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###############################################################
#### RHmm package
####
#### File: RHmm-internals.R
####
#### Author: Ollivier TARAMASCO <Ollivier.Taramasco@imag.fr>
#### Author: Sebastian BAUER <sebastian.bauer@charite.de>
####
###############################################################
setStorageMode <- function(object) UseMethod("setStorageMode")
setStorageMode.paramHMM <- function(object)
{ x <- object
storage.mode(x$nStates) <- "integer"
storage.mode(x$dimObs) <- "integer"
storage.mode(x$nMixt) <- "integer"
storage.mode(x$nLevels) <- "integer"
storage.mode(x) <- "list"
class(x) <- "paramHMM"
return(x)
}
setStorageMode.paramAlgoBW <- function(object)
{ x <- object
storage.mode(x$iter) <- "integer"
storage.mode(x$verbose) <- "integer"
storage.mode(x$nInit) <- "integer"
storage.mode(x$nIterInit) <- "integer"
if (!is.null(x$initPoint))
x$initPoint <- setStorageMode(x$initPoint)
storage.mode(x) <- "list"
class(x) <- "paramAlgoBW"
return(x)
}
setStorageMode.HMMClass <- function(object)
{ x <- object
storage.mode(x$initProb) <- "double"
if (is.list(x$transMat)) lapply(x$transMat,function(x){storage.mode(x) <- "double"})
else storage.mode(x$transMat) <- "double"
x$distribution <- setStorageMode(object$distribution)
class(x$distribution) <- class(object$distribution)
storage.mode(x) <- "list"
class(x) <- "HMMClass"
return(x)
}
setStorageMode.distributionClass <- function(object)
{ x<-NextMethod("setStorageMode", object)
storage.mode(x$nStates) <- "integer"
storage.mode(x$dis) <-"character"
class(x) <- c("distributionClass", class(x))
return(x)
}
setStorageMode.univariateNormalClass <- function(object)
{ x <- object
storage.mode(x$dimObs) <- "integer"
storage.mode(x$mean) <- "double"
storage.mode(x$var) <- "double"
storage.mode(x) <- "list"
class(x) <- "univariateNormalClass"
return(x)
}
setStorageMode.multivariateNormalClass <- function(object)
{ x <- object
storage.mode(x$dimObs) <- "integer"
storage.mode(x$mean) <- "list"
storage.mode(x$cov) <- "list"
storage.mode(x) <- "list"
class(x) <- "multivariateNormalClass"
return(x)
}
setStorageMode.mixtureUnivariateNormalClass <- function(object)
{ x <- object
storage.mode(x$dimObs) <- "integer"
storage.mode(x$nMixt) <- "integer"
storage.mode(x$mean) <- "list"
storage.mode(x$var) <- "list"
storage.mode(x$proportion) <- "list"
storage.mode(x) <- "list"
class(x) <- "mixtureUnivariateNormalClass"
return(x)
}
setStorageMode.mixtureMultivariateNormalClass <- function(object)
{ x <- object
storage.mode(x$dimObs) <- "integer"
storage.mode(x$nMixt) <- "integer"
storage.mode(x$mean) <- "list"
storage.mode(x$cov) <- "list"
storage.mode(x$proportion) <- "list"
storage.mode(x) <- "list"
class(x) <- "mixtureMultivariateNormalClass"
return(x)
}
setStorageMode.discreteClass <- function(object)
{ x <- object
storage.mode(x$nLevels) <- "integer"
storage.mode(x$proba) <- "list"
storage.mode(x$dimObs) <- "integer"
storage.mode(x) <- "list"
class(x) <- "discreteClass"
return(x)
}
GetAllLevels <- function(obs)
{
if (is.list(obs))
{ if (is.factor(obs[[1]]))
{ Aux1 <- unlist(lapply(obs, levels))
Aux2 <- sort(Aux1)
lAux <- length(Aux2)
Aux3 <- c(TRUE,(Aux2[2:lAux]!=Aux2[1:(lAux-1)]))
return(Aux2[Aux3])
}
else
{ Y <- obs
lY <- length(Y)
for ( i in 1:lY)
Y[[i]] <- as.factor(Y[[i]])
return(GetAllLevels(Y))
}
}
else
{ if (is.factor(obs))
return(levels(obs))
else
return(levels(as.factor(obs)))
}
}
TransformeListe <- function(paramHMM, obs)
{
if (paramHMM$dis=='DISCRETE')
{ if (is.null(paramHMM$Levels))
labels <- GetAllLevels(obs)
else
labels <- paramHMM$Levels
nLevels <- length(labels)
if (is.list(obs))
{ Z <- obs
lZ <- length(Z)
Zt <- rep(list(0), lZ)
for (i in 1:lZ)
{ Aux1 <- as.character(Z[[i]])
Aux2 <- factor(Aux1, levels=labels)
Zt[[i]] <- as.double(Aux2)-1.0
}
}
else
{ Z <- as.character(obs)
Z <- factor(Z, levels=labels)
Zt <- list(as.double(Z) - 1.0)
}
return(list(Zt=Zt, nLevels=nLevels, labels=labels))
}
else
{ if (is.list(obs))
{ return(list(Zt=obs, nLevels=0, labels=NULL))
}
else
{ return(list(Zt=list(obs), nLevels=0, labels=NULL))
}
}
}
TransfListe <- function(distribution, obs)
{
if (distribution$dis == 'DISCRETE')
{ Levels <- names(distribution$proba[[1]])
}
else
Levels <- NULL
paramHMM <- list(dis=distribution$dis, Levels=Levels)
return(TransformeListe(paramHMM, obs))
}
########## end of RHmm_internals
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