Add genus and family basal/root node information to a phylogeny
add_root_info.RdBased on the classification of tips, find where is the basal and root node for each genus and each family. Such information can be later used to graft new tips onto the phylogeny. This function can be used to process a user provided tree.
Usage
add_root_info(
tree,
classification,
process_all_tips = TRUE,
genus_list = NULL,
family_list = NULL,
show_warning = FALSE
)Arguments
- tree
A phylogeny with class "phylo".
- classification
A data frame of 2 columns: genus, family. It should include all genus the tips of the tree belong to.
- process_all_tips
Whether to find basal nodes for all tips? Default is
TRUE.- genus_list
An optinoal subset list of genus to find root information.
- family_list
An optinoal subset list of family to find root information. This should be for species that do not have co-genus in the tree.
- show_warning
Whether to print warning information about non-monophyletic clades or not.