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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
0.1.10
0.1.7
0.1.6
0.1.4
0.1.3
0.1.2
0.1.1
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Install
install.packages('treeplyr')
Monthly Downloads
107
Version
0.1.10
License
GPL-2 | GPL-3
Issues
3
Pull Requests
1
Stars
33
Forks
7
Repository
https://github.com/uyedaj/treeplyr
Maintainer
Josef Uyeda
Last Published
September 17th, 2020
Functions in treeplyr (0.1.10)
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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