<![CDATA[
#### <code>.EMC</code> -- Examples of <code>.EMControl()</code></font></b>
<code>.EMC</code> is a reserved object storing all options for
<code>phyclust()</code>, <code>find.best()</code>, and other related
functions, and it is created by a function <code>.EMControl()</code>
providing default values for EM steps and initialization.
Examples are given in the following, copy and paste to R to see the results,
and the details are available by using <code>help(.EMControl)</code>.
```
.EMControl() # This gives a return object as .EMC.
.show.option() # This prints all options.
# These lines provide EMC.1 which is exactly the same as
# EMC.2 using "HKY85" for the Q matrix, and time t is varied
# for clusters. EMC.1 and EMC.2 can be used in phyclust() or
# find.best().
EMC.1 <- .EMC
EMC.1$substitution.model <- "HKY85"
EMC.1$identifier <- "EV"
EMC.2 <- .EMControl(substitution.model = "HKY85",
identifier = "EV")
# These 4 lines provide EMC.3 which is exactly the same as
# EMC.4 using "SNP_JC69" for the Q matrix, HAMMING distance
# for initialization, and the data should be SNP sequences.
EMC.3 <- .EMC
EMC.3$substitution.model <- "SNP_JC69"
EMC.3$edist.model <- "HAMMING"
EMC.3$code.type <- "SNP"
EMC.4 <- .EMControl(substitution.model = "SNP_JC69",
edist.model = "HAMMING",
code.type = "SNP")
# This line changes more options including initialization
# procedure, initialization method, model for the Q matrix,
# identifier, and the EM algorithm.
EMC.5 <- .EMControl(init.procedure = "RndEM",
init.method = "randomNJ",
substitution.model = "K80",
identifier = "EV",
em.method = "ACEM")
# This line uses a convergent condition looser than the
# default, and originally conditions in optim() for the
# Nelder-Mead method.
EMC.6 <- .EMControl(EM.eps = 1e-8,
nm.abstol.Mu.given.QA = 1e-16,
nm.reltol.Mu.given.QA = 1e-8,
nm.maxit.Mu.given.QA = 500,
nm.abstol.QA.given.Mu = 1e-16,
nm.reltol.QA.given.Mu = 1e-8,
nm.maxit.QA.given.Mu = 500)
```
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