SSplotComparisons: plot model comparisons
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

Creates a user-chosen set of plots comparing model output from a summary of multiple models, where the collection was created using the SSsummarize function.

SSplotComparisons(summaryoutput,subplots=1:20,
  plot=TRUE,print=FALSE,png=print,pdf=FALSE,
  models="all",
  endyrvec="default",
  indexfleets=NULL,
  indexUncertainty=FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4, 
  indexSEvec="default",
  indexPlotEach=FALSE,         
  labels=c("Year",             
    "Spawning biomass (mt)",   
    "Spawning depletion",      
    "Age-0 recruits (1,000s)", 
    "Recruitment deviations",  
    "Index",                   
    "Log index",               
    "SPR ratio",
    "Density",
    "Management target",
    "Minimum stock size threshold"),
  col="default", shadecol="default",
  pch="default", lty=1, lwd=2,
  spacepoints = 10, staggerpoints = 1, 
  xlim="default", ylimAdj=1,
  xaxs="r", yaxs="r",
  type="o", uncertainty=TRUE, shadealpha=0.1,
  legend=TRUE, legendlabels="default", legendloc="topright",
  legendorder="default",legendncol=1,
  btarg=0.4, minbthresh=0.25, sprtarg=1,
  pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
  plotdir=NULL,
  densitynames=c("SPB_Virgin","R0"),
  densityxlabs="default",
  densityscalex=1,
  densityscaley=1,
  densityadjust=1,
  densitysymbols = TRUE,
  densitytails = TRUE,
  fix0=TRUE,
  new=TRUE,
  add=FALSE,
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose=TRUE,
  mcmcVec="default")

`summaryoutput`	List created by `SSsummarize`
`subplots`	Vector of subplots to be created.
`plot`	Plot to active plot device?
`print`	Send plots to PNG files in directory specified by `plotdir`?
`png`	Has same result as `print`, included for consistency with `SS_plots`.
`pdf`	Write output to PDF file? Can't be used in conjunction with `png` or `print`.
`models`	Optional subset of the models described in `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.
`indexfleets`	Vector of fleets for each model for which to compare indices of abundance. Only necessary if any model has more than one index.
`indexUncertainty`	Show uncertainty intervals on index data? Default=FALSE because if models have any extra standard deviations added, these intervals may differ across models.
`indexQlabel`	Add catchability to legend in plot of index fits (TRUE/FALSE)?
`indexQdigits`	Number of significant digits for catchability in legend (if `indexQlabel=TRUE`)
`indexSEvec`	Optional replacement for the SE values in summaryoutput$indices to deal with the issue of differing uncertainty by models described above.
`indexPlotEach`	TRUE plots the observed index for each model with colors, or FALSE just plots observed once in black dots.
`labels`	Vector of labels for plots (titles and axis labels)
`col`	Optional vector of colors to be used for lines. Input 'default' makes use of `rich.colors.short` function.
`shadecol`	Optional vector of colors to be used for shading uncertainty intervals. Input 'default' makes use of `rich.colors.short` function with alpha transparency.
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`spacepoints`	Number of years between points shown on top of lines (for long timeseries, points every year get mashed together)
`staggerpoints`	Number of years to stagger the first point (if `spacepoints > 1`) for each line (so that adjacent lines have points in different years)
`xlim`	Optional x limits
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space to fit legend if necessary. Default=1.
`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)
`uncertainty`	Show plots with uncertainty intervals
`shadealpha`	Transparency parameter used to make default shadecol values (see ?rgb for more info)
`legend`	Add a legend?
`legendlabels`	Optional vector of labels to include in legend. Default is 'model1','model2',etc.
`legendloc`	Location of legend. See ?legend for more info.
`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.
`btarg`	Target biomass value at which to show a line (set to 0 to remove)
`minbthresh`	Minimum biomass threshhold at which to show a line (set to 0 to remove)
`sprtarg`	Target value for SPR-ratio where line is drawn in the SPR plots and phase plot.
`pwidth`	Width of plot written to PNG file
`pheight`	Height of plot written to PNG file
`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.
`densitynames`	Vector of names (or subset of names) of parameters or derived quantities contained in summaryoutput$pars$Label or summaryoutput$quants$Label for which to make density plots
`densityxlabs`	Optional vector of x-axis labels to use in the density plots (must be equal in length to the printed vector of quantities that match the `densitynames` input)
`densityscalex`	Scalar for upper x-limit in density plots (values below 1 will cut off the right tail to provide better contrast among narrower distributions
`densityscaley`	Scalar for upper y-limit in density plots (values below 1 will cut off top of highest peaks to provide better contrast among broader distributions
`densityadjust`	Multiplier on bandwidth of kernel in density function used for smoothing MCMC posteriors. See 'adjust' in ?density for details.
`densitysymbols`	Add symbols along lines in density plots. Quantiles are `c(0.025,0.1,0.25,0.5,0.75,0.9,0.975)`.
`densitytails`	Shade tails outside of 95% interval in density plots.
`fix0`	Always include 0 in the density plots?
`new`	Create new empty plot window
`add`	Allows single plot to be added to existing figure. This needs to be combined with specific 'subplots' input to make sure only one thing gets added.
`par`	list of graphics parameter values passed to the `par` function
`verbose`	Report progress to R GUI?
`mcmcVec`	Vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE