View source: R/get.tree.data.matrix.R
get.tree.data.matrix | R Documentation |
Obtain the tree data matrix from a phylogenetic tree. The tree should be a chronogram, with branch lengths representing time.
get.tree.data.matrix(phylo)
phylo |
A phylogenetic tree of class 'phylo'. The tree should be a chronogram, with branch lengths representing time. |
None
A matrix with 7 colums and number of rows = number of edges in the tree. Each row corresponds to a branch (or edge) of the tree. The columns of the matrix correspond to the following:
branch.index: The number of the branch (or edge) in the tree. parent.node: The node of the corresponding branch that is closer to the root of the tree. daughter.node: The node of the corresponding branch that is closer to the tips. branch.midage: The median age of the branch. branch.rate: The rate along the branch. It is set to NA if get.tree.data.matrix is called directly on a phylogenetic trees. The functions simulate.rate and trann2trdat fill this column with the branch-wise rates. lengths.subst: Number of substitutions along the branch. It is set to NA if get.tree.data.matrix is called directly on a phylogenetic trees. The functions simulate.rate and trann2trdat fill this column with the branch-wise rates. length.time: The branch lengths in units of time.
This function is used internally by the simulate.rate()]
David Duchene and Sebastian Duchene
None.
simulate.rate
set.seed(12345) myTree <- rcoal(10) myDataMatrix <- get.tree.data.matrix(myTree) print(myDataMatrix) ## The function is currently defined as function (phylo) { require(phangorn) require(geiger) data.matrix <- matrix(data = NA, ncol = 7, nrow = length(phylo$edge.length)) colnames(data.matrix) <- c("branch.index", "parent.node", "daughter.node", "branch.midage", "branch.rate", "length.subst", "length.time") data.matrix[, 1] <- 1:length(phylo$edge.length) data.matrix[, 2] <- phylo$edge[, 1] data.matrix[, 3] <- phylo$edge[, 2] data.matrix[, 4] <- mid.edge.ages(phylo) data.matrix[, 7] <- phylo$edge.length class(data.matrix) <- "tree.data.matrix" return(data.matrix) }
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