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-4.5)phylosem_1.1.4.zip(r-4.4)phylosem_1.1.4.zip(r-4.3)
phylosem_1.1.4.tgz(r-4.4-x86_64)phylosem_1.1.4.tgz(r-4.4-arm64)phylosem_1.1.4.tgz(r-4.3-arm64)phylosem_1.1.4.tgz(r-4.3-x86_64)
phylosem_1.1.4.tar.gz(r-4.5-noble)phylosem_1.1.4.tar.gz(r-4.4-noble)
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'))

Peer review:

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:

cpp

4.92 score 1 stars 14 scripts 239 downloads 10 exports 99 dependencies

Last updated 2 months agofrom:5ac1104dbc. Checks:2 OK, 7 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 08 2025
R-4.5-win-x86_64NOTEJan 08 2025
R-4.5-linux-x86_64OKJan 08 2025
R-4.4-win-x86_64NOTEJan 08 2025
R-4.4-mac-x86_64NOTEJan 08 2025
R-4.4-mac-aarch64NOTEJan 08 2025
R-4.3-win-x86_64NOTEJan 08 2025
R-4.3-mac-aarch64NOTEJan 08 2025
R-4.3-mac-x86_64NOTEDec 09 2024

Exports:as_fitted_DAGas_phylo4das_semaveragebestchoicecompare_phylosemlist_parametersphylosemphylosem_control

Dependencies:abindade4apearmaskpassBiocGenericsBiocManagerbootcachemclicodacodetoolscolorspacecpp11crayoncurldigestdplyrfansifarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixmemoisemgcvmimimeminqamunsellnlmenloptropensslparallellyphylobasephylolmphylopathpillarpixmappkgconfigplyrpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrnclRNeXMLscalessemspstringistringrsyssystemfontstibbletidygraphtidyrtidyselectTMBtweenrutf8uuidvctrsviridisviridisLitewithrXMLxml2

Comparison with other packages

Rendered fromcomparison.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Demonstration of selected features

Rendered fromdemonstration.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Detailed comparison with phylopath

Rendered fromphylopath.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Phylogenetic comparative methods in fisheries science

Rendered fromfisheries.Rmdusingknitr::rmarkdownon Jan 08 2025.

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