SSplotRetroDevs: Make squid plot of retrospectives of recruitment deviations.
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) References See Also

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

SSplotRetroDevs(retroSummary, endyrvec, cohorts, ylim = c(-3, 3),
uncertainty = FALSE,
labels = c("Recruitment deviation relative to recent estimate",
"Recruitment deviation", "Age"),
main = "Retrospective analysis of recruitment deviations",
mcmcVec = FALSE, relative = FALSE,
labelyears = TRUE, legend = FALSE, leg.ncols = 4)

`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.
`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.

Ian Taylor

Ianelli et al. (2011) Assessment of the walleye pollock stock in the Eastern Bering Sea. http://www.afsc.noaa.gov/REFM/docs/2011/EBSpollock.pdf. (Figure 1.31, which is on an absolute, rather than log scale.)

SSsummarize

r4ss documentation built on May 2, 2019, 4:56 p.m.