Type: Package
Package: nodeSub
Title: Simulate DNA Alignments Using Node Substitutions
Version: 1.2.9
Authors@R: person(given = "Thijs",
                      family = "Janzen",
                      role = c("aut", "cre"),
                      email = "thijsjanzen@gmail.com")
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Description: Simulate DNA sequences for the node substitution model.  In
    the node substitution model, substitutions accumulate additionally
    during a speciation event, providing a potential mechanistic
    explanation for substitution rate variation. This package provides
    tools to simulate such a process, simulate a reference process with
    only substitutions along the branches, and provides tools to infer
    phylogenies from alignments. More information can be found in Janzen
    (2021) <doi:10.1093/sysbio/syab085>.
License: GPL-3
URL: https://github.com/thijsjanzen/nodeSub
BugReports: https://github.com/thijsjanzen/nodeSub/issues
Depends: ape, Rcpp
Imports: beastier, beautier, DDD, geiger, lifecycle, pbapply, phangorn,
        phylobase, rappdirs, Rmpfr, stringr, testit, tibble, tracerer
Suggests: dplyr, ggplot2, knitr, magrittr, nLTT, rmarkdown, RPANDA,
        testthat, tidyr, TreeSim
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.2.3
NeedsCompilation: yes
Packaged: 2025-05-06 08:32:58 UTC; thijsjanzen
Author: Thijs Janzen [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 09:00:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-30 14:35:52 UTC; unix
Archs: nodeSub.so.dSYM
