Random addition of taxa — rand_absent_tippr • treestartr

Add tips not on existing tree to the tree at random, if they do not have congeners on the tree.

Usage

rand_absent_tippr(tree, absent_list, echo_subtrees = NULL,
  echo_revbayes = NULL)

Arguments

tree: Starting tree; object of type phylo
absent_list: Vector of taxa in the total dataset that are not on the tree
echo_subtrees: Boolean; Print newick subtree with missing taxa added to screen. Default FALSE.
echo_revbayes: Boolean; Print clade constraints with missing taxa added to screen, formatted for RevBayes fossilized birth-death analysis. Default FALSE.

Value

tree Phylo object containing the starting tree, and all tips that were added.

Examples

new_tree <- rand_absent_tippr(tree, absent_list)
#> Adding tips at random node: Ailurarctos_lufengensis
#> [1] 32
#> Adding tips at random node: Kretzoiarctos_beatrix
#> [1] 27
#> Adding tips at random node: Parictis_montanus
#> [1] 23
#> Adding tips at random node: Ursavus_brevirhinus
#> [1] 35
#> Adding tips at random node: Ursavus_primaevus
#> [1] 5