Jackknife {TreeSearch}

Jackknife resampling

Description

Resample trees using Jackknife resampling, i.e. removing a subset of characters.

Usage

Jackknife(
  tree,
  dataset,
  resampleFreq = 2/3,
  InitializeData = PhyDat2Morphy,
  CleanUpData = UnloadMorphy,
  TreeScorer = MorphyLength,
  EdgeSwapper = TBRSwap,
  jackIter = 5000L,
  searchIter = 4000L,
  searchHits = 42L,
  verbosity = 1L,
  ...
)

Arguments

tree

A tree of class phylo.

dataset

a dataset in the format required by TreeScorer().

resampleFreq

Double between 0 and 1 stating proportion of characters to resample.

InitializeData

Function that sets up data object to prepare for tree search. The function will be passed the dataset parameter. Its return value will be passed to TreeScorer() and CleanUpData().

CleanUpData

Function to destroy data object on function exit. The function will be passed the value returned by InitializeData().

TreeScorer

function to score a given tree. The function will be passed three parameters, corresponding to the parent and child entries of a tree's edge list, and a dataset.

EdgeSwapper

a function that rearranges a parent and child vector, and returns a list with modified vectors; for example SPRSwap().

jackIter

Integer specifying number of jackknife iterations to conduct.

searchIter

Integer specifying maximum rearrangements to perform on each bootstrap or ratchet iteration. To override this value for a single swapper function, set e.g. attr(SwapperFunction, "searchIter") <- 99

searchHits

Integer specifying maximum times to hit best score before terminating a tree search within a ratchet iteration. To override this value for a single swapper function, set e.g. attr(SwapperFunction, "searchHits") <- 99

verbosity

Numeric specifying level of detail to display in console: larger numbers provide more verbose feedback to the user.

...

further arguments to pass to TreeScorer(), e.g. ⁠dataset = ⁠.

Details

The function assumes that InitializeData() will return a morphy object; if this doesn't hold for you, post a GitHub issue or e-mail the maintainer.

Value

Jackknife() returns a list of trees recovered after jackknife iterations.

Author(s)

Martin R. Smith ([e-mail])

See Also

• JackLabels(): Label nodes of a tree with jackknife supports.

Other split support functions: JackLabels(), MaximizeParsimony(), SiteConcordance

Other custom search functions: EdgeListSearch(), MorphyBootstrap(), SuccessiveApproximations()