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
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phylosem.pdf |phylosem.html✨
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 site:https://james-thorson-noaa.github.io

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

On CRAN:

Conda:

cpp

4.78 score 1 stars 298 downloads 10 exports 102 dependencies

Last updated 20 days agofrom:321fc949e6. Checks:3 OK, 9 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKMar 20 2025
R-4.5-win-x86_64NOTEMar 20 2025
R-4.5-mac-x86_64NOTEMar 20 2025
R-4.5-mac-aarch64NOTEMar 20 2025
R-4.5-linux-x86_64OKMar 20 2025
R-4.4-win-x86_64NOTEMar 20 2025
R-4.4-mac-x86_64NOTEMar 20 2025
R-4.4-mac-aarch64NOTEMar 20 2025
R-4.4-linux-x86_64OKMar 20 2025
R-4.3-win-x86_64NOTEMar 20 2025
R-4.3-mac-x86_64NOTEMar 20 2025
R-4.3-mac-aarch64NOTEMar 20 2025

Exports:as_fitted_DAGas_phylo4das_semaveragebestchoicecompare_phylosemlist_parametersphylosemphylosem_control

Dependencies:abindade4apearmaskpassBiocGenericsBiocManagerbootcachemclicodacodetoolscolorspacecpp11crayoncurldigestdplyrfansifarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixmemoisemgcvmimimeminqamunsellnlmenloptropensslparallellyphylobasephylolmphylopathpillarpixmappkgconfigplyrpolyclipprettyunitsprogresspurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrnclRNeXMLscalessemspstringistringrsyssystemfontstibbletidygraphtidyrtidyselectTMBtweenrutf8uuidvctrsviridisviridisLitewithrXMLxml2

Comparison with other packages

James T. Thorson and Wouter van der Bijl

Rendered fromcomparison.Rmdusingknitr::rmarkdownon Mar 20 2025.

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

Demonstration of selected features

James T. Thorson

Rendered fromdemonstration.Rmdusingknitr::rmarkdownon Mar 20 2025.

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

Detailed comparison with phylopath

Wouter van der Bijl

Rendered fromphylopath.Rmdusingknitr::rmarkdownon Mar 20 2025.

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

Phylogenetic comparative methods in fisheries science

James T. Thorson

Rendered fromfisheries.Rmdusingknitr::rmarkdownon Mar 20 2025.

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