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https://github.com/james-thorson-noaa/phylosem

Phylogenetic structural equation models
https://github.com/james-thorson-noaa/phylosem

Last synced: 2 months ago
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Phylogenetic structural equation models

Host: GitHub
URL: https://github.com/james-thorson-noaa/phylosem
Owner: James-Thorson-NOAA
Created: 2022-09-08T20:41:13.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-11-09T01:32:02.000Z (2 months ago)
Last Synced: 2024-11-09T02:24:49.805Z (2 months ago)
Language: R
Homepage: https://james-thorson-noaa.github.io/phylosem/
Size: 12.7 MB
Stars: 1
Watchers: 3
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md

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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://www.r-pkg.org/badges/version/phylosem)](https://cran.r-project.org/package=phylosem)

[![](https://cranlogs.r-pkg.org/badges/phylosem)](https://cran.r-project.org/package=phylosem)

[![](https://cranlogs.r-pkg.org/badges/grand-total/phylosem)](https://cran.r-project.org/package=phylosem)

[![Codecov test coverage](https://codecov.io/gh/James-Thorson-NOAA/phylosem/branch/remove-fit_tmb/graph/badge.svg)](https://app.codecov.io/gh/James-Thorson-NOAA/phylosem/tree/remove-fit_tmb)

[![Documentation](https://img.shields.io/badge/documentation-phylosem-orange.svg?colorB=E91E63)](https://james-thorson-noaa.github.io/phylosem/)