Description Usage Arguments Author(s) References
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14  PinerPlot(summaryoutput, plot = TRUE, print = FALSE,
component = "Length_like",
main = "Changes in lengthcomposition likelihoods by fleet",
models = "all", fleets = "all", fleetnames = "default",
profile.string = "R0", profile.label = expression(log(italic(R)[0])),
exact = FALSE, ylab = "Change in loglikelihood", 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)

summaryoutput 
List created by the function

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

fleets 
Optional vector of fleet numbers to include. 
fleetnames 
Optional character vector of names for each fleet. 
profile.string 
Character string used to find parameter over which the
profile was conducted. If 
profile.label 
Label for xaxis describing the parameter over which the profile was conducted. 
exact 
Should the 
ylab 
Label for yaxis. Default is "Change in loglikelihood". 
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 xaxis. Change in likelihood is calculated relative to values within this range. 
ymax 
Maximum yvalue. Default is 10% greater than largest value plotted. 
xaxs 
The style of axis interval calculation to be used for the xaxis (see ?par for more info) 
yaxs 
The style of axis interval calculation to be used for the yaxis (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 chisquared of p=.95 with 1 degree of
freedom: 
cutoff_prob 
Probability associated with 
verbose 
Return updates of function progress to the R GUI? (Doesn't do anything yet.) 
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. 
Ian Taylor, Kevin Piner, Jim Thorson
Kevin Piner says that he's not the originator of this idea so Athol Whitten is going to add a reference here.
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