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Add tips to the tree based on taxonomy.

Source: R/present_tippr.R
present_tippR.Rd

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)
#> Tree tip names formatted correctly
#> [1] "Indarctos_arctoides" "Indarctos_vireti"   
#> Warning: 2 arguments not used by format 'Adding tip %s'
#> Adding tip Indarctos_punjabiensis
#> [1] "Ursus_americanus" "Ursus_thibetanus" "Ursus_arctos"     "Ursus_maritimus" 
#> [5] "Ursus_spelaeus"  
#> Warning: 2 arguments not used by format 'Adding tip %s'
#> Adding tip Ursus_abstrusus