Extract and estimate an arbitrary model from a phylogenetic path analysis.

Extract and estimate an arbitrary model from a phylogenetic path analysis.

Usage

choice(phylopath, choice, ...)

Arguments

phylopath

An object of class phylopath.

choice

A character string of the name of the model to be chosen, or the index in model_set.

...

Arguments to pass to phylolm::phylolm and phylolm::phyloglm. Provide boot = K parameter to enable bootstrapping, where K is the number of bootstrap replicates. If you specified other options in the original phylo_path call you don't need to specify them again.

Value

An object of class fitted_DAG.

See also

est_DAG() for what the coefficients mean.

Examples

  candidates <- define_model_set(
    A = NL ~ BM,
    B = NL ~ LS,
    .common = c(LS ~ BM, DD ~ NL)
  )
  p <- phylo_path(candidates, rhino, rhino_tree)
  my_model <- choice(p, "B")
  # Print the best model to see coefficients, se and ci:
  my_model
#> A fitted causal model: 4 variables, 3 paths.
#> 	Continuous:	 BM LS NL DD 
#> 
#> Paths — standardized regression coefficients
#>     path coefficient    se
#>  BM → LS       0.497 0.089
#>  LS → NL       0.207 0.094
#>  NL → DD       0.629 0.080
  # Plot to show the weighted graph:
  plot(my_model)