SSplotProfile: Plot likelihood profile results

Description Usage Arguments Note Author(s) See Also

View source: R/SSplotProfile.R

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

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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 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.

add_cutoff

Add dashed line at ~1.92 to indicate 95 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 Oct. 30, 2019, 11:25 a.m.