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treeplyr (version 0.1.10)

'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

46

Version

0.1.10

License

GPL-2 | GPL-3

Issues

3

Pull Requests

0

Stars

33

Forks

6

Maintainer

Josef Uyeda

Last Published

September 17th, 2020

Functions in treeplyr (0.1.10)

forceNames

Force names for rows, columns, or both
.toSimmap

internal function from bayou
paint_clades

Add regimes to a treedata object
.tipregime

Internal function to determine tip regimes:
mutate_-defunct

mutate_.treedata
slice.treedata

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

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

Function for grouping an object of class treedata
getVector

A function for returning a named vector from a data frame or matrix with row names
filter_-defunct

filter_.treedata
select_-defunct

select_.treedata
filter.treedata

Function for filtering rows from an object of class treedata
.prepare.branches

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

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

Filter a matrix, returning either all continuous or all discrete characters
reorder

Reorder a treedata object
treeplyr

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

Function for making an object of class treedata
mutate.treedata

Function for mutating an object of class treedata
hasNames

Row and column name check
group_by_-defunct

group_by_.treedata
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
treeply

Run a function on the phylogeny of a treedata object
treeplyr-defunct

Defunct functions in treeplyr
treedply

Run a function on a treedata object
summarise.treedata

Function for summarizing an object of class treedata
slice_-defunct

slice_.treedata
anolis

Anole data
.check_names_df

.check_names_df function from tibble package
.nodeHeights

nodeHeights function from phytools
.plotRegimes

Internal functions for painted_clades
.identifyBranches

Internal function taken from bayou
detectCharacterType

Function to detect whether a character is continuous or discrete
.pars2map

New version of .pars2map is faster, returns 3 elements rather than 2 named elements
.as_data_frame.data.frame

as_data_frame.data.frame function from the tibble package
detectAllCharacters

Apply detectCharacterType over an entire matrix