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.
