Package: coevolve
Title: Fit Bayesian Generalized Dynamic Phylogenetic Models using
        'Stan' or 'JAX'
Version: 1.2.1
Authors@R: 
    c(person("Scott", "Claessens", , "scott.claessens@gmail.com", 
             role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3562-6981")),
      person("Erik", "Ringen", , "erikjacob.ringen@uzh.ch", 
             role = "aut", comment = c(ORCID = "0000-0002-3565-6961")),
      person("Rob", "Moss", , "rgmoss@unimelb.edu.au",
             role = "rev", comment = c(ORCID = "0000-0002-4568-2012")),
      person("Krzysztof", "Bartoszek", , "krzbar@protonmail.ch",
             role = "rev", comment = c(ORCID = "0000-0002-5816-4345")))
Description: Fit Bayesian generalized dynamic phylogenetic models using
        'Stan' or 'JAX'. The package allows an arbitrary number of
        variables with different response distributions to coevolve on
        a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary
        process, allowing users to assess directionality between
        coevolving variables. The optional JAX backend enables
        high-performance sampling with NumPyro and potential GPU
        acceleration via 'reticulate'.
License: GPL (>= 3)
Date: 2026-06-23
URL: https://github.com/ScottClaessens/coevolve,
        https://scottclaessens.github.io/coevolve/
BugReports: https://github.com/ScottClaessens/coevolve/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd",
        "srr::srr_stats_roclet"))
Suggests: knitr, loo, rmarkdown, reticulate, testthat (>= 3.1.7),
        tibble, withr
Config/testthat/edition: 3
Imports: ape, bayesplot, cmdstanr, colorspace, dplyr, ggplot2,
        gridExtra, lifecycle, Matrix, methods, patchwork (>= 1.2.0),
        phangorn, phaseR, phytools, posterior, purrr, readr, rlang,
        stats, stringr, tidyr, whisker
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
LazyData: true
Additional_repositories: https://stan-dev.r-universe.dev/
Remotes: stan-dev/cmdstanr, mjg211/phaseR
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev libx11-dev
Repository: https://ropensci-staging.r-universe.dev
Date/Publication: 2026-10-06 19:31:38 UTC
RemoteUrl: https://github.com/ScottClaessens/coevolve
RemoteRef: HEAD
RemoteSha: 52bdfcc1cf47a5f53adb7a181e2449318b524430
NeedsCompilation: no
Packaged: 2026-10-07 08:29:35 UTC; root
Author: Scott Claessens [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3562-6981>),
  Erik Ringen [aut] (ORCID: <https://orcid.org/0000-0002-3565-6961>),
  Rob Moss [rev] (ORCID: <https://orcid.org/0000-0002-4568-2012>),
  Krzysztof Bartoszek [rev] (ORCID:
    <https://orcid.org/0000-0002-5816-4345>)
Maintainer: Scott Claessens <scott.claessens@gmail.com>