Package 'treedata.table'

Function for performing data.table operations on an object of class treedata.table

Description

This function can be used to subset rows, select and compute on columns data.table.

Usage

## S3 method for class 'treedata.table'
x[...]

Arguments

x	An object of class treedata.table
...	Arguments in the structure of data.table used to perform changes on the treedata.table object

Value

A new object of class treedata.table with ⁠$dat⁠ and ⁠$phy⁠ corresponding with the changes set to ⁠$dat⁠ using data.table's structure.

See Also

data.table

Examples

data(anolis)
anolis2 <- anolis$phy
anolis2$tip.label[1] <- "NAA"
anolis1 <- anolis$phy
anolis1$tip.label[1] <- "NAA"
trees <- list(anolis1, anolis2)
class(trees) <- "multiPhylo"
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"

# A phylo object that fully matches the data
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
td <- as.treedata.table(anolis$phy, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A multiphylo object that fully matches the data
td <- as.treedata.table(tree = treesFM, data = anolis$dat)
td <- as.treedata.table(treesFM, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A phylo object that partially matches the data
td <- as.treedata.table(tree = anolis1, data = anolis$dat)
td <- as.treedata.table(anolis1, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A multiphylo object that partially matches the data
td <- as.treedata.table(tree = trees, data = anolis$dat)
td <- as.treedata.table(trees, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

---

Function for extract a named vector from an object of class treedata.table

Description

This function extracts a named vector for any trait from an object of class treedata.table.

Usage

## S3 method for class 'treedata.table'
x[[..., exact = TRUE]]

Arguments

x	An object of class treedata.table
...	Column name in class character
exact	whether exact search should be conducted

Value

A new object of class vector with names set to labels corresponding to tip labels in the provided treedata.table object.

See Also

data.table()

Examples

data(anolis)
# With a phylo object
td <- as.treedata.table(anolis$phy, anolis$dat)
td[["SVL"]]

# With a multiPhylo object
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"
td <- as.treedata.table(treesFM, anolis$dat)
td[["SVL"]]

---

Anole data

Description

Anole data for treedata.table functions. Many of the traits (e.g. awesomeness, hostility) in this dataset retrieved from treeplyr are based on random numbers.

Usage

data(anolis)

Format

An object of class list of length 2.

Author(s)

Luke Harmon

---

Combine tree (or set of trees) and data.frame into a single treedata.table object

Description

This function takes as input a tree of class phylo or multiPhylo and a data.frame and combines them into a treedata.table. If a multiPhylo is provided, all trees must have the same tip.labels. treedata.table object is sorted such that the rows in the data.table are matched to the tip.labels of the phylogeny. Tip.labels on the tree must match a column of tip names in the input data.frame. The output of this function will be a treedata.table, which can be manipulated as a data.table.

Usage

as.treedata.table(tree, data, name_column = "detect")

Arguments

tree	A tree of class phylo or multiple trees of class multiPhylo
data	A dataset in format data.frame
name_column	A character indicating the name of taxa in data.frame. If set to detect (default) ⁠as treedata.table⁠ will auto-detect this column

Value

An object of type treedata.table containing the tree and data.table

Examples

data(anolis)
anolis2 <- anolis$phy
anolis2$tip.label[1] <- "NAA"
anolis1 <- anolis$phy
anolis1$tip.label[1] <- "NAA"
trees <- list(anolis1, anolis2)
class(trees) <- "multiPhylo"
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"

# A phylo object that fully matches the data
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
# A multiphylo object that fully matches the data
td <- as.treedata.table(tree = treesFM, data = anolis$dat)
# A phylo object that partially matches the data
td <- as.treedata.table(tree = anolis1, data = anolis$dat)
# A multiphylo object that partially matches the data
td <- as.treedata.table(tree = trees, data = anolis$dat)

---

Apply detectCharacterType over an entire matrix

Description

This function detects whether each column in a matrix is a continuous (e.g., with values 2.45, 9.35, and so on) or a discrete character (e.g., with values blue, red, yellow).

Usage

detectAllCharacters(mat, cutoff = 0.1)

Arguments

mat	A matrix of data
cutoff	Cutoff value for deciding if numeric data might actually be discrete: if nlev is the number of levels and n the length of dat, then nlev / n should exceed cutoff, or the data will be classified as discrete

Value

Vector of either "discrete" or "continuous" for each variable in matrix

Examples

data(anolis)
detectAllCharacters(anolis$dat)

---

Function to detect whether a character is continuous or discrete

Description

This function detects whether a given vector is a continuous (e.g., with values 2.45, 9.35, and so on) or a discrete (e.g., with values blue, red, yellow) character.

Usage

detectCharacterType(dat, cutoff = 0.1)

Arguments

dat	A vector of data
cutoff	Cutoff value for deciding if numeric data might actually be discrete: if nlev is the number of levels and n the length of dat, then nlev / n should exceed cutoff, or the data will be classified as discrete

Value

Either "discrete" or "continuous"

Examples

data(anolis)
detectCharacterType(anolis$dat[, 1])

---

Function dropping taxa from an object of class treedata.table

Description

This function can be used to remove species from an object of class treedata.table. The resulting treedata.table will include fully matching ⁠$dat⁠ and ⁠$phy⁠ elements. The user should confirm the changes before they are processed.

Usage

droptreedata.table(tdObject, taxa)

Arguments

tdObject	An object of class treedata.table
taxa	A vector class character containing all taxa that needs to be dropped from the original treedata.table object

Value

An object of class treedata.table with matching ⁠$dat⁠ and ⁠$phy⁠ elements based on whether taxa were dropped or not.

Examples

data(anolis)
# With a multiphylo object in the treedata.table object
td <- as.treedata.table(anolis$phy, anolis$dat)
droptreedata.table(
  tdObject = td, taxa =
    c("chamaeleonides", "eugenegrahami")
)

# With a multiphylo object in the treedata.table object
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"
td <- as.treedata.table(treesFM, anolis$dat)
droptreedata.table(
  tdObject = td, taxa =
    c("chamaeleonides", "eugenegrahami")
)

---

Returning a named vector from a treedata.table object

Description

Returning a named vector from a treedata.table object

Usage

extractVector(tdObject, ...)

Arguments

tdObject	A treedata.table object
...	The name of the column or columns to select.

Value

A named vector or a list of named vectors

Examples

data(anolis)
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
# extracts the named vector for SVL from the td object
extractVector(td, "SVL")
# extracts the named vector for SVL and ecomorph from the td object
extractVector(td, "SVL", "ecomorph")

---

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

Description

This function filters a character matrix based on continuous (e.g., with values 2.45, 9.35, and so on) or discrete characters (e.g., with values blue, red, yellow).

Usage

filterMatrix(mat, returnType = "discrete")

Arguments

mat	A character matrix of class data.frame
returnType	Either discrete or continuous

Value

data.frame with only discrete (default) or continuous characters

Examples

data(anolis)
filterMatrix(anolis$dat, "discrete")

---

Force names for rows, columns, or both

Description

This function creates column names (colnames), row.names (row.names), or both in an unnamed data.frame or matrix.

Usage

forceNames(dat, nameType = "row")

Arguments

dat	A vector of data
nameType	either: "row" Rows (default) "col" Columns "rowcol" Both rows and columns

Value

An object of type 'data.frame with labeled columns, rows, or both.

Examples

data(anolis)
forceNames(anolis$dat, "row")

---

Row and column name check

Description

This function checks whether a given data.frame or matrix has column names (colnames), row.names (row.names), or both.

Usage

hasNames(dat, nameType = "row")

Arguments

dat	A vector of data
nameType	either: "row" Rows (default) "col" Columns "rowcol" Both rows and columns

Value

TRUE or FALSE indicating if the object has names (columns, rows, or both)

Examples

data(anolis)
hasNames(anolis$dat, "row")

---

Return the first part of an treedata.table object

Description

Return the first part of an treedata.table object

Usage

## S3 method for class 'treedata.table'
head(x, ...)

Arguments

x	a treedata.table object
...	Additional arguments passed to head.data.table

Examples

data(anolis)
td <- as.treedata.table(anolis$phy, anolis$dat)
head(td)

---

Print method treedata.table objects

Description

Print method treedata.table objects

Usage

## S3 method for class 'treedata.table'
print(x, ...)

Arguments

x	an object of class "treedata.table"
...	additional arguments passed to "head.treedata.table"

Value

Function uses prints the tree and the first lines of the data.table object.

---

Returns the character matrix or phylogeny from a treedata.table object

Description

Returns the character matrix or phylogeny from a treedata.table object

Usage

pulltreedata.table(tdObject, type = c("dat", "phy"))

Arguments

tdObject	A treedata.table object
type	Whether the output of the function is a tree ('type="phylo"') or a data.table ('type="dat"')

Value

A data.table or phylo object from the original treedata.table object

Examples

data(anolis)
td <- as.treedata.table(anolis$phy, anolis$dat)
pulltreedata.table(td, type = "phy")
pulltreedata.table(td, type = "dat")

---

Summarizing treedata.table objects

Description

Summarizing treedata.table objects

Usage

## S3 method for class 'treedata.table'
summary(object, ...)

Arguments

object	an object of class "treedata.table"
...	additional arguments passed to "head.treedata.table"

Value

Function tries to be smart about summarizing the data and detecting continuous vs. discrete data, as well as whether any data have missing data. Also returns the taxa that are dropped from either the original tree or the original data.

Examples

data(anolis)
td <- as.treedata.table(anolis$phy, anolis$dat)
summary(td)

---

Return the last part of an treedata.table object

Description

Return the last part of an treedata.table object

Usage

## S3 method for class 'treedata.table'
tail(x, ...)

Arguments

x	a treedata.table object
...	Additional arguments passed to head.data.table

Examples

data(anolis)
td <- as.treedata.table(anolis$phy, anolis$dat)
tail(td)

---

Run a function on a treedata.table object

Description

Run a function on a treedata.table object

Usage

tdt(tdObject, ...)

Arguments

tdObject	A treedata.table object
...	A function call.

Details

This function allows R functions that use trees and data to be run ontreedata.table objects.

Value

Function output for a single tree (phylo) or a list of function outputs (one per each tree in the MultiPhylo object)

Examples

data(anolis)


# A treedata.table object with a phylo $phy
td <- as.treedata.table(anolis$phy, anolis$dat)
tdt(td, geiger::fitContinuous(phy, extractVector(td, "SVL"),
  model = "BM", ncores = 1
))


# A treedata.table object with a multiPhylo $phy
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"
td <- as.treedata.table(treesFM, anolis$dat)
tdt(td, geiger::fitContinuous(phy, extractVector(td, "SVL"),
  model = "BM",
  ncores = 1
))

---