The “whamMSE” package is a comprehensive toolbox designed to conduct management strategy evaluation (MSE) for supporting spatial management for complex, heterogeneous populations. The package is built upon a state-space age-structured stock assessment model - Woods Hole Assessment Model (WHAM). WHAM can incorporate time- and/or age-varying process errors (treated as random effects) on population processes, and can also incorporate environmental effects on population processes. This package provides tools to simulate and evaluate management strategies (combination of data collection methods, stock assessment models, and harvest control rules) by allowing users to explore various scenarios and their impacts on estimation and management performance for fish stocks with different life-history traits across different regions.

1. Install “whamMSE” package

Users can install multi-wham from Tim Miller’s github:

install.packages("devtools") 
devtools::install_github("timjmiller/wham", dependencies=TRUE, ref="devel")

Users can also install the meta-population version of multi-wham:

devtools::install_github("lichengxue/wham-devel", dependencies=TRUE) # "meta-population" version of wham

Now users can install “whamMSE”:

devtools::install_github("lichengxue/whamMSE", dependencies=TRUE)

Note: If you have “single-wham” installed before, it’s recommended to install “multi-wham” package in a different directory to avoid one overwriting the other:

library_paths <- .libPaths()[1]
new_folder <- "wham_old"
if (file.exists(file.path(library_paths,new_folder))){
} else {
  dir.create(file.path(library_paths,new_folder))
}

file.copy(from = file.path(library_paths,"wham"), to = file.path(library_paths,new_folder), 
          overwrite = TRUE,  recursive = TRUE, copy.mode = TRUE)

library(wham, lib.loc = file.path(library_paths,new_folder)) # Load the single wham package