SSplotComps: Plot composition data and fits.
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

Plot composition data and fits from Stock Synthesis output. Mult-figure plots depend on make_multifig.

SSplotComps(replist, subplots=1:12,
  kind="LEN", sizemethod=1, aalyear=-1, aalbin=-1, plot=TRUE,
  print=FALSE, fleets="all", fleetnames="default", sexes="all",
  datonly=FALSE, samplesizeplots=TRUE, compresidplots=TRUE, bub=FALSE,
  showsampsize=TRUE, showeffN=TRUE, minnbubble=8, pntscalar=NULL,
  scalebubbles=FALSE,bub.scale.pearson=1.5,bub.scale.dat=3,
  pwidth=7, pheight=7, punits="in", ptsize=12, res=300,
  plotdir="default", cex.main=1, linepos=1, fitbar=FALSE,
  do.sqrt=TRUE, smooth=TRUE, cohortlines=c(),
  labels = c("Length (cm)",            
             "Age (yr)",               
             "Year",                   
             "Observed sample size",   
             "Effective sample size",  
             "Proportion",             
             "cm",                     
             "Frequency",              
             "Weight",                 
             "Length",                 
             "(mt)",                   
             "(numbers x1000)",        
             "Stdev (Age) (yr)",       
             "Andre's conditional AAL plot, "),
  printmkt=TRUE,printsex=TRUE,
  maxrows=6,maxcols=6,maxrows2=2,maxcols2=4,rows=1,cols=1,
  fixdims=TRUE,fixdims2=FALSE,maxneff=5000,verbose=TRUE,
  scalebins=FALSE,addMeans=TRUE,...)

`replist`	list created by `SSoutput`
`subplots`	vector controlling which subplots to create
`kind`	indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "L@A", or "W@A".
`sizemethod`	if kind = "SIZE" then this switch chooses which of the generalized size bin methods will be plotted.
`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.
`plot`	plot to active plot device?
`print`	print to PNG files?
`fleets`	optional vector to subset fleets for which plots will be made
`fleetnames`	optional vector of fleet names to put in the labels
`sexes`	which sexes to show plots for. Default="all" which will include males, females, and unsexed. This options is not fully implemented for all plots.
`datonly`	make plots of data without fits as well as data with fits?
`samplesizeplots`	make sample size plots?
`compresidplots`	make plots of residuals for fit to composition data?
`bub`	make bubble plot for numbers at age or size?
`showsampsize`	add sample sizes to plot
`showeffN`	add effective sample sizes to plot
`minnbubble`	number of unique x values before adding buffer. see ?bubble3 for more info.
`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.
`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.
`scalebubbles`	scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.
`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
`plotdir`	directory where PNG files will be written. by default it will be the directory where the model was run.
`cex.main`	character expansion parameter for plot titles
`linepos`	should lines be added before points (linepos=1) or after (linepos=2)?
`fitbar`	show fit to bars instead of points
`do.sqrt`	scale bubbles based on sqrt of size vector. see ?bubble3 for more info.
`smooth`	add loess smoother to observed vs. expected index plots and input vs. effective sample size?
`cohortlines`	optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots
`labels`	vector of labels for plots (titles and axis labels)
`printmkt`	show market categories in plot titles?
`printsex`	show gender in plot titles?
`maxrows`	maximum (or fixed) number or rows of panels in the plot
`maxcols`	maximum (or fixed) number or columns of panels in the plot
`maxrows2`	maximum number of rows for conditional age at length plots
`maxcols2`	maximum number of columns for conditional age at length plots
`rows`	number or rows to return to as default for next plots to come or for single plots
`cols`	number or cols to return to as default for next plots to come or for single plots
`fixdims`	fix the dimensions at maxrows by maxcols or resize based on number of years of data
`fixdims2`	fix the dimensions at maxrows by maxcols in aggregate plots or resize based on number of fleets
`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.
`verbose`	return updates of function progress to the R GUI?
`scalebins`	Rescale expected and observed proportions by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.
`addMeans`	Add parameter means in addition to medians for MCMC posterior distributions in which the median and mean differ.
`...`	additional arguments that will be passed to the plotting.