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_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)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylosem/json (API)

# 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

4.64 score 1 stars 22 scripts 217 downloads 10 exports 100 dependencies

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

TargetResultTimeFilesSyslog
linux-devel-arm64OK308
linux-devel-x86_64OK322
source / vignettesOK521
linux-release-arm64OK295
linux-release-x86_64OK235
macos-release-arm64OK240
macos-release-x86_64OK570
macos-oldrel-arm64OK167
macos-oldrel-x86_64OK378
windows-develOK332
windows-releaseOK287
windows-oldrelOK377
wasm-releaseFAIL224

Exports:as_fitted_DAGas_phylo4das_semaveragebestchoicecompare_phylosemlist_parametersphylosemphylosem_control

Dependencies:abindade4apearmaskpassbase64encBiocGenericsBiocManagerbootcachemclicodacodetoolscpp11crayoncurldigestdplyrfarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixmemoisemimimeminqanlmenloptropensslparallellyphylobasephylolmphylopathpillarpixmappkgconfigplyrpolyclipprettyunitsprogresspurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrnclRNeXMLS7scalessemspstringistringrsyssystemfontstibbletidygraphtidyrtidyselectTMBtweenrutf8uuidvctrsviridisviridisLitewithrXMLxml2

Comparison with other packages
Comparison with phylolm | Generalized linear models | Poisson-distributed response | Binomial regression | Summary of PGLM results | Compare with phylopath | Comparison with sem | Comparison with Rphylopars
Rendered fromcomparison.Rmdusingknitr::rmarkdown

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

Demonstration of selected features
Estimability for multiple covariance transformations | Scaling of runtime with increased tree size
Rendered fromdemonstration.Rmdusingknitr::rmarkdown

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

Detailed comparison with phylopath
Model comparison: some important differences | Model fitting: sometimes different
Rendered fromphylopath.Rmdusingknitr::rmarkdown

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

Phylogenetic comparative methods in fisheries science
Preparing the Then et al. mortality database | Fitting and selecting among phylogenetic structural equation models | Visualizing output | Sensitivity to using taxonomic tree
Rendered fromfisheries.Rmdusingknitr::rmarkdown

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