group.clocks: pathnode

In duchene/ClockstaRX: ClockstaRX: testing molecular clock hypotheses in genomic data

pathnode

Description

This function ...

Usage

pathnode(phylo, tipsonly = T)

Arguments

phylo	A phylogenetic tree of class 'phylo'
tipsonly	A logical value (T / F) indicating whether the function should only return the root-to-tip distance and number of nodes along a lineage for the tips only. Select T for the tips only, and F for the tips and internal nodes.

Details

The function plots...

Value

A list with two items:

roottotippath	A vector with the distance from the root to the tips. If tipsonly==F, it will also include the distances for internal nodes.
nodesinpath	A vector with the number of nodes along a lineage. If tipsonly==F, it will also include the number of nodes for internal nodes. These are counted from the tips to the root.

Note

Please see the references for more detailed information.

Author(s)

David Duchene

References

Venditti, Chris, Andrew Meade, and Mark Pagel. "Detecting the node-density artifact in phylogeny reconstruction." Systematic biology 55.4 (2006): 637-643.

See Also

Pending.

Examples

set.seed(12345)
myTree <- rtree(10)

par(mfrow = c(1, 2))
plot(myTree)
nde <- pathnode(myTree)
nde



## The function is currently defined as
function (phylo, tipsonly = T) 
{
    require(phangorn)
    di.tr <- dist.nodes(phylo)
    root.tr <- phylo$edge[, 1][!(phylo$edge[, 1] %in% phylo$edge[, 
        2])][1]
    tr.depth <- max(di.tr[as.numeric(colnames(di.tr)) == root.tr, 
        ])
    if (tipsonly == TRUE) {
        roottotippath <- di.tr[as.numeric(rownames(di.tr)) == 
            root.tr, 1:length(phylo$tip.label)]
        nodesinpath <- sapply(1:length(phylo$tip.label), function(x) length(Ancestors(phylo, 
            x)))
    }
    else {
        roottotippath <- di.tr[as.numeric(rownames(di.tr)) == 
            root.tr, ]
	nodesinpath <- sapply(1:(length(phylo$tip.label)+phylo$Nnode), function(x) length(Ancestors(phylo, x)))
    }
    plot(roottotippath, nodesinpath, xlab = "Root-to-tip path length", 
        ylab = "Number of parent nodes", pch = 20)
    return(list(roottotippath = roottotippath, nodesinpath = nodesinpath))
  }

duchene/ClockstaRX documentation built on Oct. 22, 2023, 10:51 a.m.