Extract and estimate the best supported model from a phylogenetic path analysis.

best(phylopath, ...)

Arguments

phylopath: An object of class phylopath.
...: 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.

Examples

  candidates <- define_model_set(
    A = NL ~ BM,
    B = NL ~ LS,
    .common = c(LS ~ BM, DD ~ NL)
  )
  p <- phylo_path(candidates, rhino, rhino_tree)
  best_model <- best(p)
  # Print the best model to see coefficients, se and ci:
  best_model
#> $coef
#>    BM        LS        NL        DD
#> BM  0 0.4973937 0.4303443 0.0000000
#> LS  0 0.0000000 0.0000000 0.0000000
#> NL  0 0.0000000 0.0000000 0.6285344
#> DD  0 0.0000000 0.0000000 0.0000000
#> 
#> $se
#>    BM         LS         NL         DD
#> BM  0 0.08934185 0.08868688 0.00000000
#> LS  0 0.00000000 0.00000000 0.00000000
#> NL  0 0.00000000 0.00000000 0.08006703
#> DD  0 0.00000000 0.00000000 0.00000000
#> 
#> attr(,"class")
#> [1] "fitted_DAG"
  # Plot to show the weighted graph:
  plot(best_model)