View source: R/SSplotRetroRecruits.R
SSplotRetroRecruits | R Documentation |
Inspired by Jim Ianelli and named by Sean Cox, the squid plot is a way to examine retrospective patterns in estimation of recruitment deviations.
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
)
retroSummary |
List object created by |
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 labels for plots (titles and axis 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 |
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. (Figure 1.31, which is on an absolute, rather than log scale.)
SSsummarize()
## Not run:
# run retrospective analysis
retro(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)
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