A function to generate joint distributions for stock status ratios (SSB/SSBref and F/Fref where ref can be MSY, SSB40, F40, etc.) using MCMC. The function produces a Kobe plot, maximum likelihood estimates and the MVLN Monte-Carlo distributions of the Kobe values which can be input into SSplotEnsemble().
Usage
SSdiagsMCMC(
mcmc,
ss3rep,
Fref = NULL,
years = NULL,
run = "MCMC",
thin = 1,
plot = TRUE,
addprj = FALSE,
ymax = NULL,
xmax = NULL,
legendcex = 1,
verbose = TRUE
)Arguments
- mcmc
file path for folder with the derived_posteriors.sso file
- ss3rep
from r4ss::SS_output
- Fref
Choice of Fratio c("MSY","Btgt), correponding to F_MSY and F_Btgt
- years
single year or vector of years for mvln
- run
qualifier for model run
- thin
option to use additional thinning
- plot
option to show plot
- addprj
include forecast years
- ymax
ylim maximum
- xmax
xlim maximum
- legendcex
Allows to adjust legend cex
- verbose
Report progress to R GUI?
Value
output list maximum likelihood estimates and the MCMC posterier distributions of the Kobe values and a Kobe plot