PinerPlot: Make plot of likelihood contributions by fleet

In r4ss/r4ss: R Code for Stock Synthesis

Make plot of likelihood contributions by fleet

Description

This style of plot was officially named a "Piner Plot" at the CAPAM Selectivity Workshop, La Jolla March 2013. This is in honor of Kevin Piner's contributions to interpreting likelihood profiles. He's surely not the first person to make such a plot but the name seems to have stuck.

Usage

PinerPlot(
  summaryoutput,
  plot = TRUE,
  print = FALSE,
  component = "Length_like",
  main = "Changes in length-composition likelihoods by fleet",
  models = "all",
  fleets = "all",
  fleetnames = "default",
  profile.string = "R0",
  profile.label = expression(log(italic(R)[0])),
  exact = FALSE,
  ylab = "Change in -log-likelihood",
  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,
  fleetgroups = NULL,
  likelihood_type = "raw_times_lambda",
  minfraction = 0.01
)

Arguments

summaryoutput	List created by the function SSsummarize().
plot	Plot to active plot device?
print	Print to PNG files?
component	Which likelihood component to plot. Default is "Length_like".
main	Title for plot. Should match component.
models	Optional subset of the models described in summaryoutput. Either "all" or a vector of numbers indicating columns in summary tables.
fleets	Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.
fleetnames	Optional replacement for fleetnames used in data file.
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 'R0' matches the parameter 'SR_LN(R0)'. 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".
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 plot elements.
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\ 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	Add a legend?
legendloc	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.
pwidth	Default width of plots printed to files in units of punits.
pheight	Height of plots printed to png files in units of punits. Default is designed to allow two plots per page, with pheight_tall used for plots that work best with a taller format and a single plot per page.
punits	Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".
res	Resolution of plots printed to files. The default is res = 300.
ptsize	Point size for plotted text in plots printed to files (see help("png") in R for details).
cex.main	Character expansion for plot titles. The default is cex.main=1.
plotdir	Directory where PNG files will be written.
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	A logical value specifying if output should be printed to the screen.
fleetgroups	Optional character vector, with length equal to the number of declared fleets, where fleets with the same value are aggregated
likelihood_type	choice of "raw" or "raw_times_lambda" (the default) determines whether or not likelihoods plotted are adjusted by lambdas (likelihood weights)
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.

Author(s)

Ian G. Taylor, Kevin R. Piner, James T. Thorson

References

Kevin Piner says that he's not the originator of this idea so Athol Whitten is going to add a reference here.

See Also

Other profile functions: SSplotProfile(), profile()

r4ss/r4ss documentation built on April 30, 2024, 4:42 a.m.