This function calls generate_tree_vec() to generate a vector of phylogenetic trees under parsimony. It then performs ancestral state estimations on this vector.

generate_anc_states(phy_mat, start, stop, tree, lstates = FALSE,
  pstates = FALSE)

Arguments

phy_mat

Phylogenetic matrix

start

Which character to begin sampling characters at

stop

Which character to end sampling characters at

tree

Starting tree for parsimony analysis. Phylo object.

lstates

Boolean calculate and export ancestral state estimations under the Mk model

pstates

Boolean calculate and export ancestral state estimations under parsimony

Value

Vector of ancestral state reconstructions

Examples

anc_states <- generate_anc_states(bears, 1, 2, tree, lstates = TRUE)
#> Error in nrow(sample_df): object 'sample_df' not found