View source: R/SSplotProfile.R
SSplotProfile | R Documentation |
Makes a plot of change in negative-log-likelihood for each likelihood component that contributes more than some minimum fraction of change in total.
SSplotProfile(
summaryoutput,
plot = TRUE,
print = FALSE,
models = "all",
profile.string = "steep",
profile.label = "Spawner-recruit steepness (h)",
exact = FALSE,
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", "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", "Size-at-age 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,
add_no_prior_line = TRUE,
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 x-axis describing the parameter over which the profile was conducted. |
exact |
Should the |
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
|
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 type 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 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). |
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 |
pwidth |
Default width of plots printed to files in units of
|
pheight |
Height of plots printed to png files in units of |
punits |
Units for |
res |
Resolution of plots printed to files.
The default is |
ptsize |
Point size for plotted text in plots printed to files (see
|
cex.main |
Character expansion for plot titles.
The default is |
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: |
cutoff_prob |
Probability associated with |
add_no_prior_line |
Add line showing total likelihood without the prior (only appears when profiled parameter that includes a prior) |
verbose |
A logical value specifying if output should be printed to the screen. |
... |
Additional arguments passed to the |
Someday the function profile()
will be improved and
made to work directly with this plotting function, but they don't yet work
well together. Thus, even if profile()
is used, the output
should be read using SSgetoutput()
or by multiple calls to
SS_output()
.
Ian G. Taylor, Ian J. Stewart
SSsummarize()
, SSgetoutput()
Other profile functions:
PinerPlot()
,
profile()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.