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

TSCplot

R Documentation

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 = FALSE
)

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.
`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.

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.

Value

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

Author(s)

Allan Hicks

Examples

## Not run: 

# define directory
directory <- "C:\\NOAA2011\\Dover\\Models\\base_20110701"
# read model output
base <- SS_output(dir = directory, covar = FALSE, verbose = FALSE)

# 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")

# Model with MCMC results
directory <- "C:/Models"
base <- SS_output(dir = directory, dir.mcmc = "mcmc")
TSCplot(base, ylimDepl = c(0, 1.25), pchSpace = 1, MCMC = TRUE)

## End(Not run)

r4ss documentation built on May 28, 2022, 1:11 a.m.