r4ss (version 1.44.0)

SSplotPars: 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.

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")
)
# }
# NOT RUN {
# }