Package 'treeplyr'

Anole data

Description

Anole data for aRbor functions

Usage

data(anolis)

Format

An object of class list of length 2.

---

Apply detectCharacterType over an entire matrix

Description

Apply detectCharacterType over an entire matrix

Usage

detectAllCharacters(mat, repeatsAsDiscrete = TRUE, cutoff = 0.1)

Arguments

mat	A matrix of data
repeatsAsDiscrete	If TRUE, consider numeric variables that repeat values exactly as discrete; see cutoff
cutoff	Cutoff value for deciding if numeric data might actually be descrete: 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

Function to detect whether a character is continuous or discrete

Usage

detectCharacterType(dat, repeatsAsDiscrete = TRUE, cutoff = 0.1)

Arguments

dat	A vector of data
repeatsAsDiscrete	If TRUE, consider numeric variables that repeat values exactly as discrete; see cutoff
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 for filtering rows from an object of class treedata

Description

This function can be used to select a subset of species (rows) from a treedata object; see filter.

Usage

## S3 method for class 'treedata'
filter(.data, ...)

## S3 method for class 'grouped_treedata'
filter(.data, ...)

Arguments

.data	An object of class treedata
...	Additional arguments to filter by

Value

An object of class treedata with the dataset filtered by the specified criteria.

See Also

filter

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat, name_column=1)
tdfilter <- filter(td, island=="Cuba", SVL > 3.5)

---

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

Description

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

Usage

filterMatrix(mat, charType, returnType = "discrete")

Arguments

mat	A matrix of data
charType	A vector of character types (perhaps from detectAllCharacters)
returnType	Either discrete or continuous

Value

Matrix with only discrete or continuous characters

Examples

data(anolis)
aType<-detectAllCharacters(anolis$dat)
filterMatrix(anolis$dat, aType, "discrete")

---

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

Description

This function can be used to check if a treedata object contains factors and, if desired, convert all columns automatically to factors.

Usage

forceFactor(tdObject, return.factor = TRUE)

Arguments

tdObject	A treedata object
return.factor	If TRUE, then a treedata object with all factors will be returned; columns will be forced into factors using factor and any with no repeated elements will be removed.

Value

If return.factor, then an object of class "treedata" with all columns as factors.

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdforcefactor <- forceFactor(td)

---

Force names for rows, columns, or both

Description

Force names for rows, columns, or both

Usage

forceNames(dat, nameType = "row")

Arguments

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

Examples

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

---

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

Description

This function can be used to check if a treedata object contains numeric columns and, if desired, drop all non-numeric columns.

Usage

forceNumeric(tdObject, return.numeric = TRUE)

Arguments

tdObject	A treedata object
return.numeric	If TRUE, then a treedata object with all numeric columns will be returned; non-numeric columns will be removed.

Value

If return.numeric, then an object of class "treedata" with only numeric columns.

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdnumeric <- forceNumeric(td)

---

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

Description

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

Usage

getVector(td, ...)

Arguments

td	A treedata object
...	The name of the column to select

Value

A named vector

---

Function for grouping an object of class treedata

Description

This function can be used to group a treedata object by some factor.

Usage

## S3 method for class 'treedata'
group_by(.data, ..., add = FALSE)

## S3 method for class 'grouped_treedata'
ungroup(x, ...)

Arguments

.data	An object of class treedata
...	The name of the grouping factor.
add	By default, when add = FALSE, group_by will override existing groups. To instead add to the existing groups, use add = TRUE
x	An object of class treedata

Details

Groups the data frame and phylogeny by one of the factors in the data table.

Value

An object of class grouped_treedata.

See Also

summarize

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdGrouped <- group_by(td, ecomorph)
summarize(tdGrouped, ntips = length(phy$tip.label),
   totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))

---

Row and column name check

Description

Row and column name check

Usage

hasNames(dat, nameType = "row")

Arguments

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

Examples

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

---

Function for making an object of class treedata

Description

This function generates an object of class treedata that ensures that the ordering of tip labels and data remain intact. The object can be manipulated using dplyr functions.

Usage

make.treedata(tree, data, name_column = "detect")

Arguments

tree	An object of class 'phylo'
data	A data frame or matrix
name_column	An optional argument that specifies the column of data that contains the names to be matched to the tree. By default, it is set to "detect" which finds the column with the most matches to the tree (including the rownames).

Value

An object of class "treedata". The tree is pruned of tips not represented in the data, and the data is filtered for taxa not in the tree. The data is returned as a data frame tble that is compatible with dplyr functions.

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)

---

Function for mutating an object of class treedata

Description

This function can be used to add new variables to a treedata object; see mutate.

Usage

## S3 method for class 'treedata'
mutate(.data, ...)

## S3 method for class 'grouped_treedata'
mutate(.data, ...)

Arguments

.data	An object of class treedata
...	Arguments to mutate the treedata object

Value

An object of class treedata with new data added.

See Also

mutate

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdmutate <- mutate(td, lnSVL = log(SVL), badassery = awesomeness + hostility)

---

Add regimes to a treedata object

Description

This function paints clades on the phylogeny and adds a data column that specifies to which clade each species belongs

Usage

paint_clades(
  tdObject,
  nclades = 1,
  name = "clades",
  interactive = TRUE,
  type = "nodes",
  ids = NULL,
  plot = TRUE
)

Arguments

tdObject	A treedata object
nclades	The number of clades that will be specified if used interactively
name	The name of the resulting data column
interactive	If TRUE, then a plot will appear that will allow the user to click on nclades branches. The selections will then be coverted into the data table.
type	Either "nodes" or "branches" specifying if the ids provided specify the branch id (assuming a post-ordered tree) or the node number. Ignored if interactive = TRUE.
ids	A vector of node numbers of branch numbers that specify clades. Ignored if interactive=TRUE.
plot	If TRUE and interactive = FALSE then a simmap plot is produced.

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
td <- reorder(td, "postorder")
td.painted <- paint_clades(td, interactive=FALSE, type="nodes",
                                   ids=c(184, 160, 135, 122), plot=TRUE)
td.painted <- group_by(td.painted, clades)
summarise(td.painted,
             psig1 = phytools::phylosig(setNames(SVL, phy$tip.label), tree=phy),
                   meanSVL = mean(SVL))

---

Reorder a treedata object

Description

Reorders a treedata object. Both the tips and the data are automatically reordered to match.

Usage

reorder(tdObject, ...)

## S3 method for class 'treedata'
reorder(tdObject, order = "postorder", index.only = FALSE, ...)

Arguments

tdObject	An object of class treedata
...	Additional arguments to reorder.phylo
order	Method for reordering
index.only	Whether a index is returned rather than the reordered treedata object

Value

An object of class treedata

See Also

reorder.phylo

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
td <- reorder(td, "postorder")

---

Function for selecting columns from an object of class treedata

Description

This function can be used to select a subset of variables (columns) from a treedata object; see select.

Usage

## S3 method for class 'treedata'
select(.data, ...)

Arguments

.data	An object of class treedata
...	Additional arguments to select columns

Value

An object of class treedata with specified variables selected.

See Also

select

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdselect <- select(td, SVL, awesomeness)

---

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

Description

This function can be used to drop tips from tree and data; see slice.

Usage

## S3 method for class 'treedata'
slice(.data, ...)

Arguments

.data	An object of class treedata
...	Integer row values

Value

An object of class treedata.

See Also

slice

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
tdslice <- slice(td, 1:5)
tdslice

---

Function for summarizing an object of class treedata

Description

This function can be used to summarize a treedata object.

Usage

## S3 method for class 'treedata'
summarise(.data, ...)

## S3 method for class 'grouped_treedata'
summarise(.data, ...)

Arguments

.data	An object of class treedata
...	Additional expressions by which to summarize data in the treedata object

Details

Summarizing treedata objects allows expressions using the objects phy. The treedata object can also be grouped, with summary statistics being applied to the pruned groups and phylogenies.

Value

An object of class tbl_df with the requested summary data.

See Also

summarize, group_by

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
summarize(td, ntips = length(phy$tip.label), meanSVL = mean(SVL), sdSVL = sd(SVL))
tdGrouped <- group_by(td, ecomorph)
summarize(tdGrouped, ntips = length(phy$tip.label),
   totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))

---

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

Description

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

Usage

tdapply(tdObject, MARGIN, FUN, ...)

Arguments

tdObject	A treedata object
MARGIN	the margin over which the data is applied (e.g. 1 = rows, 2 = columns)
FUN	A function to apply over the data frame
...	Additional parameters passed on to FUN

Details

Note that if the parameter phy is specified in the additional parameters (i.e. '...'), then it will be substituted with the treedata object $phy.

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
td %>% forceNumeric(.) %>% tdapply(., 2, phytools::phylosig, tree=phy)

---

Run a function on a treedata object

Description

Run a function on a treedata object

Usage

treedply(tdObject, ...)

## S3 method for class 'treedata'
treedply(tdObject, ...)

Arguments

tdObject	A treedata object
...	A function call.

Details

This function allows arbitrary R functions that use trees and data to be run on treedata objects.

Value

Function output

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
treedply(td, geiger::fitContinuous(phy, getVector(td, SVL), model="BM", ncores=1))
treedply(td, phytools::phylosig(phy, getVector(td, awesomeness), "lambda", test=TRUE))
treedply(td, phytools::phenogram(phy, getVector(td, SVL), ftype="off", spread.labels=FALSE))

---

Run a function on the phylogeny of a treedata object

Description

Applies a function to the phylogeny in a treedata object. If the order of tips are changed, or if tips are dropped, then the data are automatically reordered to match the tree.

Usage

treeply(tdObject, ...)

## S3 method for class 'treedata'
treeply(tdObject, FUN, ...)

Arguments

tdObject	An object of class treedata
...	Additional arguments
FUN	A function that operates on an object of class 'phylo'

Value

An object of class treedata

Examples

data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
td2 <- treeply(td, drop.tip, 1:50)

par(mfrow=c(1,2))
plot(td$phy)
plot(td2$phy)

---

treeplyr: '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'.

Author(s)

Josef Uyeda

---

Defunct functions in treeplyr

Description

These functions have been removed to reflect changes in dplyr.

Details

• group_by_.treedata: This function is defunct, use group_by instead.

• mutate_.treedata, mutate_.grouped_treedata: This function is defunct, use mutate instead.

• slice_.treedata: This function is defunct, use slice instead.

• select_.treedata: This function is defunct, use select instead.

• filter_.treedata,filter_.grouped_treedata: This function is defunct, use filter instead.

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