Resample trees using Jackknife resampling, i.e. removing a subset of characters.
Jackknife(
tree,
dataset,
resampleFreq = 2/3,
InitializeData = PhyDat2Morphy,
CleanUpData = UnloadMorphy,
TreeScorer = MorphyLength,
EdgeSwapper = TBRSwap,
jackIter = 5000L,
searchIter = 4000L,
searchHits = 42L,
verbosity = 1L,
...
)Jackknife() returns a list of trees recovered after jackknife
iterations.
A tree of class phylo.
a dataset in the format required by TreeScorer().
Double between 0 and 1 stating proportion of characters to resample.
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().
Function to destroy data object on function exit.
The function will be passed the value returned by InitializeData().
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.
a function that rearranges a parent and child vector,
and returns a list with modified vectors; for example SPRSwap().
Integer specifying number of jackknife iterations to conduct.
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
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
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 = .
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.
JackLabels(): Label nodes of a tree with jackknife supports.
Other split support functions:
JackLabels(),
MaximizeParsimony(),
SiteConcordance
Other custom search functions:
EdgeListSearch(),
MorphyBootstrap(),
SuccessiveApproximations()