View source: R/simulate.uncor.exp.R
simulate.uncor.exp | R Documentation |
Simulate the rate of evolution along a phylogenetic tree using the exponential model described in Drummond et al. (2006)
simulate.uncor.exp(tree, params = list(mean.exp = 0.001))
tree |
A phylogenetic tree of class phylo. The branch lengths should be in units of time (chronogram) |
params |
parameters for the autocorrelation function. This should be a list with one item: |
mean.exp |
This is the mean rate of the exponential distribution. Note that this is the same as the sd for this distribution |
None
An object of class 'ratesim'. This is a list with two items:
phylogram |
The phylogenetic tree with branch lengths in units of substitutions (phylogram) |
tree.data.matrix |
This is a matrix with the number of substitutions, rates, and times along every branch in the tree. See get.tree.data.matrix for more details |
None
Sebastian Duchene. See the reference for the description of the model.
Drummond, A.J., et al. "Relaxed phylogenetics and dating with confidence." PLoS biology 4.5 (2006): e88.
None
set.seed(1234525) myTree <- rcoal(50) rateTree <- simulate.uncor.exp(tree = myTree, params = list(mean.exp = 0.01)) plot(rateTree, col.lineages = rainbow(50)) #See the histogram of the branch-wise rates hist(rateTree$tree.data.matrix[, 5]) ## The function is currently defined as function (tree, params = list(mean.exp = 0.001)) { mean.exp <- params$mean.exp data.matrix <- get.tree.data.matrix(tree) branch.rates <- rexp(n = length(tree$edge.length), rate = 1/mean.exp) data.matrix[, 5] <- branch.rates data.matrix[, 6] <- data.matrix[, 5] * data.matrix[, 7] tree$edge.length <- data.matrix[, 6] res <- list(tree, data.matrix) names(res) <- c("phylogram", "tree.data.matrix") class(res) <- "ratesim" return(res) }
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