Add tips to tree via taxon list

Add tips according to csv or tsv file of taxon names and taxa that form the clade into which you"d like to insert the tip. One column should be called 'taxon', and should contain the taxon to be placed. The other column should be called 'clade' and contain the taxon with which the taxon to be placed will form a group. Each member of the clade will be placed on its own line. An example of this file can be seen in `inst/extdat a/mrca_df.tsv`

Usage

text_placr(tree, mrca_df, echo_subtrees = NULL, echo_revbayes = NULL)

Arguments

tree

Starting tree; object of type phylo

mrca_df

Dataframe containing a column of the taxa you'd like to place and one column with the clade into which you'd like to place it

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

text_placr(tree, mrca_df)
#> Placing tip Kretzoiarctos_beatrix
#> via relatives Indarctos_arctoides, Indarctos_vireti
#>  at node 25
#> Placing tip Ursus_abstrusus
#> via relatives Ursus_arctos, Ursus_spelaeus, Ursus_americanus
#>  at node 30
#> 
#> Phylogenetic tree with 17 tips and 19 internal nodes.
#> 
#> Tip labels:
#>   Ailuropoda_melanoleuca, Agriarctos_spp, Kretzoiarctos_beatrix, Indarctos_arctoides, Indarctos_vireti, Ursus_abstrusus, ...
#> 
#> Rooted; no branch lengths.