get.lineage.time.rate: get.lineage.time.rate

In sebastianduchene/NELSI: NELSI: Nucleotide EvoLution Simulator

get.lineage.time.rate

Description

get.lineage.time.rate obtains the branch-wise rates along a lineage. It uses a taxon to trace the rates back to the root of the tree. It is used internally by plot.ratesim().

Usage

get.lineage.time.rate(taxon, sim.rate.object)

Arguments

taxon	An integer corresponding to the index of a taxon. The index is the order of the taxa in the tree, which can be obtained with tr$tip.label. See example.
sim.rate.object	An object of class ratesim. Usually produced with simulate.rate

Details

None

Value

A data frame with two colums. The rows correspond to the each of the branches from the taxon to the root of the tree. The first column of the data frame is the mid age of the branch, and the second column is the rate along the branch.

Note

None

Author(s)

Sebastian Duchene

References

None.

See Also

simulate.rate()

Examples

set.seed(123425)
myTree <- rcoal(10)
rateTree <- simulate.rate(tree = myTree, FUN = simulate.uncor.lnorm)
plot(rateTree, col.lineages = rainbow(10))

# Get the rate for the lineages ascending from the first taxon
# Find the name of the first taxon
myTree$tip.label

get.lineage.time.rate(taxon = 1, sim.rate.object = rateTree)



## The function is currently defined as
function (taxon, sim.rate.object) 
{
    tree.data.matrix <- sim.rate.object[[2]]
    chrono <- sim.rate.object[[1]]
    chrono$edge.length <- tree.data.matrix[, 7]
    taxon.init <- taxon
    if (taxon %in% tree.data.matrix[, 3]) {
        data.matrix <- tree.data.matrix
        branch.times <- vector()
        rate.time <- vector()
        repeat {
            parent <- data.matrix[, 2][data.matrix[, 3] == taxon]
            time.br <- data.matrix[, 4][data.matrix[, 3] == taxon]
            rate.br <- data.matrix[, 5][data.matrix[, 3] == taxon]
            rate.time <- c(rate.time, rate.br)
            branch.times <- c(branch.times, time.br)
            taxon <- parent
            if (!(parent %in% data.matrix[, 3])) {
                break
            }
        }
        first.rate <- rate.time[length(rate.time)]
        last.rate <- rate.time[1]
        rate.time <- c(last.rate, rate.time, first.rate)
        node.times <- allnode.times(chrono)
        root.age <- max(node.times)
        branch.times <- c(node.times[taxon.init], branch.times, 
            root.age)
        return(data.frame(branch.times, rate.time))
    }
    else {
        stop("The taxon name was not found in the tree data matrix. It should be a number between 1 and the number of nodes (internal and external)")
    }
  }

sebastianduchene/NELSI documentation built on Aug. 18, 2022, 11:45 p.m.