Make multi-figure plots of prior, posterior, and estimated asymptotic parameter distributions. MCMC not required to make function work.
Usage
SSplotPars(
replist,
plotdir = NULL,
xlab = "Parameter value",
ylab = "Density",
showmle = TRUE,
showpost = TRUE,
showprior = TRUE,
showinit = TRUE,
showdev = FALSE,
showlegend = TRUE,
fitrange = FALSE,
xaxs = "i",
xlim = NULL,
ylim = NULL,
verbose = TRUE,
debug = FALSE,
nrows = 4,
ncols = 2,
ltyvec = c(1, 1, 3, 4),
colvec = c("blue", "red", "black", "gray60", rgb(0, 0, 0, 0.5)),
add = FALSE,
plot = TRUE,
print = FALSE,
pwidth = 6.5,
pheight = 6.5,
punits = "in",
ptsize = 10,
res = 300,
strings = NULL,
exact = FALSE,
newheaders = NULL
)Arguments
- replist
A list object created by
SS_output().- plotdir
Directory where PNG files will be written.
- xlab
Label on horizontal axis.
- ylab
Label on vertical axis.
- showmle
Show MLE estimate and asymptotic variance estimate with blue lines?
- showpost
Show posterior distribution as bar graph if MCMC results are available in
replist?- showprior
Show prior distribution as black line?
- showinit
Show initial value as red triangle?
- showdev
Include devs in the plot?
- showlegend
Show the legend?
- fitrange
Fit range tightly around MLE & posterior distributions, instead of full parameter range?
- xaxs
Parameter input for x-axis. See
?parfor more info.- xlim
Optional x-axis limits to be applied to all plots. Otherwise, limits are based on the model results.
- ylim
Optional y-axis limits to be applied to all plots. Otherwise, limits are based on the model results.
- verbose
A logical value specifying if output should be printed to the screen.
- debug
Provide additional messages to help with debugging when the function fails.
- nrows
How many rows in multi-figure plot.
- ncols
How many columns in multi-figure plot.
- ltyvec
Vector of line types used for lines showing MLE and prior distributions and the median of the posterior distribution.
- colvec
Vector of colors used for lines and polygons showing MLE, initial value, prior, posterior, and median of the posterior.
- add
Add to existing plot?
- plot
Plot to active plot device?
Print to PNG files?
- 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, withpheight_tallused for plots that work best with a taller format and a single plot per page.- punits
Units for
pwidthandpheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default ispunits="in".- ptsize
Point size for plotted text in plots printed to files (see
help("png")in R for details).- res
Resolution of plots printed to files. The default is
res = 300.- strings
Subset parameters included in the plot using substring from parameter names (i.e. "SR" will get "SR_LN(R0)" and "SR_steep" if they are both estimated quantities in this model).
- exact
Should strings input match parameter names exactly? Otherwise substrings are allowed.
- newheaders
Optional vector of headers for each panel to replace the parameter names.
Examples
if (FALSE) { # \dontrun{
# read model results
model <- SS_output(dir = "c:/SS/Simple/")
# make default plots where parameter distribution plots will appear
# in the "pars" tab
SS_plots(model)
# create just the "pars" tab with control of the inputs that are
# passed to SSplotPars
SS_plots(model,
plot = 25, showmle = TRUE, showpost = TRUE,
showprior = TRUE, showinit = TRUE, showdev = FALSE, fitrange = FALSE
)
# call SSplotPars directly
SSplotPars(replist = model)
# Create plot in custom location. Note that strings can be partial match.
# File name will be "parameter_distributions.png"
# or "parameter_distributions_pageX.png" when they don't all fit on one page
SSplotPars(
replist = model, strings = c("steep", "R0"),
nrows = 2, ncols = 1, plot = FALSE, print = TRUE,
plotdir = file.path(model[["inputs"]][["dir"]], "distribution_plots")
)
} # }