# NOT RUN {
library(phyclust, quiet = TRUE)
set.seed(1234)
X <- seq.data.toy$org
(ret.1 <- find.best(X, 4))
(ret.2 <- phyclust.se.update(X, ret.phyclust = ret.1))
.EMC$se.constant <- 1e-3
(ret.3 <- phyclust.se.update(X, ret.phyclust = ret.2))
### Search optimal error
func <- function(C){
.EMC$se.constant <<- C
-phyclust.se.update(X, ret.phyclust = ret.1)$logL
}
(ret.opt <- optimize(f = func, lower = 1e-3, upper = 1e-1))
.EMC$se.constant <- ret.opt$minimum
(ret.se.opt <- phyclust.se.update(X, ret.phyclust = ret.1))
# }
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