View source: R/simulate.uncor.gamma.R
simulate.uncor.gamma | R Documentation |
Simulate the rate of evolution along a phylogenetic tree using the gamma distributed rates model described in Drummond et al. (2006)
simulate.uncor.gamma(tree, params = list(shape = 3.98, rate = 516.53))
tree |
A phylogenetic tree of class 'phylo'. The branch lengths should be in units of time (chronogram) |
params |
parameters for the uncorrelated rates function. This should be a list with two items: |
shape |
The shape of the gamma distribution. It follows the usual parametrisation of the gamma distribution |
rate |
The rate of the gamma distribution. Note that this is different from the substitution rate. Instead, this the the rate parameter typically used for the gamma 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 |
Notes
Sebastian Duchene. See the reference for the original description of the model.
Drummond, A.J., et al. "Relaxed phylogenetics and dating with confidence." PLoS biology 4.5 (2006): e88.
simulate.uncor.lnorm simulate.uncor.exp
set.seed(1234525) myTree <- rcoal(50) rateTree <- simulate.uncor.gamma(tree = myTree, params = list(shape = 3.98, rate = 516.53)) plot(rateTree, col.lineages = rainbow(50)) #See the histogram of the branch-wise rates hist(rateTree$tree.data.matrix[, 5]) ## The function is currently defined as function (tree, params = list(shape = 3.98, rate = 516.53)) { shape.gamma <- params$shape rate.gamma <- params$rate data.matrix <- get.tree.data.matrix(tree) branch.rates <- rgamma(n = length(tree$edge.length), shape = shape.gamma, rate = rate.gamma) 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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