Usage
SSplotProfile(summaryoutput, plot = TRUE, print = FALSE,
models = "all", profile.string = "steep", profile.label =
"Spawner-recruit steepness (h)", 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",
"Forecast_Recruitment", "Parm_priors", "Parm_softbounds", "Parm_devs",
"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", "Forecast recruitment", "Priors",
"Soft bounds", "Parameter deviations", "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 = 7, pheight = 7, punits = "in",
res = 300, ptsize = 12, cex.main = 1, plotdir = NULL,
verbose = TRUE)Arguments
plot
Plot to active plot device?
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. Needs to match 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_stee
profile.label
Label for x-axis describing the parameter over which the profile was
conducted.
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 does
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 liklihood components.
lty.total
Line type for the total likelihood.
lwd
Line width for the liklihood 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).
legendloc
Location of legend (see ?legend for more info).
pwidth
Width of plot written to PNG file
pheight
Height of plot written to 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.
verbose
Return updates of function progress to the R GUI? (Doesn't do
anything yet.)