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>.
README
## Phylogenetic structural equation models Package _phylosem_ combines features from structural equation models (SEM), phylogenetic comparative methods (PCM), and generalized linear mixed models (GLMM). By doing so, it incorporates a broad feature-set: * Comparing multiple evolutionary models similar to _phylopath_ * Estimating trade-offs among multiple traits similar to _phylolm_ * Predicting missing trait values (and associated standard errors) similar to _Rphylopars_ * Estimating tradeoffs including recursive (cyclic) dependencies similar to package _sem_ * Applying ordination to multiple traits, similar to phylogenetic factor analysis in package _FishLife_ _phylosem_ is specifically intended as a minimal implementation, and uses standard packages for input/output formatting: * Input: phylogenetic relatedness defined using class _phylo_ in package _ape_ * Input: structural trade-offs specified using syntax defined by package _sem_ * Output: visualizing trade-offs using _semPlot_, _diagrammeR_, and _ggraph_ * Output: assembling trait predictions and standard errors using _phylobase_ * Output: plotting trait predictions using _phylosignal_ Please see package vignettes for more details regarding syntax and features. [](https://cran.r-project.org/package=phylosem) [](https://cran.r-project.org/package=phylosem) [](https://zenodo.org/badge/latestdoi/534386257) [](https://app.codecov.io/gh/James-Thorson-NOAA/phylosem/tree/remove-fit_tmb) [](https://james-thorson-noaa.github.io/phylosem/)
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.1.4 |
rolling linux/jammy R-4.5 | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
rolling linux/noble R-4.5 | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
rolling source/ R- | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
latest linux/jammy R-4.5 | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
latest linux/noble R-4.5 | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
latest source/ R- | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
2026-04-26 source/ R- | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
2026-04-23 source/ R- | phylosem_1.1.4.tar.gz |
313.7 KiB |
1.1.4 |
2025-04-20 source/ R- | phylosem_1.1.4.tar.gz |
313.7 KiB |