Nothing
### This file contains functions to call phyclust_se_update in C.
### EM step.
phyclust.se.update <- function(X, EMC = .EMC, ret.phyclust = NULL,
K = NULL, Eta = NULL, Mu = NULL, pi = NULL, kappa = NULL, Tt = NULL,
byrow = TRUE){
label <- NULL
if(is.null(ret.phyclust)){
if(is.null(K) || is.null(Eta) || is.null(Mu) || is.null(Tt)){
stop("The parameters are not specified correctly.")
} else{
ret.phyclust <- list(K = K, Eta = Eta, Mu = Mu,
QA = list(pi = pi, kappa = kappa, Tt = Tt,
identifier = EMC$identifier),
substitution.model = EMC$substitution.model,
code.type = EMC$code.type)
}
} else{
if(!inherits(ret.phyclust, "phyclust")){
stop("The ret.phyclust should be in a phyclust class.")
}
}
if(ret.phyclust$code.type != "NUCLEOTIDE"){
stop("The sequencing error model only supports NUCLEOTIDE data.")
}
K <- ret.phyclust$K
if(byrow){
X <- t(X)
}
N.X.org <- ncol(X)
L <- nrow(X)
EMC$init.procedure <- ret.phyclust$init.procedure
EMC$init.method <- ret.phyclust$init.method
EMC$substitution.model <- ret.phyclust$substitution.model
EMC$edist.model <- ret.phyclust$edist.model
EMC$identifier <- ret.phyclust$QA$identifier
EMC$code.type <- ret.phyclust$code.type
EMC$em.method <- "EM"
EMC$boundary.method <- ret.phyclust$boundary.method
EMC$se.type <- TRUE
EMC$se.model <- "CONVOLUTION"
EMC <- check.EMC(EMC)
EMC <- translate.EMC.se(EMC)
vect <- convert.QA.to.vect(ret.phyclust)
label <- check.label(label, N.X.org, K, byrow)
ret <- .Call("R_phyclust_se_update",
as.integer(N.X.org),
as.integer(L),
as.integer(X),
EMC,
as.integer(K),
as.double(ret.phyclust$Eta),
as.integer(t(ret.phyclust$Mu)),
as.double(vect),
label,
PACKAGE = "phyclust")
if(!is.finite(ret$logL)){
stop("The logL is not finite.\n")
}
ret$class.id <- ret$class.id + 1
ret <- translate.ret.se(ret, EMC)
class(ret) <- "phyclust"
ret
} # End of phyclust.se.update().
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