Make plot of likelihood contributions by fleet

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.

References

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

Author

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

Make plot of likelihood contributions by fleet

Usage

Arguments

References

See also

Author