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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.

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