Nothing
seqintegration <- function(...){
msg.stop("Seqintegration is obsolete, use seqintegr instead!")
}
seqintegr <- function(seqdata, state=NULL, pow=1, with.missing=FALSE){
if (!inherits(seqdata, "stslist")) {
stop("[!] seqdata is not a sequence object, see seqdef function to create one")
}
alph <- alphabet(seqdata)
nr <- attr(seqdata, "nr")
if (with.missing) {
alph <- c(alph, nr)
}
if (length(state)>1)
msg.stop("When non null, 'state' must be a single state")
if (!is.null(state)){
if (!state %in% alph){
msg.stop("state ", state, " not in the alphabet!")
}
}
nbstat <- ifelse(is.null(state),length(alph),1)
nbseq <- nrow(seqdata)
iseqtab <- matrix(nrow = nbseq, ncol = nbstat)
if (is.null(state))
colnames(iseqtab) <- alph
else
colnames(iseqtab) <- state
rownames(iseqtab) <- rownames(seqdata)
## message(" [>] computing state distribution for ", nbseq, " sequences ...")
integVector <- (1:ncol(seqdata))^pow
suminteg <- sum(integVector, na.rm = TRUE)
## when with.missing=FALSE we do not account for positions occupied by missings
miss <- c(nr, attr(seqdata,"void"))
if(!with.missing)
suminteg <- suminteg - apply(seqdata, 1, function(x) sum(integVector[x %in% miss], na.rm = TRUE))
if(is.null(state)){
for(i in 1:nbstat) {
iseqtab[, i] <- apply(seqdata, 1, function(x) sum(integVector[x == alph[i]], na.rm =
TRUE))/suminteg
}
} else {
iseqtab[, 1] <- apply(seqdata, 1, function(x) sum(integVector[x == state], na.rm = TRUE))/suminteg
}
return(iseqtab)
}
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