Package: phylosem 1.1.4

James Thorson

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>.

Authors:James Thorson [aut, cre], Wouter van der Bijl [ctb]

phylosem_1.1.4.tar.gz
phylosem_1.1.4.zip(r-4.7)phylosem_1.1.4.zip(r-4.6)phylosem_1.1.4.zip(r-4.5)
phylosem_1.1.4.tgz(r-4.6-x86_64)phylosem_1.1.4.tgz(r-4.6-arm64)phylosem_1.1.4.tgz(r-4.5-x86_64)phylosem_1.1.4.tgz(r-4.5-arm64)
phylosem_1.1.4.tar.gz(r-4.7-arm64)phylosem_1.1.4.tar.gz(r-4.7-x86_64)phylosem_1.1.4.tar.gz(r-4.6-arm64)phylosem_1.1.4.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
phylosem/json (API)
NEWS

# Install 'phylosem' in R:
install.packages('phylosem', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/james-thorson-noaa/phylosem/issues

Pkgdown/docs site:https://james-thorson-noaa.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

4.56 score 1 stars 18 scripts 243 downloads 10 exports 100 dependencies

Last updated from:321fc949e6. Checks:12 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK340
linux-devel-x86_64OK324
source / vignettesOK505
linux-release-arm64OK311
linux-release-x86_64OK340
macos-release-arm64OK179
macos-release-x86_64OK604
macos-oldrel-arm64OK209
macos-oldrel-x86_64OK379
windows-develOK296
windows-releaseOK305
windows-oldrelOK300
wasm-releaseFAIL222

Exports:as_fitted_DAGas_phylo4das_semaveragebestchoicecompare_phylosemlist_parametersphylosemphylosem_control

Dependencies:abindade4apearmaskpassbase64encBiocGenericsBiocManagerbootcachemclicodacodetoolscpp11crayoncurldigestdplyrfarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixmemoisemimimeminqanlmenloptropensslparallellyphylobasephylolmphylopathpillarpixmappkgconfigplyrpolyclipprettyunitsprogresspurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrnclRNeXMLS7scalessemspstringistringrsyssystemfontstibbletidygraphtidyrtidyselectTMBtweenrutf8uuidvctrsviridisviridisLitewithrXMLxml2

Comparison with other packages

James T. Thorson and Wouter van der Bijl

Rendered fromcomparison.Rmdusingknitr::rmarkdownon May 17 2026.

Last update: 2024-02-01
Started: 2023-01-27

Demonstration of selected features

James T. Thorson

Rendered fromdemonstration.Rmdusingknitr::rmarkdownon May 17 2026.

Last update: 2024-02-01
Started: 2023-06-13

Detailed comparison with phylopath

Wouter van der Bijl

Rendered fromphylopath.Rmdusingknitr::rmarkdownon May 17 2026.

Last update: 2024-02-01
Started: 2023-02-03

Phylogenetic comparative methods in fisheries science

James T. Thorson

Rendered fromfisheries.Rmdusingknitr::rmarkdownon May 17 2026.

Last update: 2024-02-01
Started: 2023-10-07