Package index • ScrambledTreeBuilder

All functions

ConvenientTblTree: Convenient tbl_trees

FocalCladeList(): List of focal clades

Haloarchaea Halo_DF Halo_PercentDiff Halo_FocalClades Halo_Tree: Example Haloarchaea data objects

MRCA_2D_plot(): 2D MRCA plot

MRCAs(): Most recent common ancestors

averageResults(): Average results

childSpecies(): Children species of an ancestor

ellipsePlot(): Ellipse plots

eog(): Run eog on a plot for a clade

extractValues(): Extract values from a matrix.

focalClade(): Focal clades

formatStats(): Consolidate YAML reports in one data frame

getStats(): Get statistical information from .yaml files.

makeMatrix(): Pairwise comparison matrix

makeTidyTree(): Make a tidy tree

makeValueTibble(): Make new tibble dataset with added value column from a matrix

oikData: Oikopleura data

orderWithTree(): Order a comparison matrix

recordAncestor(): Record ancestor node ID of a pair

recordClades(): Record clade metadata in results table

resultFiles(): List YAML result files

subMatrix(): Subset a matrix with a subtree

subTree(): Extract a subtree

visualizeTree(): Plot a phylogenetic tree and its node data