==params$its[1]) { mtext(side=2, "Vulnerability/Retention", las=3, outer=TRUE, line=2) } if (yr == yr.vert[1]) { text(1, 1, "Simulation", xpd=NA, col=cnt, pos=4) axis(side=2) } if (yr != yr.vert[1]) axis(side=2, labels=FALSE) polygon(x=c(1:Pars$maxage, rev(1:Pars$maxage)), y=c(Pars$V[sim,, yr], rev(Pars$retA[sim,, yr])), col="gray", border=FALSE) lines(1:Pars$maxage, Pars$V[sim,, yr], col=2, lwd=params$plotPars$lwd, lty=2, type='l') lines(1:Pars$maxage, Pars$retA[sim,, yr], col=4, lwd=params$plotPars$lwd, lty=3, type='l') if (yr == max(yr.vert) & sim == params$its[1]) { minval <- min(c(Pars$V[sim,Pars$maxage, yr], Pars$retA[sim,Pars$maxage, yr])) if (minval >= 0.5) loc <- "bottomright" if (minval < 0.5) loc <- "topright" legend(loc, legend = c("Vulnerability", "Realized Selection", "Retention"), lwd=2, col=c(1, 2, 4), bty="n", lty=c(1,2,3)) } } }
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