phyclust (version 0.1-9)

gen.equal.star.anc.dec: Generate comprehensive trees.

Description

Generate comprehensive trees for simulation studies.

Usage

gen.equal.star.anc.dec(K, N.K, rate.f = 0.5)

Arguments

K

number of clusters, $K$.

N.K

number of sequences for each cluster, a vector with length K.

rate.f

$r_f$, growth rate ratio of ancestral and descendent trees.

Value

• A list contains all information of generation and results including:
• 'K'
  number of clusters.
• 'N.K
  number of sequences for each cluster.
• 'rate.f'
  $r_f$, growth rate ratio of ancestral and descendent trees.
• 'anc'
  an ancestral tree.
• 'dec'
  all descendent trees.
• 'equalstar'
  a tree that descendants are equal star trees.

Details

These functions generates an ancestral tree in K tips and generates descendent trees according to N.K tips. All trees, ancestral and descendent, are coerced to star shapes and scaled their heights to fit the ratio rate.f, and the final tree has total height 1. The returns are stored in a list, and the final tree is stored with a name equal.star.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

gen.unit.K.

Examples

set.seed(1234)
tree.K <- gen.equal.star.anc.dec(6, rep(3:5, 2),
                                 rate.f = 0.7)
X.class <- as.numeric(gsub("d(.).(.)", "\\1",
                           tree.K$equal.star$tip.label))

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