SSplotRetroRecruits: Make squid plot of retrospectives of recruitment deviations.

In r4ss: R Code for Stock Synthesis

Make squid plot of retrospectives of recruitment deviations.

Description

Inspired by Jim Ianelli and named by Sean Cox, the squid plot is a way to examine retrospective patterns in estimation of recruitment deviations.

Usage

SSplotRetroRecruits(
  retroSummary,
  endyrvec,
  cohorts,
  ylim = NULL,
  uncertainty = FALSE,
  labels = c("Recruitment deviation", "Recruitment (billions)",
    "relative to recent estimate", "Age"),
  main = "Retrospective analysis of recruitment deviations",
  mcmcVec = FALSE,
  devs = TRUE,
  relative = FALSE,
  labelyears = TRUE,
  legend = FALSE,
  leg.ncols = 4
)

Arguments

retroSummary	List object created by SSsummarize() that summarizes the results of a set of retrospective analysis models.ss
endyrvec	Vector of years representing the final year of values to show for each model.
cohorts	Which cohorts to show in plot.
ylim	Limits of y-axis.
uncertainty	Show uncertainty intervals around lines? (This can get a bit busy.)
labels	Vector of plot labels.
main	Title for plot.
mcmcVec	Either vector of TRUE/FALSE values indicating which models use MCMC. Or single value applied to all models.
devs	Plot deviations instead of absolute recruitment values?
relative	Show deviations relative to most recent estimate or relative to 0.
labelyears	Label cohorts with text at the end of each line?
legend	Add a legend showing which color goes with which line (as alternative to labelyears).
leg.ncols	Number of columns for the legend.

Author(s)

Ian Taylor

References

Ianelli et al. (2011) Assessment of the walleye pollock stock in the Eastern Bering Sea. (Figure 1.31, which is on an absolute, rather than log scale.)

See Also

SSsummarize()

Examples

## Not run: 
# run retrospective analysis
SS_doRetro(olddir = "2013hake_12", years = 0:-10)
# read in output
retroModels <- SSgetoutput(dirvec = paste("retrospectives/retro", -10:0, sep = ""))
# summarize output
retroSummary <- SSsummarize(retroModels)

# set the ending year of each model in the set
endyrvec <- retroModels[[1]][["endyr"]] - 10:0
# make comparison plot
pdf("retrospectives/retrospective_comparison_plots.pdf")
SSplotComparisons(retroSummary, endyrvec = endyrvec, new = FALSE)
dev.off()

# make Squid Plot of recdev retrospectives
pdf("retrospectives/retrospective_dev_plots.pdf", width = 7, height = 10)
par(mfrow = c(2, 1))
# first scaled relative to most recent estimate
SSplotRetroRecruits(retroSummary,
  endyrvec = endyrvec, cohorts = 1999:2012,
  relative = TRUE, legend = FALSE
)
# second without scaling
SSplotRetroDevs(retroSummary,
  endyrvec = endyrvec, cohorts = 1999:2012,
  relative = FALSE, legend = FALSE
)
dev.off()

## End(Not run)

r4ss documentation built on May 28, 2022, 1:11 a.m.