Package: phylosem
Type: Package
Title: Phylogenetic Structural Equation Model
Version: 1.1.4
Date: 2024-04-02
Authors@R: 
    c(person(given = "James",
             family = "Thorson",
             role = c("aut", "cre"),
             email = "James.Thorson@noaa.gov",
             comment = c(ORCID = "0000-0001-7415-1010")),
      person(given = "Wouter",
             family = "van der Bijl",
             role = c("ctb"),
             email = "wouter@zoology.ubc.ca",
             comment = c(ORCID = "0000-0002-7366-1868"))
    )
Imports: sem, ape, phylobase, phylopath, methods
Depends: TMB, R (>= 4.0.0),
Suggests: semPlot, TreeTools, Rphylopars, phylolm, fishtree, phyr,
        knitr, rmarkdown, ggplot2, testthat, phylosignal, adephylo
Enhances: phytools, DiagrammeR
LinkingTo: RcppEigen, TMB
Description: Applies phylogenetic comparative methods (PCM) and
        phylogenetic trait imputation using structural equation models
        (SEM), extending methods from Thorson et al. (2023)
        <doi:10.1111/2041-210X.14076>. This implementation includes a
        minimal set of features, to allow users to easily read all of
        the documentation and source code.  PCM using SEM includes
        phylogenetic linear models and structural equation models as
        nested submodels, but also allows imputation of missing values.
        Features and comparison with other packages are described in
        Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.1
VignetteBuilder: knitr
URL: https://james-thorson-noaa.github.io/phylosem/
BugReports: https://github.com/James-Thorson-NOAA/phylosem/issues
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libxml2-dev libssl-dev
Repository: https://james-thorson-noaa.r-universe.dev
Date/Publication: 2026-09-24 07:37:08 UTC
RemoteUrl: https://github.com/james-thorson-noaa/phylosem
RemoteRef: HEAD
RemoteSha: 1ff457f318ecb3606234824cff5f73ab6ba98ee4
NeedsCompilation: yes
Packaged: 2026-10-09 11:26:32 UTC; root
Author: James Thorson [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7415-1010>),
  Wouter van der Bijl [ctb] (ORCID:
    <https://orcid.org/0000-0002-7366-1868>)
Maintainer: James Thorson <James.Thorson@noaa.gov>