R/CustomSearch.R
, R/IWScore.R
, R/TreeSearch_utilities.R
TreeSearch.Rd
Run standard search algorithms (NNI, SPR or TBR) to search for a more parsimonious tree.
For detailed documentation of the "TreeSearch" package, including full instructions for loading phylogenetic data into R and initiating and configuring tree search, see the package documentation.
EdgeListSearch(
edgeList,
dataset,
TreeScorer = MorphyLength,
EdgeSwapper = RootedTBRSwap,
maxIter = 100,
maxHits = 20,
bestScore = NULL,
stopAtScore = NULL,
stopAtPeak = FALSE,
stopAtPlateau = 0L,
verbosity = 1L,
...
)
TreeSearch(
tree,
dataset,
InitializeData = PhyDat2Morphy,
CleanUpData = UnloadMorphy,
TreeScorer = MorphyLength,
EdgeSwapper = RootedTBRSwap,
maxIter = 100L,
maxHits = 20L,
stopAtPeak = FALSE,
stopAtPlateau = 0L,
verbosity = 1L,
...
)
IWTreeSearch(...)
EmptyPhyDat(tree)
DoNothing(...)
a list containing the following: - vector of integers corresponding to the parent of each edge in turn - vector of integers corresponding to the child of each edge in turn - (optionally) score of the tree - (optionally, if score provided) number of times this score has been hit
A phylogenetic data matrix of phangorn class
phyDat
, whose names correspond to the labels of any accompanying tree.
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()
.
Numeric specifying maximum number of iterations to perform before abandoning the search.
Numeric specifying maximum times to hit the best pscore before abandoning the search.
Logical specifying whether to terminate search once a
subsequent iteration recovers a sub-optimal score.
Will be overridden if a passed function has an attribute stopAtPeak
set by
attr(FunctionName, "stopAtPeak") <- TRUE
.
Integer. If > 0, tree search will terminate if the score
has not improved after stopAtPlateau
iterations.
Will be overridden if a passed function has an attribute stopAtPlateau
set
by attr(FunctionName, "stopAtPlateau") <- TRUE
.
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 =
.
A fully-resolved starting tree in phylo
format,
with the desired outgroup.
Edge lengths are not supported and will be removed.
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()
.
TreeSearch()
returns a tree, with an attribute pscore
conveying its
parsimony score.
#" Note that the parsimony score will be inherited from the tree"s
attributes, which is only valid if it was generated using the same
data
that is passed here.
EmptyPhyDat()
returns a phyDat
object comprising a single
null character, coded with state zero for every leaf in tree
.
EdgeListSearch()
: Tree search from edge lists
Fitch
, calculates parsimony score;
RootedNNI
, conducts tree rearrangements;
Ratchet
, alternative heuristic, useful to escape local
optima.
Other custom search functions:
Jackknife()
,
MorphyBootstrap()
,
SuccessiveApproximations()
data("Lobo", package="TreeTools")
njtree <- TreeTools::NJTree(Lobo.phy)
## Only run examples in interactive R sessions
if (interactive()) {
TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = NNISwap)
TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = RootedSPRSwap)
TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = TBRSwap)
}