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# Automatically generated from all.nw using noweb
survfit <- function(formula, ...) {
UseMethod("survfit", formula)
}
dim.survfit <- function(x) {
if (is.null(x$strata)) {
if (is.matrix(x$surv)) ncol(x$surv)
else 1
}
else {
nr <- length(x$strata)
if (is.matrix(x$xurv)) c(nr, ncol(x$surv))
else nr
}
}
"[.survfit" <- function(x, ..., drop=TRUE) {
nmatch <- function(indx, target) {
# This function lets R worry about character, negative, or logical subscripts
# It always returns a set of positive integer indices
temp <- 1:length(target)
names(temp) <- target
temp[indx]
}
if (missing(..1)) i<- NULL else i <- ..1
if (missing(..2)) j<- NULL else j <- ..2
if (is.null(i) && is.null(j)) return (x) #no subscripts present!
if (!is.matrix(x$surv) && !is.null(j))
stop("survfit object does not have 2 dimensions")
if (is.null(x$strata)) {
if (is.matrix(x$surv)) {
if (is.null(j) && !is.null(i)) j <- i #special case noted above
x$surv <- x$surv[,j,drop=drop]
if (!is.null(x$std.err)) x$std.err <- x$std.err[,j,drop=drop]
if (!is.null(x$upper)) x$upper <- x$upper[,j,drop=drop]
if (!is.null(x$lower)) x$lower <- x$lower[,j,drop=drop]
if (!is.null(x$cumhaz)) x$cumhaz <- x$cumhaz[,j,drop=drop]
}
else warning("survfit object has only a single survival curve")
}
else {
if (is.null(i)) keep <- seq(along.with=x$time)
else {
indx <- nmatch(i, names(x$strata)) #strata to keep
if (any(is.na(indx)))
stop(paste("strata",
paste(i[is.na(indx)], collapse=' '),
'not matched'))
# Now, indx may not be in order: some can use curve[3:2] to reorder
# The list/unlist construct will reorder the data
temp <- rep(1:length(x$strata), x$strata)
keep <- unlist(lapply(indx, function(x) which(temp==x)))
if (length(indx) <=1 && drop) x$strata <- NULL
else x$strata <- x$strata[i]
x$n <- x$n[indx]
x$time <- x$time[keep]
x$n.risk <- x$n.risk[keep]
x$n.event <- x$n.event[keep]
x$n.censor<- x$n.censor[keep]
if (!is.null(x$enter)) x$enter <- x$enter[keep]
}
if (is.matrix(x$surv)) {
# If the curve has been selected by strata and keep has only
# one row, we don't want to lose the second subscript too
if (!is.null(i) && (is.null(j) ||length(j) >1)) drop <- FALSE
if (is.null(j)) {
x$surv <- x$surv[keep,,drop=drop]
if (!is.null(x$std.err))
x$std.err <- x$std.err[keep,,drop=drop]
if (!is.null(x$upper)) x$upper <-x$upper[keep,,drop=drop]
if (!is.null(x$lower)) x$lower <-x$lower[keep,,drop=drop]
if (!is.null(x$cumhaz)) x$cumhaz <-x$cumhaz[keep,,drop=drop]
}
else {
x$surv <- x$surv[keep,j, drop=drop]
if (!is.null(x$std.err))
x$std.err <- x$std.err[keep,j, drop=drop]
if (!is.null(x$upper)) x$upper <- x$upper[keep,j, drop=drop]
if (!is.null(x$lower)) x$lower <- x$lower[keep,j, drop=drop]
if (!is.null(x$cumhaz)) x$cumhaz <- x$cumhaz[keep,j, drop=drop]
}
}
else {
x$surv <- x$surv[keep]
if (!is.null(x$std.err)) x$std.err <- x$std.err[keep]
if (!is.null(x$upper)) x$upper <- x$upper[keep]
if (!is.null(x$lower)) x$lower <- x$lower[keep]
if (!is.null(x$cumhaz)) x$cumhaz <- x$cumhaz[keep]
}
}
x
}
survfit.formula <- function(formula, data, weights, subset,
na.action, etype, id, istate, ...) {
Call <- match.call()
Call[[1]] <- as.name('survfit') #make nicer printout for the user
# create a copy of the call that has only the arguments we want,
# and use it to call model.frame()
indx <- match(c('formula', 'data', 'weights', 'subset','na.action',
'istate', 'id', "etype"), names(Call), nomatch=0)
#It's very hard to get the next error message other than malice
# eg survfit(wt=Surv(time, status) ~1)
if (indx[1]==0) stop("a formula argument is required")
temp <- Call[c(1, indx)]
temp[[1]] <- as.name("model.frame")
m <- eval.parent(temp)
Terms <- terms(formula, c("strata", "cluster"))
ord <- attr(Terms, 'order')
if (length(ord) & any(ord !=1))
stop("Interaction terms are not valid for this function")
n <- nrow(m)
Y <- model.extract(m, 'response')
if (!is.Surv(Y)) stop("Response must be a survival object")
casewt <- model.extract(m, "weights")
if (is.null(casewt)) casewt <- rep(1,n)
if (!is.null(attr(Terms, 'offset'))) warning("Offset term ignored")
id <- model.extract(m, 'id')
istate <- model.extract(m,"istate")
temp <- untangle.specials(Terms, "cluster")
if (length(temp$vars)>0) {
if (length(temp$vars) > 1) stop("can not have two cluster terms")
if (!is.null(id)) stop("can not have both a cluster term and an id variable")
id <- m[[temp$vars]]
Terms <- Terms[-temp$terms]
}
ll <- attr(Terms, 'term.labels')
if (length(ll) == 0) X <- factor(rep(1,n)) # ~1 on the right
else X <- strata(m[ll])
if (!is.Surv(Y)) stop("y must be a Surv object")
# Backwards support for the now-depreciated etype argument
etype <- model.extract(m, "etype")
if (!is.null(etype)) {
if (attr(Y, "type") == "mcounting" ||
attr(Y, "type") == "mright")
stop("cannot use both the etype argument and mstate survival type")
if (length(istate))
stop("cannot use both the etype and istate arguments")
status <- Y[,ncol(Y)]
etype <- as.factor(etype)
temp <- table(etype, status==0)
if (all(rowSums(temp==0) ==1)) {
# The user had a unique level of etype for the censors
newlev <- levels(etype)[order(-temp[,2])] #censors first
}
else newlev <- c(" ", levels(etype)[temp[,1] >0])
status <- factor(ifelse(status==0,0, as.numeric(etype)),
labels=newlev)
if (attr(Y, 'type') == "right")
Y <- Surv(Y[,1], status, type="mstate")
else if (attr(Y, "type") == "counting")
Y <- Surv(Y[,1], Y[,2], status, type="mstate")
else stop("etype argument incompatable with survival type")
}
# At one point there were lines here to round the survival
# times to a certain number of digits. This approach worked
# almost all the time, but only almost. The better logic is
# now in the individual compuation routines
if (attr(Y, 'type') == 'left' || attr(Y, 'type') == 'interval')
temp <- survfitTurnbull(X, Y, casewt, ...)
else if (attr(Y, 'type') == "right" || attr(Y, 'type')== "counting")
temp <- survfitKM(X, Y, casewt, ...)
else if (attr(Y, 'type') == "mright" || attr(Y, "type")== "mcounting")
temp <- survfitCI(X, Y, weights=casewt, id=id, istate=istate, ...)
else {
# This should never happen
stop("unrecognized survival type")
}
if (is.null(temp$states)) class(temp) <- 'survfit'
else class(temp) <- c("survfitms", "survfit")
if (!is.null(attr(m, 'na.action')))
temp$na.action <- attr(m, 'na.action')
temp$call <- Call
temp
}
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