SSplotProfile: Plot likelihood profile results

In r4ss: R Code for Stock Synthesis

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)

Ian Taylor, Ian Stewart

See Also

SSsummarize(), SS_profile(), SS_output(), SSgetoutput()

r4ss documentation built on May 28, 2022, 1:11 a.m.