TSCplot: Create a plot for the TSC report

Description

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

Usage

TSCplot(SSout, yrs = "default", ylimBar = "default", ylimDepl = c(0,
  1.025), colBar = "yellow", cexBarLabels = 1.1, cex.axis = 1.1,
  space = 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)

Arguments

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.

Height of the plot in inches

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.

Value

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

Details

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.

Examples

Run this code

# NOT RUN {
  
# }
# 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)


  ###############################################
  
# }
# NOT RUN {
# }