SSplotPars: Plot distributions of priors, posteriors, and estimates.

In r4ss: R Code for Stock Synthesis

Plot distributions of priors, posteriors, and estimates.

Description

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	A path to the folder where the plots will be saved. The default is NULL, which leads to the plots being created in the folder that contains the results.
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 ?par for 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	Controls amount of text output (maybe).
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	Print to PNG files?
pwidth	Default width of plots printed to files in units of punits. Default=7.
pheight	Default height width of plots printed to files in units of punits. Default=7.
punits	Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".
ptsize	Point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.
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.

Author(s)

Ian G. Taylor, Cole C. Monnahan

Examples

## Not run: 
# 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")
)

## End(Not run)

r4ss documentation built on May 28, 2022, 1:11 a.m.