plotKobe_compare: plotKobe_compare terminal kobe plot. check out FLR.

Description Usage Arguments

View source: R/plotKobe_compare.R

Description

plotKobe_compare terminal kobe plot. check out FLR.

Usage

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plotKobe_compare(
  rootdir,
  axes.limits = c(2, 2),
  terminal_year = c(2017, 2017, 2016, 2017),
  kobe.type = c(NA, "ISC")[1],
  mq_csv = NA,
  b.name = NA,
  f.name = NA,
  pattern = NA,
  subpattern = NA,
  saveplot = T,
  plotloc = NA,
  doDistrib = FALSE,
  doLegend = T
)

Arguments

rootdir

home directory

axes.limits

x and y maximums for kobe plot, default to 2

terminal_year

Either a value or vector corresponding to the terminal year in each model.

kobe.type

if 'ISC', will have pale orange coloring in place of orange/yellow

mq_csv

optional; if you already generated a MQ csv using extractResults it will read from that, otherwise need pattern/subpattern

b.name

the character column name of the biomass ref point; can rename to change y lab

f.name

the character column name of the fishing ref point

pattern

1st order directory character

subpattern

2nd order directory character

saveplot

logical, do you want to save the plot

plotloc

where to save plot

doDistrib

logical. Do you want to have FLR style distributions on outer margins? Only works if models run with hessian.

doLegend

logical. do you want to write a legend (not advised for huge rep sets)


mkapur/kaputils documentation built on Nov. 14, 2021, 3:23 a.m.