Package: phylosem 1.1.4

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://james-thorson-noaa.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 191 downloads 10 exports 100 dependencies

Last updated from:321fc949e6. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK352
linux-devel-x86_64OK335
source / vignettesOK567
linux-release-arm64OK291
linux-release-x86_64OK327
macos-release-arm64OK231
macos-release-x86_64OK347
macos-oldrel-arm64OK284
macos-oldrel-x86_64OK498
windows-develOK340
windows-releaseOK278
windows-oldrelOK324
wasm-releaseFAIL218

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 Jun 01 2026.

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

Demonstration of selected features

James T. Thorson

Rendered fromdemonstration.Rmdusingknitr::rmarkdownon Jun 01 2026.

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

Detailed comparison with phylopath

Wouter van der Bijl

Rendered fromphylopath.Rmdusingknitr::rmarkdownon Jun 01 2026.

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

Phylogenetic comparative methods in fisheries science

James T. Thorson

Rendered fromfisheries.Rmdusingknitr::rmarkdownon Jun 01 2026.

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