Nothing
## creating rf sequence object
seqrf <- function(seqdata, diss, k=NULL, sortv="mds", weights=NULL,
weighted=TRUE,
grp.meth = "prop", squared = FALSE, pow = NULL){
if (is.null(weights) & weighted) weights <- attr(seqdata,"weights")
if (!weighted) weights <- NULL
## computing sortv
if (!is.null(sortv)) {
if (length(sortv)==1){
if (sortv %in% c("from.start", "from.end")) {
end <- if (sortv=="from.end") { max(seqlength(seqdata)) } else { 1 }
beg <- if (sortv=="from.end") { 1 } else { max(seqlength(seqdata)) }
sortv <- do.call(order, as.data.frame(seqdata)[,end:beg])
sortv <- order(sortv)
} else if (sortv != "mds") {
stop(call.=FALSE, "If of length one, sortv must be one of 'mds', 'from.start', and 'from.end'")
}
} else if (length(sortv)!=nrow(seqdata)) {
stop(call.=FALSE, "sortv must contain one value for each row in the sequence object ")
} else {
if (is.factor(sortv)) { sortv <- as.integer(sortv) }
}
}
rf <- dissrf(diss, k=k, sortv=sortv, weights=weights,
grp.meth = grp.meth, squared = squared, pow = pow)
seqtoplot <- seqdata[rf[["medoids"]],]
attr(seqtoplot,"weights") <- rf[["heights"]]
srf <- list(seqtoplot=seqtoplot,rf=rf)
class(srf) <- c("seqrf",class(srf))
if (inherits(rf,"dissrfprop")){
class(srf) <- c("seqrfprop",class(srf))
}
else
class(srf) <- c("seqrfcrisp",class(srf))
return(srf)
}
######
print.seqrf <- function(x, ...){
print(x[["seqtoplot"]], ...)
}
#####
summary.seqrf <- function(object, format="SPS", dist.idx = 1:10, ...){
#limit <- max(seqlength(seqdss(x[["seqtoplot"]])))
sry <- summary(object[["rf"]], dist.idx = dist.idx)
meds <- suppressMessages(seqformat(object[["seqtoplot"]], to=format, compress=TRUE,
SPS.out = list(xfix = "", sdsep = "/")))
mnames <- sub("\\..","",x=rownames(meds))
##print(id)
medoids <- data.frame(index=sry[["medoids"]],names=mnames,medoids=meds)
rownames(medoids)<-NULL
sry[["medoids"]] <- medoids
return(sry)
}
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