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treeplyr (version 0.1.7)

'dplyr' Functionality for Matched Tree and Data Objects

Description

Matches phylogenetic trees and trait data, and allows simultaneous manipulation of the tree and data using 'dplyr'.

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Version

Install

install.packages('treeplyr')

Monthly Downloads

141

Version

0.1.7

License

GPL-2 | GPL-3

Issues

3

Pull Requests

0

Stars

33

Forks

6

Maintainer

Josef Uyeda

Last Published

July 25th, 2019

Functions in treeplyr (0.1.7)

filterMatrix

Filter a matrix, returning either all continuous or all discrete characters
make.treedata

Function for making an object of class treedata
.toSimmap

internal function from bayou
mutate_.treedata

Function for mutating an object of class treedata
.tipregime

Internal function to determine tip regimes:
hasNames

Row and column name check
group_by_.treedata

Function for grouping an object of class treedata
.identifyBranches

Internal function taken from bayou
forceNumeric

Function for checking whether a treedata object contains only numeric columns and for forcing data columns into numeric format
slice_.treedata

Choose rows by their ordinal position in the tbl for an object of class treedata
filter_.treedata

Function for filtering rows from an object of class treedata
forceFactor

Function for checking whether a treedata object contains only factors and for forcing data columns into factor format
forceNames

Force names for rows, columns, or both
tdapply

Apply a function over all treedata object columns and return a list of results, analogously to the normal apply function
select_.treedata

Function for selecting columns from an object of class treedata
select.treedata

Function for selecting columns from an object of class treedata
detectAllCharacters

Apply detectCharacterType over an entire matrix
getVector

A function for returning a named vector from a data frame or matrix with row names
treedply

Run a function on a treedata object
paint_clades

Add regimes to a treedata object
reorder

Reorder a treedata object
summarise.treedata

Function for summarizing an object of class treedata
treeply

Run a function on the phylogeny of a treedata object
treeplyr

treeplyr: 'dplyr' Functionality for Matched Tree and Data Objects
.pars2map

New version of .pars2map is faster, returns 3 elements rather than 2 named elements
.check_names_df

.check_names_df function from tibble package
anolis

Anole data
.plotRegimes

Internal functions for painted_clades
detectCharacterType

Function to detect whether a character is continuous or discrete
.prepare.branches

This is an internal function modified from geiger's function .prepare.bm.univariate for use with OU models.
.nodeHeights

nodeHeights function from phytools
.as_data_frame.data.frame

as_data_frame.data.frame function from the tibble package