PlotASAP: Plot ASAP

In cmlegault/ASAPplots: Creates Standard Plots and PDFs for ASAP3

Description

This function calls all the other functions to create the desired outputs.

Usage

PlotASAP(
  wd,
  asap.name,
  nyrs.ave = 5,
  correlation.limit = 0.9,
  scale.catch.bubble.resid = 2,
  scale.index.bubble.resid = 2,
  scale.catch.bubble.data = 6,
  scale.index.bubble.data = 6,
  orig.bubble.colors = FALSE,
  pspr = c(),
  mcmc.burn = 0,
  mcmc.thin = 1,
  first.age = -999,
  save.plots = TRUE,
  plotf = "png",
  make.one.pdf = TRUE
)

Arguments

wd	directory where ASAP run is located
asap.name	Base name of original dat file (without the .dat extension)
nyrs.ave	number of years to average for calculating Reference Points (defaults to 5)
correlation.limit	will return parameter combos where |correlation| > value (defaults to 0.9)
scale.catch.bubble.resid	larger values increase size of catch age comp bubbles (defaults to 2)
scale.index.bubble.resid	larger values increase size of catch age comp bubbles (defaults to 2)
scale.catch.bubble.data	larger values increase size of catch age comp bubbles (defaults to 6)
scale.index.bubble.data	larger values increase size of catch age comp bubbles (defaults to 6)
orig.bubble.colors	logical TRUE = red, white, FALSE = red, blue (defaults to FALSE)
pspr	user defined value(s) of spr, e.g. 0.4 or c(0.4, 0.43, 0.46); if empty (default), calculated at seq(0.2, 0.5, by=0.1)
mcmc.burn	number of realizations to remove from start of MCMC (defaults to 0)
mcmc.thin	thinning parameter for MCMC (defaults to 1)
first.age	youngest age to use in catch curves, -999 finds peak age (defaults to -999)
save.plots	saves indivdual plots (defaults to TRUE)
plotf	format for individual plots (defaults to 'png')
make.one.pdf	diagnostics/results/ref pts/MCMC/data are all saved as one pdf (defaults to TRUE)

Examples

PlotASAP("C:\\main.dir\\my.asap.results.dir","simple") 

cmlegault/ASAPplots documentation built on March 29, 2021, 8:28 p.m.