SS_plots: plot many quantities related to output from Stock Synthesis
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) References See Also

Creates a user-chosen set of plots, including biological quantities, time series, and fits to data. Plots are sent to R GUI, single PDF file, or multiple PNG files. This is now just a wrapper which calls on separate functions to make all the plots.

SS_plots(
  replist=NULL, plot=1:24, print=NULL, pdf=FALSE, png=FALSE, html=png,
  printfolder="plots", dir="default", fleets="all", areas="all",
  fleetnames="default", fleetcols="default", fleetlty=1, fleetpch=1,
  lwd=1, areacols="default", areanames="default",
  verbose=TRUE, uncertainty=TRUE, forecastplot=FALSE,
  datplot=FALSE, Natageplot=TRUE, samplesizeplots=TRUE,
  compresidplots=TRUE, sprtarg="default", btarg="default",
  minbthresh="default", pntscalar=NULL,
  bub.scale.pearson=1.5,bub.scale.dat=3,pntscalar.nums=2.6,
  minnbubble=8, aalyear=-1, aalbin=-1, aalresids=FALSE, maxneff=5000,
  cohortlines=c(), smooth=TRUE, showsampsize=TRUE, showeffN=TRUE,
  showlegend=TRUE, pwidth=7, pheight=7, punits="in", ptsize=12, res=300,
  cex.main=1,selexlines=1:5, rows=1, cols=1, maxrows=6, maxcols=6,
  maxrows2=2, maxcols2=4, tagrows=3, tagcols=3, fixdims=TRUE, new=TRUE,
  SSplotDatMargin=8, filenotes=NULL, catchasnumbers=NULL,
  catchbars=TRUE, legendloc="topleft", minyr=NULL, maxyr=NULL,
  scalebins=FALSE, scalebubbles=FALSE,...)

`replist`	List created by `SS_output`
`plot`	Plot sets to be created, see list of plots below. Use to specify only those plot sets of interest, e.g., c(1,2,5,10). Plots for data not available in the model run will automatically be skipped, whether called or not.
`print`	Deprecated input for backward compatability, now replaced by `png = TRUE/FALSE`.
`pdf`	Send plots to PDF file instead of R GUI?
`png`	Send plots to PNG files instead of R GUI?
`html`	Run `SS_html` on completion? By default has same value as `png`.
`printfolder`	Name of subfolder to create within the working directory into which any PNG files specified by `print` will be saved. By default the working directory is used with no subfolder. Default="".
`dir`	The directory in which any PNG files requested by `print` are created. By default it will be the same directory that the report file was read from by the `SS_output` function. Default="default".
`fleets`	Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys for which plots should be made. By default, plots will be made for all fleets and surveys. Default="all".
`areas`	Either the string "all", or a vector of numerical values, like c(1,3), listing areas for which plots should be made in a multi-area model. By default, plots will be made for all areas (excepting cases where the function has not yet been updated for multi-area models). Default="all".
`fleetnames`	Either the string "default", or a vector of characters strings to use for each fleet name. Default="default".
`fleetcols`	Either the string "default", or a vector of colors to use for each fleet. Default="default".
`fleetlty`	Vector of line types used for each fleet in some plots. Default=1.
`fleetpch`	Vector of point types used for each fleet in some plots. Default=1.
`lwd`	Line width for some plots. Default=1.
`areacols`	Either the string "default", or a vector of colors to use for each area. Default="default".
`areanames`	Optional vector of names for each area used in titles. Default="default".
`verbose`	Return updates of function progress to the R GUI? Default=T.
`uncertainty`	Include values in plots showing estimates of uncertainty (requires positive definite hessian in model and `covar`=T in `SS_output`)? Default=T.
`forecastplot`	Include forecast years in the plots? Obviously requires forecast options to have been used in the model. Default=T.
`datplot`	Plot the data by itself? This is useful in document preparation. Setting datplot=F is equivalent to leaving off plots 15 and 16. Default=F.
`Natageplot`	Plot the expected numbers at age bubble plots and mean-age time series? Default=T.
`samplesizeplots`	Show sample size plots? Default=T.
`compresidplots`	Show residuals for composition plots?
`sprtarg`	Specify the F/SPR proxy target. Default=0.4.
`btarg`	Target depletion to be used in plots showing depletion. May be omitted by setting to NA. Default=0.4.
`minbthresh`	Threshold depletion to be used in plots showing depletion. May be omitted by setting to NA. Default=0.25.
`pntscalar`	This scalar defines the maximum bubble size for bubble plots. This option is still available but a better choice is to use bub.scale.pearson and bub.scale.dat, which are allow the same scaling throughout all plots.
`pntscalar.nums`	This scalar defines the maximum bubble size for numbers-at-age and numbers-at-length plots.
`bub.scale.pearson`	Character expansion (cex) value for a proportion of 1.0 in bubble plot of Pearson residuals. Default=1.5.
`bub.scale.dat`	Character expansion (cex) value for a proportion of 1.0 in bubble plot of composition data. Default=3.
`minnbubble`	This defines the minimum number of years below which blank years will be added to bubble plots to avoid cropping. Default=8.
`aalyear`	Years to plot multi-panel conditional age-at-length fits for all length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking the fit of a dominant year class, critical time period, etc. Default=-1.
`aalbin`	The length bin for which multi-panel plots of the fit to conditional age-at-length data will be produced for all years. Useful to see if growth curves are ok, or to see the information on year classes move through the conditional data. Default=-1.
`aalresids`	Plot the full set of conditional age-at-length Pearson residuals? Default=F.
`maxneff`	The maximum value to include on plots of input and effective sample size. Occasionally a calculation of effective N blows up to very large numbers, rendering it impossible to observe the relationship for other data. Default=5000.
`cohortlines`	Optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots. Default=c().
`smooth`	Add loess smoother to observed vs. expected index plots and input vs. effective sample size? Default=T.
`showsampsize`	Display sample sizes on composition plots? Default=T.
`showeffN`	Display effective sample sizes on composition plots? Default=T.
`showlegend`	Display legends in various plots? Default=T.
`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. Default=300.
`cex.main`	Character expansion parameter for plot titles (not yet implemented for all plots). Default=1.
`selexlines`	Vector controling which lines should be shown on selectivity plots if the model includes retention. Default=1:5.
`rows`	Number of rows to use for single panel plots. Default=1.
`cols`	Number of columns to use for single panel plots. Default=1.
`maxrows`	Maximum number of rows to for multi-panel plots. Default=6.
`maxcols`	Maximum number of columns for multi-panel plots. Default=6.
`maxrows2`	Maximum number of rows for conditional age at length multi-panel plots. Default=2.
`maxcols2`	Maximum number of rows for conditional age at length multi-panel plots. Default=4.
`tagrows`	Number of rows for tagging-related plots. Default=3.
`tagcols`	Number of columns for tagging-related plots. Default=3.
`fixdims`	Control whether multi-panel plots all have dimensions equal to maxrows by maxcols, or resized within those limits to fit number of plots. Default=T.
`new`	Open a new window or add to existing plot windows. Default=T.
`SSplotDatMargin`	Size of right-hand margin in data plot (may be too small if fleet names are long)
`filenotes`	Optional vector of character strings to be added to intro HTML page (if created) with notes about the model.
`catchasnumbers`	Is catch input in numbers instead of biomass? Default=F.
`catchbars`	show catch by fleet as barplot instead of stacked polygons (default=TRUE)
`legendloc`	Location for all legends. Default="topleft".
`minyr`	First year to show in time-series plots (changes xlim parameters).
`maxyr`	Last year to show in time-series plots (changes xlim parameters).
`scalebins`	Rescale expected and observed proportions in composition plots by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.
`scalebubbles`	scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.
`...`	Additional arguments that will be passed to some subfunctions.

Ian Stewart, Ian Taylor

Walters, Hilborn, and Christensen, 2008, Surplus production dynamics in declining and recovering fish populations. Can. J. Fish. Aquat. Sci. 65: 2536-2551.

SS_output, SSplotBiology, SSplotCatch, SSplotComps, SSplotDiscard, SSplotIndices, SSplotMnwt, SSplotNumbers, SSplotRecdevs, SSplotSelex, SSplotSpawnrecruit, SSplotSPR, SSplotTags, SSplotTimeseries, SSplotYield