phylosem: Phylogenetic Structural Equation Model

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>.

Version: 1.1.4
Depends: TMB, R (≥ 4.0.0)
Imports: sem, ape, phylobase, phylopath, methods
LinkingTo: RcppEigen, TMB
Suggests: semPlot, TreeTools, Rphylopars, phylolm, fishtree, phyr, knitr, rmarkdown, ggplot2, testthat, phylosignal, adephylo
Enhances: phytools, DiagrammeR
Published: 2024-04-02
Author: James Thorson ORCID iD [aut, cre], Wouter van der Bijl ORCID iD [ctb]
Maintainer: James Thorson <James.Thorson at noaa.gov>
BugReports: https://github.com/James-Thorson-NOAA/phylosem/issues
License: GPL-3
URL: https://james-thorson-noaa.github.io/phylosem/
NeedsCompilation: yes
Citation: phylosem citation info
Materials: README NEWS
CRAN checks: phylosem results

Documentation:

Reference manual: phylosem.pdf
Vignettes: Comparison with other packages
Demonstration of selected features
Phylogenetic comparative methods in fisheries science
Detailed comparison with 'phylopath'

Downloads:

Package source: phylosem_1.1.4.tar.gz
Windows binaries: r-devel: phylosem_1.1.4.zip, r-release: phylosem_1.1.4.zip, r-oldrel: phylosem_1.1.4.zip
macOS binaries: r-release (arm64): phylosem_1.1.4.tgz, r-oldrel (arm64): phylosem_1.1.4.tgz, r-release (x86_64): phylosem_1.1.4.tgz
Old sources: phylosem archive

Linking:

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