SSplotProfile: Plot likelihood profile results
In r4ss: R code for Stock Synthesis

Description Usage Arguments Note Author(s) See Also

Makes a plot of change in negative-log-likelihood for each likelihood component that contributes more than some minimum fraction of change in total.

SSplotProfile(summaryoutput, plot = TRUE, print = FALSE,
models = "all", profile.string = "steep", profile.label =
"Spawner-recruit steepness (h)", ylab = "Change in -log-likelihood",
components = c("TOTAL", "Catch", "Equil_catch", "Survey", "Discard",
"Mean_body_wt", "Length_comp", "Age_comp", "Size_at_age", "SizeFreq",
"Morphcomp", "Tag_comp", "Tag_negbin", "Recruitment",
"Forecast_Recruitment", "Parm_priors", "Parm_softbounds", "Parm_devs",
"Crash_Pen"),
component.labels = c("Total", "Catch", "Equilibrium catch",
"Index data", "Discard", "Mean body weight", "Length data",
"Age data", "Size-at-age data", "Generalized size data",
"Morph composition data", "Tag recapture distribution",
"Tag recapture total", "Recruitment", "Forecast recruitment", "Priors",
"Soft bounds", "Parameter deviations", "Crash penalty"),
minfraction = 0.01,
sort.by.max.change = TRUE, col = "default", pch = "default", lty = 1,
lty.total = 1, lwd = 2, lwd.total = 3, cex = 1, cex.total = 1.5, xlim =
"default", ymax = "default", xaxs = "r", yaxs = "r", type = "o", legend
= TRUE, legendloc = "topright", pwidth = 7, pheight = 7, punits = "in",
res = 300, ptsize = 12, cex.main = 1, plotdir = NULL,
verbose = TRUE)

`summaryoutput`	List created by the function `SSsummarize`.
`plot`	Plot to active plot device?
`print`	Print to PNG files?
`models`	Optional subset of the models described in `summaryoutput`. Either "all" or a vector of numbers indicating columns in summary tables.
`profile.string`	Character string used to find parameter over which the profile was conducted. Needs to match substring of one of the SS parameter labels found in the Report.sso file. For instance, the default input 'steep' matches the parameter 'SR_BH_steep'.
`profile.label`	Label for x-axis describing the parameter over which the profile was conducted.
`ylab`	Label for y-axis. Default is "Change in -log-likelihood".
`components`	Vector of likelihood components that may be included in plot. List is further refined by any components that are not present in model or have little change over range of profile (based on limit `minfraction`). Hopefully this doesn't need to be changed.
`component.labels`	Vector of labels for use in the legend that matches the vector in `components`.
`minfraction`	Minimum change in likelihood (over range considered) as a fraction of change in total likelihood for a component to be included in the figure.
`sort.by.max.change`	Switch giving option to sort components in legend in order of maximum amount of change in likelihood (over range considered). Default=TRUE.
`col`	Optional vector of colors for each line.
`pch`	Optional vector of plot characters for the points.
`lty`	Line total for the liklihood components.
`lty.total`	Line type for the total likelihood.
`lwd`	Line width for the liklihood components.
`lwd.total`	Line width for the total likelihood.
`cex`	Character expansion for the points representing the likelihood components.
`cex.total`	Character expansion for the points representing the total likelihood.
`xlim`	Range for x-axis. Change in likelihood is calculated relative to values within this range.
`ymax`	Maximum y-value. Default is 10% greater than largest value plotted.
`xaxs`	The style of axis interval calculation to be used for the x-axis (see ?par for more info)
`yaxs`	The style of axis interval calculation to be used for the y-axis (see ?par for more info).
`type`	Line type (see ?plot for more info).
`legend`	Include legend?
`legendloc`	Location of legend (see ?legend for more info).
`pwidth`	Width of plot written to PNG file
`pheight`	Height of plot written to PNG file
`punits`	Units for PNG file
`res`	Resolution for PNG file
`ptsize`	Point size for PNG file
`cex.main`	Character expansion for plot titles
`plotdir`	Directory where PNG files will be written. by default it will be the directory where the model was run.
`verbose`	Return updates of function progress to the R GUI? (Doesn't do anything yet.)

Someday the function SS_profile will be improved and made to work directly with this plotting function, but they don't yet work well together. Thus, even if SS_profile is used, the output should be read using SSgetoutput or by multiple calls to SS_output.

Ian Taylor, Ian Stewart

SSsummarize, SS_profile, SS_output, SSgetoutput

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