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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.