Installation

Overview

The SPASAM.MSE package (Spatial Processes and Stock Assessment Methods – Management Strategy Evaluation) is a comprehensive toolbox for conducting spatially explicit Management Strategy Evaluation (MSE) to support fisheries management under complex population structure and movement dynamics.

SPASAM.MSE is built upon the Woods Hole Assessment Model (WHAM), a state-space, age-structured stock assessment framework. WHAM supports time- and/or age-varying process error (treated as random effects) on key population processes and can incorporate environmental covariate effects. By embedding WHAM within a closed-loop MSE framework, SPASAM.MSE provides tools to simulate and evaluate management strategies (combinations of data collection, stock assessment models, and harvest control rules) under realistic spatial and temporal complexity.

The platform enables systematic exploration of estimation and management performance across scenarios involving spatial heterogeneity, movement, connectivity, and alternative population structures for fish stocks with diverse life-history traits across multiple regions.

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1. Install WHAM

SPASAM.MSE depends on WHAM, which must be installed separately.

Install the development version of WHAM

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

(Optional) Meta-population / spatial development version of WHAM

For users working with spatial or meta-population extensions of WHAM,
the development branch (lab) can be installed directly from GitHub:

devtools::install_github(
  "lichengxue/wham",
  ref = "lab",
  dependencies = TRUE
)

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2. Install SPASAM.MSE

Once WHAM is installed, install SPASAM.MSE from GitHub:

devtools::install_github(
  "lichengxue/SPASAM.MSE",
  dependencies = TRUE
)

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3. Notes on Multiple WHAM Installations

If you have previously installed a single-stock version of WHAM and wish to retain it alongside a multi-stock or spatial version, it is recommended to store them in separate library directories to avoid overwriting.

Example workflow:

library_paths <- .libPaths()[1]
new_folder <- "wham_old"

if (!file.exists(file.path(library_paths, new_folder))) {
  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)
)

This approach allows users to switch between WHAM versions as needed for different modeling workflows.