| present_tippr {treestartr} | R Documentation |
Add tips to the tree based on taxonomy.
Description
Add tips not on existing tree to the tree via an MRCA node, if they have congeners. This function will look to see if any tips on the tree have the same genus as the tip to be added. If there are multiple members of the genus, the tip will be added subtending the MRCA of all present congeners. If there is member of the genus, the tip will be added subtending the parent node of the congener.
Usage
present_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
genera_tree <- present_tippr(tree, absent_list)