Nothing
knitr::opts_chunk$set(echo = TRUE) library(dplyr) Pars <- params$Pars$Hist nsim <- dim(Pars@TSdata$VB)[1] nyears <- dim(Pars@TSdata$VB)[2] CurrentYr <- params$Pars$CurrentYr histYr <- (CurrentYr-nyears+1):CurrentYr futYr <- (CurrentYr+1):(CurrentYr+proyears) Years <- histYr
if (params$tabs) { cat('### Spawning Biomass {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Spawning Biomass') }
Time-series plots of SB/SB0:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Depletion <- apply(Pars@TSdata$SBiomass, 1:2, sum)/matrix(Pars@Ref$ReferencePoints$SSB0, nrow=nsim, ncol=nyears) ylim <- c(0, max(c(1, max(Depletion)))) matplot(Years, t(Depletion), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Depletion (spawning biomass)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i') maxL <- ceiling(max(ylim/0.2))*0.2 abline(h=seq(0.2, maxL, by=0.2), lwd=1, col="lightgray")
Time-series plots of absolute SB:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) SSB <- apply(Pars@TSdata$SBiomass, 1:2, sum) ylim <- c(0, max(SSB)) matplot(Years, t(SSB), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="SSB", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i')
if (params$tabs) { cat('### Vulnerable Biomass {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Vulnerable Biomass') }
Time-series plots of VB/VB0:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Depletion <- apply(Pars@TSdata$VBiomass, 1:2, sum)/matrix(Pars@Ref$ReferencePoints$VB0, nrow=nsim, ncol=nyears) ylim <- c(0, max(c(1, max(Depletion)))) matplot(Years, t(Depletion), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Depletion (vulnerable biomass)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i') maxL <- ceiling(max(ylim/0.2))*0.2 abline(h=seq(0.2, maxL, by=0.2), lwd=1, col="lightgray")
Time-series plots of absolute VB:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Vb <- apply(Pars@TSdata$VBiomass, 1:2, sum) ylim <- c(0, max(Vb)) matplot(Years, t(Vb), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Vuln. Biomass", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i')
if (params$tabs) { cat('### Total Biomass {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Total Biomass') }
Time-series plots of B/B0:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Depletion <- apply(Pars@TSdata$Biomass, 1:2, sum)/matrix(Pars@Ref$ReferencePoints$B0, nrow=nsim, ncol=nyears) ylim <- c(0, max(c(1, max(Depletion)))) matplot(Years, t(Depletion), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Depletion (total biomass)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i') maxL <- ceiling(max(ylim/0.2))*0.2 abline(h=seq(0.2, maxL, by=0.2), lwd=1, col="lightgray")
Time-series plots of absolute B:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) B <- apply(Pars@TSdata$Biomass, 1:2, sum) ylim <- c(0, max(B)) matplot(Years, t(B), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Total Biomass", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i')
if (params$tabs) { cat('### Recruitment {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Recruitment') }
Time-series plot of recruitment relative to R0:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Depletion <- apply(Pars@AtAge$Number[,1,,], 1:2, sum)/matrix( Pars@SampPars$Stock$R0, nrow=nsim, ncol=nyears) ylim <- c(0, max(c(1,Depletion))) matplot(Years, t(Depletion), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Recruitment (relative to R0)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i') maxL <- ceiling(max(ylim/0.2))*0.2 abline(h=seq(0.2, maxL, by=0.2), lwd=1, col="lightgray")
Time-series plot of absolute recruitment:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Rec <- apply(Pars@AtAge$Number[,1,,], 1:2, sum) ylim <- c(0, max(Rec)) matplot(Years, t(Rec), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Recruitment", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i')
if (params$tabs) { cat('### Catch {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Catch') }
Time-series of catch relative to the current year:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Depletion <- apply(Pars@TSdata$Landings, 1:2, sum)/matrix(apply(Pars@TSdata$Landings[,nyears,], 1, sum), nrow=nsim, ncol=nyears) Depletion[!is.finite(Depletion)] <- 0 ylim <- c(0, max(c(1,max(Depletion)))) matplot(Years, t(Depletion), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Catch (relative to current year)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i', axes=F) axis(side=1) maxL <- ceiling(max(ylim/0.5))*0.5 yax <- seq(0, maxL, by=0.25*maxL) axis(side=2, at=yax, las=1) abline(h=yax, lwd=1, col="lightgray")
Time-series of absolute catch:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Catch <- apply(Pars@TSdata$Landings, 1:2, sum) ylim <- c(0, max(Catch)) matplot(Years, t(Catch), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Catch", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i')
if (params$tabs) { cat('### Historical Fishing Mortality {.tabset .tabset-fade .tabset-pills}' ) } else { cat('### Historical Fishing Mortality') }
Time-series of historical fishing mortality:
par(mfrow=c(1,1), oma=c(3,3,1,1), mar=c(1,1,1,1)) Find <- Pars@TSdata$Find * Pars@SampPars$Fleet$qs ylim <- c(0, max(c(1, max(Find)))) matplot(Years, t(Find), type="l", lty=1, bty="l", main="", lwd=params$plotPars$lwd, ylab="Fishing mortality rate (apical)", xlab="Historical Years", las=1, xpd=NA, ylim=ylim, yaxs = 'i') maxL <- ceiling(max(ylim/0.2))*0.2 abline(h=seq(0.2, maxL, by=0.2), lwd=1, col="lightgray")
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