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) . 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) .

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.