R: Plot likelihood profile results

SSplotProfile {r4ss}

R Documentation

Plot likelihood profile results

Description

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

Usage

SSplotProfile(
  summaryoutput,
  plot = TRUE,
  print = FALSE,
  models = "all",
  profile.string = "steep",
  profile.label = "Spawner-recruit steepness (h)",
  exact = FALSE,
  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", "InitEQ_Regime", "Forecast_Recruitment", "Parm_priors",
    "Parm_softbounds", "Parm_devs", "F_Ballpark", "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", "Initital equilibrium recruitment",
    "Forecast recruitment", "Priors", "Soft bounds", "Parameter deviations",
    "F Ballpark", "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 = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  add_cutoff = FALSE,
  cutoff_prob = 0.95,
  verbose = TRUE,
  ...
)

Arguments

`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. If `exact=FALSE`, this can be a 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'. If `exact=TRUE`, then profile.string needs to be an exact match to the parameter label.
`profile.label`	Label for x-axis describing the parameter over which the profile was conducted.
`exact`	Should the `profile.string` have to match the parameter label exactly, or is a substring OK.
`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 likelihood components.
`lty.total`	Line type for the total likelihood.
`lwd`	Line width for the likelihood 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
`pheight`	Height of plot
`punits`	Units for PNG file
`res`	Resolution of plots printed to files. The default is `res = 300`.
`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.
`add_cutoff`	Add dashed line at ~1.92 to indicate 95% confidence interval based on common cutoff of half of chi-squared of p=.95 with 1 degree of freedom: `0.5*qchisq(p=cutoff_prob, df=1)`. The probability value can be adjusted using the `cutoff_prob` below.
`cutoff_prob`	Probability associated with `add_cutoff` above.
`verbose`	Return updates of function progress to the R GUI? (Doesn't do anything yet.)
`...`	Additional arguments passed to the `plot` command.

Note

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().

Author(s)