Package: wham
Title: Woods Hole Assessment Model (WHAM)
Version: 2.1.0.9006
Authors@R: c(
    person("Tim", "Miller", role = c("aut", "cre"),
           email = "timothy.j.miller@noaa.gov",
           comment = c(ORCID = "0000-0003-1411-1206")),
    person("Brian", "Stock", role = c("aut"),
           comment = c(ORCID = "0000-0002-2393-6747")),
    person("Liz", "Brooks", role = c("ctb"),
           email = "liz.brooks@noaa.gov"),
    person("Chris", "Legault", role = c("ctb"),
           email = "chris.legault@noaa.gov"),
    person("Jim", "Thorson", role = c("ctb"),
           email = "james.thorson@noaa.gov"))
Description: The Woods Hole Assessment Model (WHAM) is a general
        age-structured stock assessment framework that can be
        configured to estimate assessment models that range in
        complexity from statistical catch-at-age (SCAA) model with
        annual recruitments as fixed effects, to state-space,
        multi-stock, multi-region, age-structured models where many
        parameters can be treated as time- and age-varying process
        errors and/or allowing effects of environmental covariates.
        WHAM is a generalization of code from Miller et al. (2016),
        Miller and Hyun (2018), and Miller et al. (2018). WHAM also has
        many similarities of input data sources with ASAP (Legault and
        Restrepo 1999) and provides functions to generate a WHAM input
        file from an ASAP3 dat file, although this is not a
        requirement. Many of the plotting functions for input data,
        results, and diagnostics have modified from code written by
        Chris Legault and Liz Brooks.
Depends: R (>= 4.2.2)
Imports: Deriv (>= 4.1.6), dplyr (>= 1.1.4), ellipse (>= 0.5.0),
        ggplot2 (>= 3.5.1), kableExtra (>= 1.4.0), knitr (>= 1.48),
        mnormt (>= 2.1.1), rmarkdown (>= 2.28), tidyr (>= 1.3.1), TMB
        (>= 1.9.17), viridis (>= 0.6.5), viridisLite (>= 0.4.2)
Remotes: kaskr/adcomp/TMB
LinkingTo: TMB, RcppEigen
URL: https://timjmiller.github.io/wham/,
        https://github.com/timjmiller/wham,
        https://doi.org/10.1016/j.fishres.2021.105967,
        https://doi.org/10.1139/cjfas-2025-0097
BugReports: https://github.com/timjmiller/wham/issues
License: GPL-3
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Encoding: UTF-8
Suggests: testthat, devtools, here, parallel, snowfall
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev
        libuv1-dev libxml2-dev
Repository: https://noaa-fisheries-integrated-toolbox.r-universe.dev
Date/Publication: 2026-06-16 13:45:24 UTC
RemoteUrl: https://github.com/timjmiller/wham
RemoteRef: HEAD
RemoteSha: 3b16618f8de5ac7b5f0b6dc63dd6b4c359e717fc
NeedsCompilation: yes
Packaged: 2026-06-16 18:14:20 UTC; root
Author: Tim Miller [aut, cre] (ORCID: <https://orcid.org/0000-0003-1411-1206>),
  Brian Stock [aut] (ORCID: <https://orcid.org/0000-0002-2393-6747>),
  Liz Brooks [ctb],
  Chris Legault [ctb],
  Jim Thorson [ctb]
Maintainer: Tim Miller <timothy.j.miller@noaa.gov>