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 (In press).

Version: 1.1.1
Depends: TMB (≥ 1.9.7), R (≥ 4.0.0)
Imports: sem, ape, phylobase, phylopath
LinkingTo: RcppEigen, TMB
Suggests: semPlot, TreeTools, Rphylopars, phylolm, fishtree, phyr, knitr, rmarkdown, ggplot2, testthat, phylosignal
Enhances: phytools, DiagrammeR
Published: 2023-11-26
Author: James Thorson ORCID iD [aut, cre], Wouter van der Bijl ORCID iD [ctb]
Maintainer: James Thorson <James.Thorson at>
License: GPL-3
NeedsCompilation: yes
Citation: phylosem citation info
Materials: README NEWS
CRAN checks: phylosem results


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


Package source: phylosem_1.1.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): phylosem_1.1.1.tgz, r-oldrel (arm64): phylosem_1.1.1.tgz, r-release (x86_64): phylosem_1.1.1.tgz, r-oldrel (x86_64): phylosem_1.1.0.tgz
Old sources: phylosem archive


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