In DLMtool/DLMtool: Data-Limited Methods Toolkit

suppressMessages(library(dplyr))
if (params$tabs) {
  cat('### Natural Mortality Parameters {.tabset .tabset-fade .tabset-pills}' )
} else {
  cat('### Natural Mortality Parameters')
}

dd <- params$Pars$M_ageArray %>% dim()
nsim <- dd[1]
maxage <- dd[2]

nsamp <- length(params$its)
nyears <- params$nyears
proyears <- params$proyears

Sampled Parameters

Histograms of r nsim simulations of M, Mexp, and Msd parameters, with vertical colored lines indicating r nsamp randomly drawn values used in other plots:

par(mfrow=c(1,3))
hist2(Pars$M, main="M", col=params$plotPars$col, axes=params$plotPars$axes,
      breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main)
abline(v=Pars$M[params$its], col=1:nsamp, lwd=params$plotPars$lwd)
axis(side=1) 

hist2(Pars$Mexp, main="Mexp", col=params$plotPars$col, axes=params$plotPars$axes,
      breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main)
abline(v=Pars$Mexp[params$its], col=1:nsamp, lwd=params$plotPars$lwd)
axis(side=1) 

hist2(Pars$Msd, main="Msd", col=params$plotPars$col, axes=params$plotPars$axes,
      breaks=params$plotPars$breaks, cex.main=params$plotPars$cex.main)
abline(v=Pars$Msd[params$its], col=1:nsamp, lwd=params$plotPars$lwd)
axis(side=1) 

Time-Series

The average natural mortality rate by year for adult fish 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$Marray[params$its,]), type="l", lty=1, bty="l", main="M by Year", 
         lwd=params$plotPars$lwd, ylab="M", xlab="Years", las=1)
abline(v=0, col="darkgray", lty=2)

M-at-Age

Natural mortality-at-age for r nsamp simulations in the first historical year, the last historical year (i.e., current year), and the last projected year:

par(mfrow=c(1,3))
lims <- range(Pars$M_ageArray[params$its,, ])
ylab <- "Natural Mortality"
matplot(t(Pars$M_ageArray[params$its,,1]), type="l", lty=1, bty="l", 
        lwd=params$plotPars$lwd, ylim=lims, ylab=ylab, las=1)
mtext(side=3, "First historical year", cex=0.8, line=-1)
mtext(side=1, "Age", line=2, cex=0.7)

matplot(t(Pars$M_ageArray[params$its,,nyears]), type="l", lty=1, bty="l", 
        main="M-at-age", lwd=params$plotPars$lwd, ylim=lims, axes=FALSE,
        ylab="")
mtext(side=3, "Last historical year", cex=0.8, line=-1)
axis(side=1)
mtext(side=1, "Age", line=2, cex=0.7)
matplot(t(Pars$M_ageArray[params$its,,nyears+proyears]), type="l", lty=1, 
        bty="l", lwd=params$plotPars$lwd, ylim=lims, axes=FALSE,
        ylab="")
mtext(side=3, "Last projected year", cex=0.8, line=-1)
axis(side=1)
mtext(side=1, "Age", line=2, cex=0.7)

M-at-Length

Natural mortality-at-length for r nsamp simulations in the first historical year, the last historical year (i.e., current year), and the last projected year:

```r par(mfrow=c(1,3)) lims <- range(Pars$M_ageArray[params$its,, ]) xlims <- range(Pars$Len_age[params$its,,]) matplot(t(Pars$Len_age[params$its,,1]), t(Pars$M_ageArray[params$its,,1]), type="l", lty=1, bty="l", lwd=params$plotPars$lwd, ylim=lims, xlim=xlims, ylab="Natural Mortality", xlab="", las=1) mtext(side=3, "First historical year", cex=0.8, line=-1) mtext(side=1, "Length", line=2, cex=0.7)

matplot(t(Pars$Len_age[params$its,,nyears]), t(Pars$M_ageArray[params$its,,nyears]), type="l", lty=1, bty="l", main="M-at-length", lwd=params$plotPars$lwd, ylim=lims, xlim=xlims, axes=FALSE, ylab="", xlab="") axis(side=1) mtext(side=1, "Length", line=2, cex=0.7) mtext(side=3, "Last historical year", cex=0.8, line=-1)

matplot(t(Pars$Len_age[params$its,,nyears+proyears]), t(Pars$M_ageArray[params$its,,nyears+proyears]), type="l", lty=1, bty="l", lwd=params$plotPars$lwd, ylim=lims, axes=FALSE, xlim=xlims, ylab="", xlab="")

mtext(side=3, "Last projected year", cex=0.8, line=-1) axis(side=1) mtext(side=1, "Length", line=2, cex=0.7) ```

DLMtool/DLMtool documentation built on June 20, 2021, 5:20 p.m.