SSplotRetroRecruits {r4ss} | R Documentation |
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 |
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 |
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
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)