TSCplot: Create a plot for the TSC report
In r4ss: R code for Stock Synthesis

Description Usage Arguments Details Value Author(s) See Also Examples

Creates a plot of catch and spawning biomass from the output of SS_output for the NOAA TSC report.

TSCplot(SSout,yrs="default",ylimBar="default",ylimDepl=c(0,1.025),
colBar="yellow",cexBarLabels=1.1,cex.axis=1.1,space=0.0,pchDepl=19,
colDepl="red",lwdDepl=3,shiftDepl = 0.25,pchSpace = 5,ht=4,wd=7,
labelLines=2.8,makePDF=NULL,makePNG=NULL,MCMC=F)

`SSout`	The output from `SS_output`
`yrs`	The vector of years to plot
`ylimBar`	y-axis limits for catch barplot
`ylimDepl`	y-axis limits for depletion line
`colBar`	colors of the bars
`cexBarLabels`	character expansion for the labels underneath the bars (years)
`cex.axis`	character expansion for the axis labels
`space`	space between bars (see space argument of `barplot`)
`pchDepl`	character type for points on the depletion line
`colDepl`	color of the points on the depletion line
`lwdDepl`	width of the depletion line
`shiftDepl`	shift from beginning of the year for the points on the depletion line. Helps to guide the eye for exactly which year it corresponds to.
`pchSpace`	number of years between points on the depletion line. Higher numbers help tidy up the plot when plotting many years.
`ht`	Height of the plot in inches
`wd`	Width of the plot in inches
`labelLines`	line argument for `mtext` to move the axis labels
`makePDF`	filename for a pdf file. If NULL it does not make a pdf. Can specify a pdf filename or a png filename. Not both at the same time.
`makePNG`	filename for a png image. If NULL it does not make a png. Can specify a pdf filename or a png filename. Not both at the same time.
`MCMC`	If TRUE, will use mcmc results. It needs a list element called 'mcmc' on SSout.

It creates a plot on the current graphics device, in a pdf file, or as a png image of the figure used in the TSC report produced by the NWFSC. It expects the SS results read in by SS_output. If MCMC results are to be plotted, a 'mcmc' list element should be added using the SSgetMCMC function. See the examples below.

Returns a data frame with the years, spawning biomass, depletion, and total dead catch.

Allan Hicks

SS_output SSgetMCMC

  ## Not run: 
  ######################################
  #DO NOT RUN
    library(r4ss)
    update_r4ss_files()

    # ** CHANGE TO THE BASE DIRECTORY
    directory <- "C:\NOAA2011\Dover\Models\base_20110701"

    base <- SS_output(dir=directory,covar=F,verbose=F)

    #show the plot in R
    TSCplot(base)
    TSCplot(base,yrs=2000:2011,pchSpace = 1)
    #Create the plot as a PNG file
    TSCplot(base,makePNG="C:\NOAA2012\Assessments\TSCdover.png")
    #Create the plot as a PDF file
    TSCplot(base,makePDF="C:\NOAA2012\Assessment\TSCdover.pdf")

    # ** Hake model with MCMC results
    SSdir <- "C:/NOAA2012/Hake/Models"
    base <- SS_output(dir=paste(SSdir,"81_base_MCMC",sep="/"),covar=F)
    tmp <- SSgetMCMC(dir=paste(SSdir,"81_base_MCMC",sep="/"),writecsv=F)
    base$mcmc <- data.frame(tmp$model1)
    TSCplot(base,ylimDepl = c(0,1.25),pchSpace=1,MCMC=T)


  ###############################################
  
## End(Not run)