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treestartr (version 0.1.0)

Generate Starting Trees for Combined Molecular, Morphological and Stratigraphic Data

Description

Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.

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Version

Install

install.packages('treestartr')

Monthly Downloads

101

Version

0.1.0

License

MIT + file LICENSE

Maintainer

April Wright

Last Published

January 9th, 2019

Functions in treestartr (0.1.0)

echo_rb

Print RevBayes-formatted clade constriants.
genera_strippr

Check if tip is on tree
echo_subtree

Print subtrees with tips added.
fileformat

Utility function to check if file is a csv or tsv.
get_found

Get dataframe of tips that do not have congeners on tree.
text_placr

Add tips to tree via taxon list
treestartr

treestartr: A package for generating reasonable starting trees for phylogenetic analysis.
absent_tippr

Add tips to tree via user input
bears

bears
rand_absent_tippr

Random addition of taxa
taxon_testr

Utility function to check taxon_names in parsed data file
get_lost

Determine if a tip is present on a tree
make_absentdf

Determine which tips are not on the tree, and get their genera.
make_treedf

Determine which tips are on the tree, and get their genera.
present_tippr

Add tips to the tree based on taxonomy.
dataf_parsr

Detect file format of taxon file