| gen.equal.star.anc.dec {phyclust} | R Documentation |
Generate comprehensive trees for simulation studies.
gen.equal.star.anc.dec(K, N.K, rate.f = 0.5)
K |
number of clusters, K. |
N.K |
number of sequences for each cluster, a vector with length |
rate.f |
r_f, growth rate ratio of ancestral and descendent trees. |
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.
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. |
Wei-Chen Chen wccsnow@gmail.com
Phylogenetic Clustering Website: http://snoweye.github.io/phyclust/
## Not run:
library(phyclust, quiet = TRUE)
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)
## End(Not run)