R: Generate Comprehensive Trees.

gen.unit.K {phyclust} | R Documentation

## Generate Comprehensive Trees.

### Description

Generate comprehensive trees for simulation studies.

### Usage

    gen.unit.K(K, N.K, rate.anc = 10, rate.dec = 10)

### Arguments

`K` | number of clusters, K.
`N.K` | number of sequences for each cluster, a vector with length `K`.
`rate.anc` | r_a, growth rate of ancestral tree.
`rate.dec` | r_d, growth rate of descendent tree.

### Details

These functions generates an ancestral tree in K tips and generates descendent trees according to `N.K` tips, and returns several types of trees, `org`, `equal`, `max`, and `star`, as the following:

- 'org': original tree, adjacent the descendent trees to the ancestral tree.

- 'equal': descendent trees are scaled to the average height and attached to the ancestral tree, then scale the total height to be 1.

- 'max': descendent trees are attached to the ancestral tree, then scale the maximum height to be 1.

- 'star': descendent trees are applied `as.star.tree` and attached to the ancestral tree, then scale the maximum height to be 1.

### Value

A list contains all information of generation and results including:

`'K'` | number of clusters.
`'N.K` | number of sequences for each cluster.
`'rate.anc'` | r_a, growth rate of ancestral tree.
`'rate.dec'` | r_d, growth rate of descendent tree.
`'height.anc'` | height of ancestral tree.
`'height.dec'` | height of all descendent trees.
`'anc'` | an ancestral tree.
`'dec'` | all descendent trees.
`'org'` | an original tree.
`'equal'` | a three that descendants are all equal height.
`'max'` | a tree that descendants are scaled by the maximum height.
`'star'` | a tree that descendants are star trees.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`gen.equal.star.anc.dec`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    # For gen.unit.K()
    set.seed(1234)
    tree.K <- gen.unit.K(6, rep(3:5, 2),
                         rate.anc = 0.7, rate.dec = 1.1)
    X.class <- as.numeric(gsub("d(.)(.*)", "\\1",
                               tree.K$org$tip.label))

    # Plot results
    par(mfrow = c(2, 2))
    plotnj(tree.K$org, X.class, type = "p",
           edge.width.class = 2, main = "org")
    axis(1)
    plotnj(tree.K$equal, X.class, type = "p",
           edge.width.class = 2, main = "equal")
    axis(1)
    plotnj(tree.K$max, X.class, type = "p",
           edge.width.class = 2, main = "max")
    axis(1)
    plotnj(tree.K$star, X.class, type = "p",
           edge.width.class = 2, main = "star")
    axis(1)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]