SSplotRetro: SSplotRetro() Retrospective-Forecast with one-step ahead...
In jabbamodel/ss3diags: What the Package Does (One Line, Title Case)

SSplotRetro

R Documentation

SSplotRetro() Retrospective-Forecast with one-step ahead hindcasting

Description

Plots retrospective pattern, including (optional) one-step ahead forecast and computes Mohn's Rho

Usage

SSplotRetro(
  summaryoutput,
  subplots = c("SSB", "F"),
  plot = TRUE,
  print = FALSE,
  png = print,
  pdf = FALSE,
  models = "all",
  endyrvec = "default",
  xlim = NULL,
  xmin = NULL,
  labels = NULL,
  ylim = NULL,
  forecast = TRUE,
  forecastrho = TRUE,
  showrho = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.7,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = grey(0.4, 0.6),
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE
)

Arguments

`summaryoutput`	List created by r4ss::SSsummarize()
`subplots`	Vector of subplots to be created
`plot`	plot to active plot device?
`print`	print to PNG files?
`pdf`	not tested for TRUE
`models`	Optional subset of the models described in r4ss function summaryoutput(). Either "all" or a vector of numbers indicating columns in summary tables.
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
`xlim`	optional xlim, which overwrites xmin
`xmin`	optional minimum year shown in plot (default first yr)
`labels`	yaxis lable for biomass (bony fish and sharks)
`ylim`	option to specify ylim range
`forecast`	if true one-step ahead forecasts are shown in plot
`forecastrho`	if true one-step ahead forecast rho value is denoted in plot
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	TRUE/FALSE switch to turn on/off extra axis mark at final year in timeseries plots.
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space
`xaxs`	Choice of xaxs parameter (see ?par for more info)
`yaxs`	Choice of yaxs parameter (see ?par for more info)
`type`	Type parameter passed to points (default 'o' overplots points on top of lines)
`legend`	Add a legend?
`legendlabels`	Optional vector of labels to include in 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 ?legend for more info on the string options.
`legendorder`	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
`legendncol`	Number of columns for the legend.
`legendsp`	Space between legend labels
`legendindex`	Allows to add lengend for selected indices (plots)
`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 or PDF files will be written. By default it will be the directory where the model was run.
`filenameprefix`	Additional text to append to PNG or PDF file names. It will be separated from default name by an underscore.
`par`	list of graphics parameter values passed to par() function
`verbose`	Report progress to R GUI?
`shadecol`	uncertainty shading of hcxval horizon
`new`	Create new empty plot window
`add`	surpresses par() to create multiplot figs
`mcmcVec`	NOT TESTED Vector of TRUE/FALSE values (or single value) indicating
`legendcex=1`	Allows to adjust legend cex
`shadecol1`	uncertainty shading of early years not affected by hindcast
`indexQlabel`	Add catchability to legend in plot of index fits (TRUE/FALSE)?
`indexQdigits`	Number of significant digits for catchability in legend