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library(phyclust, quiet = TRUE)
### Examples to use EM functions.
data.path <- paste(.libPaths()[1], "/phyclust/data/pony524.phy", sep = "")
my.seq <- read.phylip(data.path)
X <- my.seq$org
### Directly use phyclust().
set.seed(1234)
ret <- phyclust(X, 2)
### One EM step.
ret.em <- phyclust.em.step(X, ret)
### One E- and M- step.
ret.e <- phyclust.e.step(X, ret)
ret$Z.normalized <- ret.e
ret.m <- phyclust.m.step(X, ret)
ret.e.m <- phyclust.m.step(X, K = ret$K, Tt = ret$QA$Tt,
Z.normalized = ret.e,
substitution.model = ret$substitution.model,
identifier = ret$QA$identifier,
code.type = ret$code.type)
### Check logL.
phyclust.logL(X, ret.em)
phyclust.logL(X, ret.m)
phyclust.logL(X, ret.e.m)
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