Description Usage Arguments Note Author(s) See Also
View source: R/SSplotProfile.R
Makes a plot of change in negativeloglikelihood for each likelihood component that contributes more than some minimum fraction of change in total.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  SSplotProfile(summaryoutput, plot = TRUE, print = FALSE,
models = "all", profile.string = "steep",
profile.label = "Spawnerrecruit steepness (h)", exact = FALSE,
ylab = "Change in loglikelihood", 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", "Sizeatage 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, ...)

summaryoutput 
List created by the function 
plot 
Plot to active plot device? 
print 
Print to PNG files? 
models 
Optional subset of the models described in

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". 
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

component.labels 
Vector of labels for use in the legend that matches
the vector in 
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 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.) 
... 
Additional arguments passed to the 
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
.
Ian Taylor, Ian Stewart
SSsummarize
, SS_profile
,
SS_output
, SSgetoutput
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