Description Usage Arguments Examples
This function calls all the other functions to create the desired outputs.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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
)
|
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) |
1 | PlotASAP("C:\\main.dir\\my.asap.results.dir","simple")
|
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