a4aPlotRunstest: plot function for runs test plot
In Henning-Winker/a4adiags: Diagnostic Toolbox for a4a

Description Usage Arguments Author(s)

View source: R/a4aPlotRunstest.R

Residual diagnostics with runs test p-value and 3xsigma limits for Indices and meanL

a4aPlotRunstest(
  obs,
  hat,
  mixing = "less",
  subplots = c("combined.n", "age", "bio")[1],
  ylab = NULL,
  plot = TRUE,
  print = FALSE,
  png = print,
  pdf = FALSE,
  indexselect = NULL,
  miny = 1,
  pch = 21,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = "default",
  ylimAdj = 1.4,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  legend = TRUE,
  legendloc = "top",
  legendcex = 1,
  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,
  new = TRUE,
  add = FALSE
)

`mixing`	c("less","greater","two.sided"). Default less is checking for postive autocorrelation only
`subplots`	optional use of c("cpue","len","age"), yet to be tested for age.
`plot`	plot to active plot device?
`print`	print to PNG files?
`pdf`	not tested for TRUE
`indexselect`	Vector of fleet numbers for each model for which to compare
`miny`	minimum abs values of ylim
`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?
`legendloc`	Location of legend. Either a string like "topleft" or a vector
`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?
`new`	Create new empty plot window
`add`	surpresses par() to create multiplot figs
`fit`	from r4ss::SSgetoutput()$replist1
`idx`	from r4ss::SSgetoutput()$replist1
`legendcex=1`	Allows to adjust legend cex