A function to generate joint distributions for stock status ratios (SSB/SSBref and F/Fref where ref can be MSY, SSB40, F40, etc.) using a Multivariate Log-Normal Distribution. 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
SSdeltaMVLN(
ss3rep,
Fref = NULL,
years = NULL,
mc = 5000,
weight = 1,
run = "MVLN",
plot = TRUE,
addprj = FALSE,
ymax = NULL,
xmax = NULL,
legendcex = 1,
verbose = TRUE,
variance_method = "ww2019",
bias_correct_mean = FALSE
)Arguments
- 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
- mc
number of monte-carlo simulations
- weight
weighting option for model ensembles weight*mc
- run
qualifier for model run
- 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?
- variance_method
Specify method for approximating the variance and covariance of the multivariate lognormal distribution
- ww2019
Use the approximation from Walter and Winker 2019 (Default for backwards compatibility).
- 2T
Use the delta-method and a 2nd order Taylor series approximation.
- bias_correct_mean
Specify if the Stock Synthesis MLE estimates should be bias corrected when used to specify the mean of the multivariate lognormal distribution
- FALSE
Do not apply bias correction (Default for backwards compatibility).
- TRUE
Apply bias correction.