### This file contains functions for print and summary.
### Print phyclust
print.phyclust <- function(x, digits = max(4, getOption("digits") - 3), ...){
ret.phyclust <- x
op.org <- options()
options(digits = digits)
init <- NULL
if(!is.null(ret.phyclust$conv)){
my.cat("Phyclust Results:\n",
"code type: ", ret.phyclust$code.type,
", em method: ", ret.phyclust$em.method,
", boundary method: ", ret.phyclust$boundary.metho, ".\n",
"init procedure: ", ret.phyclust$init.procedure,
", method: ", ret.phyclust$init.method, ".\n",
"model substitution: ", ret.phyclust$substitution.model,
", distance: ", ret.phyclust$edist.model, ".\n",
"label method: ", ret.phyclust$label.method, ".\n",
"iter: ", ret.phyclust$conv$iter,
" ", ret.phyclust$conv$inner.iter,
" ", ret.phyclust$conv$cm.iter,
", convergence: ", ret.phyclust$conv$flag,
", check.param: ", ret.phyclust$conv$check.param, ".\n",
"eps: ", ret.phyclust$conv$eps,
", error: ", ret.phyclust$conv$error, ".\n")
}
my.cat("N.X.org: ", ret.phyclust$N.X.org,
", N.X: ", ret.phyclust$N.X,
", L: ", ret.phyclust$L,
", K: ", ret.phyclust$K,
", p: ", ret.phyclust$p,
", N.seg.site: ", ret.phyclust$N.seg.site, ".\n",
"logL: ", ret.phyclust$logL)
if(!is.null(ret.phyclust$bic)) my.cat(", bic: ", ret.phyclust$bic)
if(!is.null(ret.phyclust$aic)) my.cat(", aic: ", ret.phyclust$aic)
if(!is.null(ret.phyclust$icl)) my.cat(", icl: ", ret.phyclust$icl)
my.cat("\n")
my.cat("identifier: ", ret.phyclust$QA$identifier, "\n")
cat(" Eta:", ret.phyclust$Eta, "\n")
if(!is.null(ret.phyclust$Q$pi)){
my.cat(" pi:\n")
my.print(ret.phyclust$Q$pi)
}
if(!is.null(ret.phyclust$Q$kappa)) cat(" kappa:", ret.phyclust$Q$kappa, "\n")
cat(" Tt:", ret.phyclust$Q$Tt, "\n")
if(!is.null(ret.phyclust$n.class)) cat(" n.class:", ret.phyclust$n.class, "\n")
if(!is.null(ret.phyclust$SE)){
my.cat("SE_model: ", ret.phyclust$SE$model,
", SE_constant: ", ret.phyclust$SE$constant, "\n")
my.print(ret.phyclust$SE$f.err)
}
options(op.org)
invisible()
} # End of print.phyclust().
summary.phyclust <- function(object, ...){
ret.phyclust <- object
print.phyclust(ret.phyclust)
cat("Mu:\n")
for(i in 1:ret.phyclust$K){
cat(" ", as.character(.nucleotide$code[ret.phyclust$Mu[i,] + 1]), "\n")
}
cat("Class id:", ret.phyclust$class.id, "\n")
} # End of summary.phyclust().
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