vbgfCI_time: VBGF plot and CI

In rschwamborn/fishboot: Bootstrap-based methods for the study of fish stocks and aquatic populations

Description

VBGF plot and CI

Usage

vbgfCI_time(res, CI = 95, agemax = NULL, add_legend = TRUE,
  add_max_dens_legend = TRUE, xlab = "Relative time",
  ylab = "Length", perm.col = adjustcolor("grey50", 0.1),
  perm.lwd = 1, ci.col = 1, ci.lty = 2, ci.lwd = 1, maxd.col = 1,
  maxd.lty = 1, maxd.lwd = 2)

Arguments

res	list of class 'lfqBoot'
CI	vector. Confidence interval levels to plot
agemax	numeric. Maximum number of years to project.
add_legend	logical. Should CI and max. density legend be added (Default: 'add_legend = TRUE').
add_max_dens_legend	logical. Should maximum density line be added (Default: 'add_max_dens_legend = TRUE').
xlab	Label for x-axis
ylab	Label for y-axis
perm.col	Color for each resample estimate line. See '?par'.
perm.lwd	Line width for each resample estimate line. See '?par'.
ci.col	Color for CI line. See '?par'.
ci.lty	Line type for CI line. See '?par'.
ci.lwd	Line width for CI line. See '?par'.
maxd.col	Color for maximum density line. See '?par'.
maxd.lty	Line type maximum density line. See '?par'.
maxd.lwd	Line width maximum density line. See '?par'.

Value

plot and list containing: 'limCI' - data.frame with CI limits by time, 'inCi' - data.frame with logical values defining whether bootstrapping samples are within each of the defined CIs, 'density' - the multivariate kernel density estimates for each sample, and 'max_dens' is a list with the VBGF parameter combination having the maximum density estimate.

Examples

data(alba_boot)
CIinfo <- vbgfCI_time(
  res = alba_boot,
  agemax = 2, CI = 95,
  perm.col = adjustcolor("grey50",0.2)
)

# plot more CI levels
CIinfo <- vbgfCI_time(
  res = alba_boot,
  agemax = 2, CI = c(95, 50),
  ci.lty = 1, ci.lwd = 2, ci.col = c("red", "orange"),
  perm.col = adjustcolor("grey50",0.2)
)

# using output in lfq plot (see ?TropFishR::plot.lfq)
library(TropFishR)
data(alba)
alba <- lfqRestructure(alba, MA = 7)
plot(alba, Fname = "rcounts", ylim=c(0,15))
for(i in seq(nrow(alba_boot$bootRaw))){
  x <- as.list(alba_boot$bootRaw[i,])
  tmp <- lfqFitCurves(
    lfq = alba, par = x,
    col = adjustcolor("grey50",0.1), draw = TRUE, lty=1
  )
}
for(j in seq(CIinfo$limCI)){
  usr <- par()$usr
  tmax <- diff(range(CIinfo$limCI[[j]]$t))
  date_start <- as.Date(usr[1], origin = "1970-01-01")
  yeardec_start <- date2yeardec(date_start)
  date_end <- as.Date(usr[2], origin = "1970-01-01")
  yeardec_end <- date2yeardec(date_end)
  years <- (floor(yeardec_start)-tmax):ceiling(yeardec_end)

  for(y in years){
    time <- y + CIinfo$limCI[[j]]$t
    time <- as.numeric(yeardec2date(time))
    lines(time, CIinfo$limCI[[j]]$min, lty = 2, col=2+j)
    lines(time, CIinfo$limCI[[j]]$max, lty = 2, col=2+j)
  }

  tmp <- lfqFitCurves(lfq = alba, par = CIinfo$max_dens,
    col = 1, draw = TRUE, lty=1, lwd=2
  )
}

rschwamborn/fishboot documentation built on July 27, 2019, 12:36 a.m.