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R/phreg.R
In mets: Analysis of Multivariate Event Times
Defines functions
phreg
phreg01
Documented in
phreg
###{{{ phreg01
phreg01 <- function(X,entry,exit,status,id=NULL,strata=NULL, offset=NULL,weights=NULL,strata.name=NULL,cumhaz=TRUE,
beta,stderr=TRUE,method="NR",no.opt=FALSE,Z=NULL,propodds=NULL,AddGam=NULL,
case.weights=NULL,no.var=0,augmentation=0,...) {
p <- ncol(X)
if (missing(beta)) beta <- rep(0,p)
if (p==0) X <- cbind(rep(0,length(exit)))
if (is.null(strata)) { strata <- rep(0,length(exit)); nstrata <- 1; strata.level <- NULL; } else {
strata.level <- levels(strata)
ustrata <- sort(unique(strata))
nstrata <- length(ustrata)
strata.values <- ustrata
if (is.numeric(strata)) strata <- fast.approx(ustrata,strata)-1 else {
strata <- as.integer(factor(strata,labels=seq(nstrata)))-1
}
}
if (is.null(offset)) offset <- rep(0,length(exit))
if (is.null(weights)) weights <- rep(1,length(exit))
strata.call <- strata
Zcall <- matrix(1,1,1) ## to not use for ZX products when Z is not given
if (!is.null(Z)) Zcall <- Z
## possible casewights to use for bootstrapping and other things
if (is.null(case.weights)) case.weights <- rep(1,length(exit))
trunc <- (!is.null(entry))
if (!trunc) entry <- rep(0,length(exit))
call.id <- id
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(entry))-1;
## orginal id coding into integers
id.orig <- id+1;
dd <- .Call("FastCoxPrepStrata", entry,exit,status,X,id,trunc,strata,weights,offset,Zcall,case.weights,PACKAGE="mets")
dd$nstrata <- nstrata
obj <- function(pp,U=FALSE,all=FALSE) {# {{{
if (length(dd$jumps) >0) {
if (is.null(propodds) & is.null(AddGam)) {
val <- with(dd, .Call("FastCoxPLstrata",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,caseweights,PACKAGE="mets"))
} else if (is.null(AddGam))
val <- with(dd, .Call("FastCoxPLstrataPO",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,propodds,PACKAGE="mets"))
else val <- with(dd, .Call("FastCoxPLstrataAddGam",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,
AddGam$theta,AddGam$dimthetades,AddGam$thetades,AddGam$ags,AddGam$varlink,AddGam$dimjumprv,AddGam$jumprv,
AddGam$JumpsCauses,PACKAGE="mets"))
val$gradient <- val$gradient+augmentation
} else {
val <- list(jumps=NULL,ploglik=NULL,U=NULL,gradient=NULL,hessian=NULL,hessiantime=NULL,S2S0=NULL,E=NULL,S0=NULL)
}
if (all) {
val$time <- dd$time
### plus 1 for R index
val$ord <- dd$ord+1
val$jumps <- dd$jumps+1
val$jumptimes <- val$time[val$jumps]
val$weightsJ <- dd$weights[val$jumps]
val$case.weights <- dd$case.weights[val$jumps]
val$nevent <- length(val$S0)
val$nstrata <- dd$nstrata
val$strata <- dd$strata
val$strata.jumps <- val$strata[val$jumps]
return(val)
}
n <- length(dd$time)
with(val,structure(-ploglik/n,gradient=-gradient/n,hessian=-hessian/n))
}# }}}
opt <- NULL
if (p>0) {
if (no.opt==FALSE) {
if (tolower(method)=="nr") {
tim <- system.time(opt <- lava::NR(beta,obj,...))
opt$timing <- tim
opt$estimate <- opt$par
} else {
opt <- nlm(obj,beta,...)
opt$method <- "nlm"
}
cc <- opt$estimate; names(cc) <- colnames(X)
if (!stderr) return(cc)
val <- c(list(coef=cc), obj(opt$estimate,all=TRUE))
} else val <- c(list(coef=beta), obj(beta,all=TRUE))
} else {
val <- obj(0,all=TRUE)
}
se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL
II <- NULL
if (no.opt==FALSE & p!=0) {
II <- - tryCatch(solve(val$hessian),error=function(e) matrix(0,nrow(val$hessian),ncol(val$hessian)) )
} else II <- matrix(0,p,p)
## Brewslow estimator, to handle also possible weights, caseweights that are 0
ww <- val$caseweightsJ * val$weightsJ
val$S0[abs(ww)<.00000001] <- 0
### computes Breslow estimator
if (cumhaz==TRUE & (length(val$jumps)>0)) { # {{{
strata <- val$strata[val$jumps]
nstrata <- val$nstrata
jumptimes <- val$jumptimes
## Brewslow estimator, to handle also possible weights/case-weights, and caseweights that are 0
S0i2 <- S0i <- rep(0,length(val$S0))
wwJ <- val$caseweightsJ*val$weightsJ
S0i[val$S0>0] <- 1/val$S0[val$S0>0]
S0i2[val$S0>0] <- 1/(val$S0[val$S0>0]^2*wwJ[val$S0>0])
cumhaz <- cbind(jumptimes,cumsumstrata(S0i,strata,nstrata))
if ((no.opt==FALSE & p!=0)) {
DLambeta.t <- apply(val$E*S0i,2,cumsumstrata,strata,nstrata)
varbetat <- rowSums((DLambeta.t %*% II)*DLambeta.t)
### covv <- apply(covv*DLambeta.t,1,sum) Covariance is "0" by construction
} else varbetat <- 0
var.cumhaz <- cumsumstrata(S0i2,strata,nstrata)+varbetat
se.cumhaz <- cbind(jumptimes,(var.cumhaz)^.5)
colnames(cumhaz) <- c("time","cumhaz")
colnames(se.cumhaz) <- c("time","se.cumhaz")
} # }}}
else {cumhaz <- se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL}
res <- c(val,
list(cox.prep=dd,
strata.call=strata.call, strata.level=strata.level,
entry=entry,
exit=exit,
status=status,
p=p,
X=X,
offsets=offset,
weights=weights,
id=id.orig, call.id=call.id,
opt=opt,
no.opt=no.opt,
cumhaz=cumhaz, se.cumhaz=se.cumhaz,
lcumhaz=lcumhaz, lse.cumhaz=lse.cumhaz,
ihessian=II,
II=II,strata.name=strata.name,propodds=propodds))
class(res) <- "phreg"
## also computing robust variance
if (p>0 & no.var==0) {
beta.iid <- iid(res)
phvar <- crossprod(beta.iid)
colnames(phvar) <- rownames(phvar) <- names(res$coef)
res$var <- phvar
res$beta.iid <- beta.iid
} else res$var <- 0
return(res)
}
###}}} phreg0
###{{{ phreg
##' Fast Cox PH regression
##'
##' Fast Cox PH regression
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for Cox model
##' @param weights weights for Cox score equations
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases phreg phreg.par robust.phreg readPhreg IIDbaseline.phreg conftype plotO.predictphreg plotpredictphreg predictO.phreg predictrecreg summarybase.phreg
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##' ## robust standard errors default
##' summary(out1)
##'
##' par(mfrow=c(1,2))
##' plot(out1)
##'
##' ## computing robust variance for baseline
##' rob1 <- robust.phreg(out1)
##' plot(rob1,se=TRUE,robust=TRUE)
##'
##' ## taking iid decomposition of regression parameters
##' betaiiid <- lava::iid(out1)
##'
##' ## making iid decomposition of baseline at a specific time-point
##' Aiiid <- mets::IIDbaseline.phreg(out1,time=30)
##'
##' @export
phreg <- function(formula,data,offset=NULL,weights=NULL,...) {# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
### if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (!inherits(Y,c("Event","Surv"))) stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
} else pos.cluster <- NULL
if (!is.null(attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
pos.strata <- ts$terms
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else { strata.name <- NULL; pos.strata <- NULL}
### if (!is.null(attributes(Terms)$specials$offset)) {
### ts <- survival::untangle.specials(Terms, "offset")
### pos.offset <- ts$terms
### Terms <- Terms[-ts$terms]
### offset <- m[[ts$vars]]
### } else pos.offset <- NULL
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
res <- c(phreg01(X,entry,exit,status,id,strata,offset,weights,strata.name,...),
list(call=cl,model.frame=m,formula=formula,strata.pos=pos.strata,
cluster.pos=pos.cluster,n=length(exit)))
class(res) <- "phreg"
res
}# }}}
##' @export
readPhreg <- function (object, newdata, nr=TRUE, ...)
{# {{{
exit <- entry <- status <- clusters <- NULL
if (missing(newdata)) { # {{{
X <- object$X
strataNew <- object$strata
if (!nr) {
exit <- object$exit; entry <- object$entry; status <- object$status;
clusters <- object$id
}
} else { ## make design for newdata
xlev <- lapply(object$model.frame,levels)
ff <- unlist(lapply(object$model.frame,is.factor))
upf <- update(object$formula,~.)
tt <- terms(upf)
if (nr) tt <- delete.response(tt)
X <- model.matrix(tt,data=newdata,xlev=xlev)[,-1,drop=FALSE]
if (!nr) {
allvar <- all.vars(tt)
pr <- length(allvar)-ncol(object$model.frame)+1
if (pr==2) {
exit <- newdata[,allvar[1]]
status <- newdata[,allvar[2]]
} else {
entry <- newdata[,allvar[1]]
exit <- newdata[,allvar[2]]
status <- newdata[,allvar[3]]
}
}
clusterTerm<- grep("^cluster[(][A-z0-9._:]*",colnames(X),perl=TRUE)
## remove clusterTerm from design
if (length(clusterTerm)==1) {
clusters <- X[,clusterTerm]
X <- X[,-clusterTerm,drop=FALSE]
id <- clusters
id.orig <- id;
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
clusters <- id
} else clusters <- (1:nrow(newdata))-1
}
strataTerm<- grep("^strata[(][A-z0-9._:]*",colnames(X),perl=TRUE)
## remove strataTerm from design, and construct numeric version of strata
if (length(strataTerm)>=1) {
strataNew <- X[,strataTerm,drop=FALSE]
whichstrata <- paste(object$strata.name,object$strata.level,sep="")
if (length(strataTerm)>=1) { ## construct strata levels numeric
mm <- match(colnames(X)[strataTerm], whichstrata)-1
strataNew <- c(strataNew %*% mm )
}
X <- X[,-strataTerm,drop=FALSE]
} else strataNew <- rep(0,nrow(X))
}# }}}
return(list(X=X,strata=strataNew,entry=entry,exit=exit,status=status,clusters=clusters))
}# }}}
###}}} phreg
###{{{ phregR
##' Fast Cox PH regression and calculations done in R to make play and adjustments easy
##'
##' Fast Cox PH regression with R implementation to play and adjust in R function: FastCoxPLstrataR
##'
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for cox model
##' @param weights weights for Cox score equations
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases FastCoxPLstrataR
##'
##' @export
phregR <- function(formula,data,offset=NULL,weights=NULL,...) {# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
} else pos.cluster <- NULL
if (!is.null(attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
pos.strata <- ts$terms
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else { strata.name <- NULL; pos.strata <- NULL}
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
res <- c(phreg01R(X,entry,exit,status,id,strata,offset,weights,strata.name,...),
list(call=cl,model.frame=m,formula=formula,strata.pos=pos.strata,cluster.pos=pos.cluster,
n=length(exit)))
class(res) <- "phreg"
res
}# }}}
phreg01R <- function(X,entry,exit,status,id=NULL,strata=NULL,offset=NULL,weights=NULL,
strata.name=NULL,cumhaz=TRUE,
beta,stderr=TRUE,method="NR",no.opt=FALSE,Z=NULL,propodds=NULL,AddGam=NULL,
case.weights=NULL,...) {# {{{
p <- ncol(X)
if (missing(beta)) beta <- rep(0,p)
if (p==0) X <- cbind(rep(0,length(exit)))
if (is.null(strata)) { strata <- rep(0,length(exit)); nstrata <- 1; strata.level <- NULL; } else {
strata.level <- levels(strata)
ustrata <- sort(unique(strata))
nstrata <- length(ustrata)
strata.values <- ustrata
if (is.numeric(strata)) strata <- fast.approx(ustrata,strata)-1 else {
strata <- as.integer(factor(strata,labels=seq(nstrata)))-1
}
}
if (is.null(offset)) offset <- rep(0,length(exit))
if (is.null(weights)) weights <- rep(1,length(exit))
strata.call <- strata
Zcall <- matrix(1,1,1) ## to not use for ZX products when Z is not given
if (!is.null(Z)) Zcall <- Z
## possible casewights to use for bootstrapping and other things
if (is.null(case.weights)) case.weights <- rep(1,length(exit))
trunc <- (!is.null(entry))
if (!trunc) entry <- rep(0,length(exit))
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(entry))-1;
## orginal id coding into integers
id.orig <- id+1;
dd <- .Call("FastCoxPrepStrata", entry,exit,status,X, id,trunc,strata,weights,offset,Zcall,case.weights,PACKAGE="mets")
dd$nstrata <- nstrata
obj <- function(pp,U=FALSE,all=FALSE) {# {{{
if (is.null(propodds) & is.null(AddGam))
cc <- system.time(
val <- with(dd, FastCoxPLstrataR(pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,caseweights))
)
else if (is.null(AddGam))
val <- with(dd, .Call("FastCoxPLstrataPO",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,propodds,PACKAGE="mets"))
else val <- with(dd, .Call("FastCoxPLstrataAddGam",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,
AddGam$theta,AddGam$dimthetades,AddGam$thetades,AddGam$ags,AddGam$varlink,AddGam$dimjumprv,AddGam$jumprv,AddGam$JumpsCauses,PACKAGE="mets"))
if (all) {
val$time <- dd$time
val$ord <- dd$ord+1
val$jumps <- dd$jumps+1
val$jumptimes <- val$time[val$jumps]
val$weightsJ <- dd$weights[val$jumps]
val$case.weights <- dd$case.weights[val$jumps]
val$strata.jumps <- val$strata[val$jumps]
val$nevent <- length(val$S0)
val$nstrata <- dd$nstrata
val$strata <- dd$strata
return(val)
}
with(val,structure(-ploglik,gradient=-gradient,hessian=-hessian))
}# }}}
opt <- NULL
if (p>0) {
if (no.opt==FALSE) {
if (tolower(method)=="nr") {
tim <- system.time(opt <- lava::NR(beta,obj,...))
opt$timing <- tim
opt$estimate <- opt$par
} else {
opt <- nlm(obj,beta,...)
opt$method <- "nlm"
}
cc <- opt$estimate; names(cc) <- colnames(X)
if (!stderr) return(cc)
val <- c(list(coef=cc),obj(opt$estimate,all=TRUE))
} else val <- c(list(coef=beta),obj(beta,all=TRUE))
} else {
val <- obj(0,all=TRUE)
}
se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL
II <- NULL
### computes Breslow estimator
if (cumhaz==TRUE) { # {{{
if (no.opt==FALSE & p!=0) {
II <- - tryCatch(solve(val$hessian),error=
function(e) matrix(0,nrow(val$hessian),ncol(val$hessian)) )
} else II <- matrix(0,p,p)
strata <- val$strata[val$jumps]
nstrata <- val$nstrata
jumptimes <- val$jumptimes
## Brewslow estimator
cumhaz <- cbind(jumptimes,cumsumstrata(1/val$S0,strata,nstrata))
if ((no.opt==FALSE & p!=0)) {
DLambeta.t <- apply(val$E/c(val$S0),2,cumsumstrata,strata,nstrata)
varbetat <- rowSums((DLambeta.t %*% II)*DLambeta.t)
### covv <- apply(covv*DLambeta.t,1,sum) Covariance is "0" by construction
} else varbetat <- 0
var.cumhaz <- cumsumstrata(1/val$S0^2,strata,nstrata)+varbetat
se.cumhaz <- cbind(jumptimes,(var.cumhaz)^.5)
colnames(cumhaz) <- c("time","cumhaz")
colnames(se.cumhaz) <- c("time","se.cumhaz")
} # }}}
else {cumhaz <- se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL}
res <- c(val,
list(cox.prep=dd,
strata.call=strata.call, strata.level=strata.level,
entry=entry,
exit=exit,
status=status,
p=p,
X=X,
offsets=offset,
weights=weights,
id=id.orig,
opt=opt,
cumhaz=cumhaz, se.cumhaz=se.cumhaz,
lcumhaz=lcumhaz, lse.cumhaz=lse.cumhaz,
II=II,strata.name=strata.name,propodds=propodds))
class(res) <- "phreg"
## also computing robust variance
if (p>0) {
phvar <- crossprod(iid(res))
colnames(phvar) <- rownames(phvar) <- names(res$coef)
res$var <- phvar
} else res$var <- 0
return(res)
}# }}}
##' @export
FastCoxPLstrataR <- function(beta, X, XX, Sign, Jumps, strata, nstrata, weights, offsets, ZX, caseweights)
{# {{{
p=length(beta)
strata=c(strata)
Xb = c(X %*% beta+offsets)
eXb = c(exp(Xb)*weights);
if (nrow((Sign))==length(eXb)) { ## Truncation
eXb = c(Sign)*eXb;
}
S0 = c(revcumsumstrata(eXb,strata,nstrata))
E=apply(eXb*X,2,revcumsumstrata,strata,nstrata)/S0;
Jumps=Jumps+1
E = E[Jumps,];
E2=.Call("vecMatMat",E,E)$vXZ;
XX2=apply(XX*eXb,2,revcumsumstrata,strata,nstrata)/S0;
## mat XX2=revcumsumstrataMatCols(XX,eXb,S0,strata,nstrata);
XX2 = XX2[Jumps,];
weightsJ=weights[Jumps];
caseweightsJ=caseweights[Jumps];
S0 = S0[Jumps];
grad = (X[Jumps,]-E); ## Score
val = (Xb[Jumps]-log(S0)); ## Partial log-likelihood
## colvec iweightsJ=1/weightsJ;
S02 = S0/(caseweightsJ*weightsJ); ## S0 with weights to estimate baseline
grad2= grad*(caseweightsJ*weightsJ); ## score with weights
gradient=apply(grad2,2,sum)
val2 = caseweightsJ*weightsJ*val; ## Partial log-likelihood with weights
hesst = -(XX2-E2); ## hessian contributions in jump times
hesst2 = hesst*(caseweightsJ*weightsJ); ## hessian over time with weights
hess2 = matrix(apply(hesst2,2,sum),p,p); ## hessian with weights
out=list(jumps=Jumps, ploglik=sum(val2),U=grad2,
gradient=matrix(gradient,1,p), hessian=hess2, hessianttime=hesst2, S2S0=XX2, E=E, S0=S02 )
return(out)
}# }}}
###}}}
###{{{ iid & Robust variances
##' @export
IC.phreg <- function(x,type="robust",all=FALSE,baseline=FALSE,...) {# {{{
if (baseline) {
if (inherits(x, "cifreg")) {
res <- IIDbaseline.cifreg(x, ...)$base.iid
} else {
res <- IIDbaseline.phreg(x, ...)$base.iid
}
tryCatch(rownames(res) <- rownames(x$X), error=function(...) NULL)
return(res*NROW(res))
}
classes1 <- "mlogit"
if ((length(class(x))==1) || inherits(x, classes1)) {
invhess <- -solve(x$hessian)
orig.order <- FALSE
if (is.null(x$propodds)) {
if (type=="robust") { # {{{ cox model
xx <- x$cox.prep
ii <- invhess
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
cumhaz <- cbind(xx$time,cumsumstrata(S0i,xx$strata,xx$nstrata))
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz[,2]-EdLam0)*rr*c(xx$weights)
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of iid variable
MGt <- MGt[oo,,drop=FALSE] ## sum after id later so not needed
id <- xx$id[oo]
} else id <- xx$id
} else {
MGt <- x$U; MG.base <- 1/x$S0;
}# }}}
} else { # {{{ prop-odds model logitSurv
xx <- x$cox.prep
ii <- invhess
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
cumhazA <- cumsumstratasum(S0i,xx$strata,xx$nstrata,type="all")
cumhaz <- c(cumhazA$sum)
cumhazm <- cumhazA$lagsum
###
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
rro <- c(exp(Z %*% coef(x) + xx$offset))
S0star <- revcumsumstrata(rr/(1+rro*cumhazm),xx$strata,xx$nstrata)
S0 <- revcumsumstrata(rr,xx$strata,xx$nstrata)
S1 <- apply(Z*rr,2,revcumsumstrata,xx$strata,xx$nstrata)
Et <- S1/c(S0)
lt <- apply((Z-Et)*c(rr*rro/(1+rro*cumhazm)),2,revcumsumstrata,xx$strata,xx$nstrata)
Estar <- S0star/S0
EstardLam <- cumsumstrata(Estar*S0i,xx$strata,xx$nstrata)
k <- exp(-EstardLam)
basecor <- apply(lt*c(k*S0i),2,revcumsumstrata,xx$strata,xx$nstrata)
basecor <- basecor/c(k*S0)
www <- x$propoddsW*x$weightsJ
U[xx$jumps+1,] <- U[xx$jumps+1,]-c(www)*basecor[xx$jumps+1,]
MGt <- U;
if (type=="robust") {
baseDLam0 <- apply(basecor*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz-EdLam0-baseDLam0)*rr*c(xx$weights) ### -baseIII
} else MGt <- MGt[xx$jumps+1,]
MG.base <- 1/x$S0;
id <- xx$id
}# }}}
ncluster <- NULL
if (type == "robust" & (!is.null(x$id) | any(x$entry > 0))) {
if (type == "martingale") id <- x$id[x$jumps]
### ii <- mets::cluster.index(id)
UU <- apply(MGt, 2, sumstrata, id, max(id) + 1)
### names of clusters given in call
ncluster <- nrow(UU)
} else {
UU <- MGt
}
res <- structure(UU %*% invhess, invhess = invhess, ncluster = ncluster)
if (is.null(colnames(res)))
colnames(res) <- names(coef(x))
tryCatch(rownames(res) <- rownames(x$X), error=function(...) NULL)
res <- res*NROW(res)
return(res)
} else if (inherits(x,c("cifreg","recreg","IPTW"))) {
if (inherits(x,c("IPTW"))) res <- x$IID else res <- x$iid
if (is.null(colnames(res)))
colnames(res) <- names(coef(x))
res <- res*NROW(res)
return(res)
}
} # }}}
##' @export IIDbaseline.phreg
IIDbaseline.phreg <- function(x,time=NULL,ft=NULL,fixbeta=NULL,beta.iid=NULL,...)
{# {{{
### sum_i int_0^t f(s)/S_0(s) dM_{ki}(s) - P(t) \beta_k
### with possible strata and cluster "k", and i in clusters
if (!inherits(x,"phreg")) stop("Must be phreg object\n");
if (is.null(time)) stop("Must give time for iid of baseline")
if (!is.null(x$propodds)) stop("Only for Cox model")
### sets fixbeta based on wheter xr has been optimized in beta (so cox case)
if (is.null(fixbeta))
if ((x$no.opt) | is.null(x$coef)) fixbeta<- 1 else fixbeta <- 0
xx <- x$cox.prep
btimexx <- c(1*(xx$time < time))
S0i2 <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
ww <- xx$caseweights*xx$weights
S0i2[xx$jumps+1] <- 1/(x$S0^2*ww[xx$jump+1])
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
### only up to time t for A
if (is.null(ft)) ft <- rep(1,length(xx$time))
if (is.matrix(ft)) ft <- c(ft)
cumhaz <- c(cumsumstrata(ft*S0i,xx$strata,xx$nstrata))
cumS0i2 <- c(cumsumstrata(ft*S0i2*btimexx,xx$strata,xx$nstrata))
if (fixbeta==0) {
EdLam0 <- apply(ft*E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
Ht <- apply(ft*E*S0i*btimexx,2,cumsumstrata,xx$strata,xx$nstrata)
} else Ht <- NULL
if (fixbeta==0) rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset)) else rr <- c(xx$sign*exp(xx$offset))
id <- xx$id
mid <- max(id)+1
MGAiid <- ft*S0i*btimexx-cumS0i2*rr*c(xx$weights)
MGtiid <- NULL
if (fixbeta==0) {# {{{
if (!is.null(beta.iid)) MGtiid <- beta.iid else {
invhess <- -solve(x$hessian)
MGt <- ft*U[,drop=FALSE]-(Z*cumhaz-EdLam0)*rr*c(xx$weights)
MGt <- MGt %*% invhess
MGtiid <- apply(MGt,2,sumstrata,id,mid)
}
## Ht efter strata
Htlast <- tailstrata(xx$strata,xx$nstrata)
HtS <- Ht[Htlast,,drop=FALSE]
}# }}}
### \hat beta - \beta = \sum_i \beta_i (iid)
### iid after baseline:
### \hat A_s-A_s=\sum_{i clusters} \sum_{j: i(j)=i, s(j)=s} \int_0^t 1/S_0 dM^s_{i,j} - P^s(t) \sum_i \beta_i
### = \sum_{i clusters} ( \sum_{j \in i(j)=i, s(j)=s} \int_0^t 1/S_0 dM^s_j - P^s(t) \beta_i )
## sum after id's within strata and order
MGAiids <- c()
sus <- sort(unique(xx$strata))
for (i in sus) {
wi <- which(xx$strata==i)
MGAiidl <- sumstrata(MGAiid[xx$strata==i],xx$id[xx$strata==i],mid)
if (fixbeta==0) {
UU <- apply(HtS[i+1,]*t(MGtiid),2,sum)
MGAiidl <- MGAiidl - UU
}
MGAiids <- cbind(MGAiids,MGAiidl)
}
MGAiid <- MGAiids
colnames(MGAiid) <- paste("strata",sus,sep="")
return(list(time=time,base.iid=MGAiid,strata=xx$strata,nstrata=xx$nstrata,
id=id,beta.iid=MGtiid,model.frame=x$model.frame,formula=x$formula))
} # }}}
##' @export
residuals.phreg <- function(object,cumsum=FALSE,...) {# {{{
orig.order <- FALSE
x <- object
if (is.null(x$propodds)) { # {{{ cox model
xx <- x$cox.prep
dN <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
dN[xx$jumps+1] <- 1
cumhaz <- cumsumstrata(S0i,xx$strata,xx$nstrata)
Z <- xx$X
if (is.null(coef(x)))
rr <- c(xx$sign*exp(xx$offset))
else
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
### dMartingale as a function of time and for all subjects to handle strata
Lamt <- (cumhaz)*rr*c(xx$weights)
dMGt <- dN-Lamt
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of iid variable
dMGt <- dMGt[oo,,drop=FALSE] ## sum after id later so not needed
id <- xx$id[oo]
} else id <- xx$id
} else { ## }}}
# {{{ prop-odds model logitSurv
xx <- x$cox.prep
dN <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
dN[xx$jumps+1] <- 1
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
cumhazA <- cumsumstratasum(S0i,xx$strata,xx$nstrata,type="all")
cumhaz <- c(cumhazA$sum)
cumhazm <- cumhazA$lagsum
###
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
rro <- c(exp(Z %*% coef(x) + xx$offset))
S0star <- revcumsumstrata(rr/(1+rro*cumhazm),xx$strata,xx$nstrata)
S0 <- revcumsumstrata(rr,xx$strata,xx$nstrata)
S1 <- apply(Z*rr,2,revcumsumstrata,xx$strata,xx$nstrata)
Et <- S1/c(S0)
lt <- apply((Z-Et)*c(rr*rro/(1+rro*cumhazm)),2,revcumsumstrata,xx$strata,xx$nstrata)
Estar <- S0star/S0
EstardLam <- cumsumstrata(Estar*S0i,xx$strata,xx$nstrata)
k <- exp(-EstardLam)
basecor <- apply(lt*c(k*S0i),2,revcumsumstrata,xx$strata,xx$nstrata)
basecor <- basecor/c(k*S0)
www <- x$propoddsW*x$weightsJ
U[xx$jumps+1,] <- U[xx$jumps+1,] - c(www)* basecor[xx$jumps+1,]
baseDLam0 <- apply(basecor*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz-EdLam0-baseDLam0)*rr*c(xx$weights)
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of data-set
MGt <- MGt[oo,,drop=FALSE]
id <- xx$id[oo]
} else id <- xx$id
}# }}}
ncluster <- NULL
if (!cumsum) {
mid <- max(id)+1
Mt <- sumstrata(dMGt,id,mid)
cumhaz <- sumstrata(Lamt,id,mid)
out <- list(residuals=c(Mt),cumhaz=c(cumhaz))
} else {
mid <- max(id)+1
out <- data.frame(dMGt=c(dMGt),Lamt=Lamt,status=dN,
time=c(xx$time),id=c(xx$id)+1,sign=xx$sign)
dsort(out) <- ~time+status+id-sign
Mt <- cumsumstrata(out$dMGt,out$id-1,mid)
cumhaz <- cumsumstrata(out$Lamt,out$id-1,mid)
out <- cbind(out,Mt,cumhaz)
out <- subset(out,sign==1)
ddrop(out) <- ~sign+dMGt+Lamt
}
return(out)
} # }}}
##' @export
robust.basehaz.phreg <- function(x,type="robust",fixbeta=NULL,...) {# {{{
IsdM <- squareintHdM(x,ft=NULL,fixbeta=fixbeta,...)
varA <- IsdM$varInt[x$jumps]
strata <- x$strata[x$jumps]
cumhaz <- x$cumhaz
se.cumhaz <- cbind(cumhaz[,1],varA^.5)
colnames(se.cumhaz) <- c("time","se.cumhaz")
return(list(cumhaz=cumhaz,se.cumhaz=se.cumhaz,strata=strata))
} # }}}
##' @export robust.phreg
robust.phreg <- function(x,fixbeta=NULL,...) {
if (is.null(fixbeta))
if ((x$no.opt) | is.null(x$coef)) fixbeta<- 1 else fixbeta <- 0
if (fixbeta==0) {
beta.iid <- iid(x)
robvar <- crossprod(beta.iid)
} else robvar <- beta.iid <- NULL
baseline <- robust.basehaz.phreg(x,fixbeta=fixbeta,...);
## add arguments so that we can call basehazplot.phreg
res <- c(x,list(beta.iid=beta.iid,robvar=robvar,robse.cumhaz=baseline$se.cumhaz))
class(res) <- "phreg"
return(res)
}
###}}}
###{{{ phreg: coef vcov print summary print.summary plot lines
##' @export
coef.phreg <- function(object,...) { ## {{{
object$coef
} ## }}}
##' @export
vcov.phreg <- function(object,...) { ## {{{
if ((length(class(object))==1) & inherits(object,"phreg")) {
res <- as.matrix(object$var) ### objectcrossprod(ii <- iid(object,...))
### attributes(res)$ncluster <- attributes(ii)$ncluster
### attributes(res)$invhess <- attributes(ii)$invhess
colnames(res) <- rownames(res) <- names(coef(object))
} else { ##if ((length(class(object))==2) & class(object)[2]=="cifreg") {
res <- as.matrix(object$var)
colnames(res) <- rownames(res) <- names(coef(object))
}
res
} ## }}}
##' @export
summary.phreg <- function(object,type=c("robust","martingale"),augment.type=c("var.augment.times","var.augment"),...) { ## {{{
expC <- cc <- ncluster <- V <- NULL
if (length(object$p)>0 & object$p>0 & (!object$no.opt)) {
I <- -solve(object$hessian)
if ( (length(class(object))==2) && ( inherits(object,c("cifreg","recreg")))) {
V <- object$var
ncluster <- object$ncluster ## nrow(object$Uiid)
if (!is.null(object$augmentation)) { V <- object[[augment.type[1]]]; }
} else { ## phreg
V <- vcov(object,type=type[1])
ncluster <- object$n
}
cc <- cbind(coef(object),diag(V)^0.5,diag(I)^0.5)
cc <- cbind(cc,2*(pnorm(abs(cc[,1]/cc[,2]),lower.tail=FALSE)))
colnames(cc) <- c("Estimate","S.E.","dU^-1/2","P-value")
if (length(class(object))==1) if (!is.null(ncluster <- attributes(V)$ncluster))
rownames(cc) <- names(coef(object))
expC <- exp(lava::estimate(coef=coef(object),vcov=V)$coefmat[,c(1,3,4),drop=FALSE])
}
Strata <- levels(object$strata)
n <- object$n
res <- list(coef=cc,n=n,nevent=object$nevent,strata=Strata,ncluster=ncluster,var=V,exp.coef=expC)
class(res) <- "summary.phreg"
res
} ## }}}
##' @export
summarybase.phreg <- function(object,robust=FALSE,...) { ## {{{
out <- summaryRecurrentobject(object,robust=robust,...)
class(out) <- "summary.recurrent"
return(out)
}# }}}
##' @export
print.phreg <- function(x,...) { ## {{{
cat("Call:\n")
dput(x$call)
print(summary(x),...)
} ## }}}
##' Plotting the baselines of stratified Cox
##'
##' Plotting the baselines of stratified Cox
##' @param x phreg object
##' @param ... Additional arguments to baseplot funtion
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases basehazplotO.phreg baseplot bplot basecumhaz plotConfRegion plotConfRegionSE plotstrata kmplot plotConfregion
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##'
##' par(mfrow=c(2,2))
##' plot(out1)
##' plot(out1,stratas=c(0,3))
##' plot(out1,stratas=c(0,3),col=2:3,lty=1:2,se=TRUE)
##' plot(out1,stratas=c(0),col=2,lty=2,se=TRUE,polygon=FALSE)
##' plot(out1,stratas=c(0),col=matrix(c(2,1,3),1,3),lty=matrix(c(1,2,3),1,3),se=TRUE,polygon=FALSE)
##' @aliases plotConfRegion plotConfRegionSE plotstrata kmplot plotConfregion
##' @export
plot.phreg <- function(x,...) baseplot(x,...)
##' @export
lines.phreg <- function(x,...,add=TRUE) plot(x,...,add=add)
##' @export
bplot <- function(x,...,add=TRUE) plot(x,...,add=add)
##' @export
print.summary.phreg <- function(x,max.strata=5,...) { ## {{{
if (length(class(x))==2 & inherits(x,"cifreg")) cat("Competing risks regression \n");
if (!is.null(x$propodds)) {
cat("Proportional odds model, log-OR regression \n");
} else cat("\n")
nn <- cbind(x$n, x$nevent)
rownames(nn) <- levels(x$strata); colnames(nn) <- c("n","events")
if (is.null(rownames(nn))) rownames(nn) <- rep("",NROW(nn))
if (length(x$strata)>max.strata) {
nn <- rbind(c(colSums(nn),length(x$strata)));
colnames(nn) <- c("n","events","stratas")
rownames(nn) <- ""
}
print(nn,quote=FALSE)
if (!is.null(x$ncluster)) cat("\n ", x$ncluster, " clusters\n",sep="")
if (!is.null(x$coef)) {
cat("coeffients:\n")
printCoefmat(x$coef,...)
cat("\n")
cat("exp(coeffients):\n")
printCoefmat(x$exp.coef,...)
}
cat("\n")
## for binreg ATE
if (!is.null(x$ateDR)) {
cat("Average Treatment effects (G-formula) :\n")
printCoefmat(x$ateG,...)
cat("\n")
cat("Average Treatment effects (double robust) :\n")
printCoefmat(x$ateDR,...)
cat("\n")
### if (!is.null(x$attc)) {
### cat("Average Treatment effects on Treated/Non-Treated (DR) :\n")
### printCoefmat(x$attc,...)
### cat("\n")
### }
}
cat("\n")
} ## }}}
###}}}
##' @export
conftype <- function(x,std.err,conf.type=c("log","plain"),restrict=c("positive","prob","none"),conf.int=0.95)
{ ## {{{
zval <- qnorm(1 - (1 - conf.int)/2, 0, 1)
if (conf.type[1] == "plain") {# {{{
temp1 <- x + zval * std.err
temp2 <- x - zval * std.err
if (restrict[1]=="prob") cix <- list(upper = pmin(temp1, 1), lower = pmax(temp2, 0), conf.type = "plain", conf.int = conf.int)
if (restrict[1]=="positive") cix <- list(upper = pmax(temp1, 0), lower = pmax(temp2, 0), conf.type = "plain", conf.int = conf.int)
if (restrict[1]=="none") cix <- list(upper = temp1, lower = temp2, conf.type = "plain", conf.int = conf.int)
}
if (conf.type[1] == "log") {
xx <- ifelse(x <= 0, NA, x)
temp1 <- ifelse(x <= 0, NA, exp(log(xx) + zval * std.err/xx))
temp2 <- ifelse(x <= 0, NA, exp(log(xx) - zval * std.err/xx))
if (restrict[1]=="prob") cix <- list(upper = pmin(temp1, 1), lower = temp2, conf.type = "log", conf.int = conf.int)
else cix <- list(upper = temp1, lower = temp2, conf.type = "log", conf.int = conf.int)
}
### if (conf.type[1] == "log-log") {
### who <- (x == 0 | x == 1)
### xx <- ifelse(who, NA, x)
### temp1 <- exp(-exp(log(-log(xx)) + zval * std.err/log(xx)))
### temp2 <- exp(-exp(log(-log(xx)) - zval * std.err/log(xx)))
### if (restrict[1]=="prob") {
### temp3 <- ifelse(x == 0, NA, 1)
### temp1 <- ifelse(who, temp3, temp1)
### temp2 <- ifelse(who, temp3, temp2)
### } else {
### cix <- list(upper = temp1, lower = temp2, conf.type = "log-log", conf.int = conf.int)
### }
### }# }}}
return(cix)
}# }}}
##' @export
basecumhaz <- function(x,type=c("list"),only=0,joint=0,cumhaz="cumhaz",
se.cumhaz="se.cumhaz",robust=FALSE,...) {# {{{
## all strata
stratobs <- x$strata[x$jumps]
ustratobs <- sort(unique(stratobs))
stratas <- 0:(x$nstrata-1)
se.cum <- cum <- c()
se.cum <- cum <- x[[cumhaz]]
if (robust==TRUE) {
## take robse if there otherwise stay with se.cumhaz
secum <- x$robse.cumhaz
if (is.null(secum)) secum <- x[[se.cumhaz]]
} else secum <- x[[se.cumhaz]]
if (is.null(secum)) nose <- TRUE else nose <- FALSE
out <- rep(list(NULL),x$nstrata)
if (length(ustratobs)>0)
for (i in ustratobs) {
if (!is.null(x[[cumhaz]])) {
cumhazard <- x[[cumhaz]][stratobs==i,,drop=FALSE]
nr <- nrow(cumhazard)
if (nr>=1) {
if (!nose) se.cum <- secum[stratobs==i,,drop=FALSE] else se.cum <- NULL
if (only==0) {
if (joint==0) out[[i+1]] <- list(cumhaz=cumhazard,se.cumhaz=se.cum,strata=i) else
out[[i+1]] <- list(cumhaz=cbind(cumhazard,se.cum[,2],i))
} else out[[i+1]] <- cumhazard
}
}
}
attr(out,"stratobs") <- ustratobs
return(out)
}# }}}
###
###basecumhaz <- function(x,type=c("list"),only=0,joint=0,robust=FALSE,...) {# {{{
### ## all strata
### stratobs <- x$strata[x$jumps]
### ustratobs <- sort(unique(stratobs))
### stratas <- 0:(x$nstrata-1)
###
### se.cum <- cum <- c()
### se.cum <- cum <- x$cumhaz
### if (robust==TRUE) {
### ## take robse if there otherwise stay with se.cumhaz
### secum <- x$robse.cumhaz
### if (is.null(secum)) secum <- x$se.cumhaz
### } else secum <- x$se.cumhaz
### if (is.null(secum)) nose <- TRUE else nose <- FALSE
###
### out <- rep(list(NULL),x$nstrata)
### if (length(ustratobs)>0)
### for (i in ustratobs) {
### if (!is.null(x$cumhaz)) {
### cumhazard <- x$cumhaz[stratobs==i,,drop=FALSE]
### nr <- nrow(cumhazard)
### if (nr>=1) {
### if (!nose) se.cum <- secum[stratobs==i,,drop=FALSE] else se.cum <- NULL
### if (only==0) {
### if (joint==0) out[[i+1]] <- list(cumhaz=cumhazard,se.cumhaz=se.cum,strata=i) else
### out[[i+1]] <- list(cumhaz=cbind(cumhazard,se.cum[,2],i))
### } else out[[i+1]] <- cumhazard
### }
### }
### }
###
### attr(out,"stratobs") <- ustratobs
### return(out)
###}# }}}
###
##' @export
baseplot <- function(x,se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,
lty=NULL,col=NULL,lwd=NULL,legend=TRUE,ylab="Cumulative hazard",xlab="time",
polygon=TRUE,level=0.95,stratas=NULL,robust=FALSE,cumhaz="cumhaz",se.cumhaz="se.cumhaz",
conf.type=c("log","plain"),restrict = c("positive","prob", "none"),...) {# {{{
base <- basecumhaz(x,joint=1,robust=robust,cumhaz=cumhaz,se.cumhaz=se.cumhaz)
nstrata <- x$nstrata
stratobs <- attr(base,"stratobs")
###
if (is.null(stratas)) stratas <- stratobs else {
wm <- match(stratas,stratobs)
wm <- wm[!is.na(wm)]
if (length(wm)==0) stratas <- rep(0,0) else stratas <- stratobs[wm]
}
## all confidence intervals for relevant strata to make ylim
if (length(stratobs)>0) {
xx <- conftype(x$cumhaz[,2],x$se.cumhaz[,2],conf.type=conf.type[1],restrict=restrict[1],conf.int=level)
if (is.null(xlim)) {
xlim <- range(x$cumhaz[,1],na.rm=TRUE)
}
if (se) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz)) stop("phreg must be with cumhazard=TRUE\n");
rrse <- range(c(xx$lower,xx$upper),na.rm=TRUE)
if (is.null(ylim))
{
if (Inf %in% abs(rrse)) ylim <- range(x$cumhaz[,2],na.rm=TRUE) else ylim <- rrse
}
} else {
if (is.null(ylim)) ylim <- range(x$cumhaz[,2],na.rm=TRUE)
}
## all strata
## {{{
ltys <- lty; cols <- col; lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) lty <- ltys <- 1:length(stratas)
if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) col <- cols <- 1:length(stratas)
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas)) else cols <- col
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwd <- lwds <- rep(1,length(stratas))
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas)) else lwds <- lwd
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
## }}}
first <- 1
j <- 1
for (i in stratas) {
if (!is.null(base[[i+1]])) {
cumhazard <- base[[i+1]]$cumhaz
if (nrow(cumhazard)>1) {
if (add | first==0) lines(cumhazard,type="s",lty=ltys[j,1],col=cols[j,1],lwd=lwds[j,1])
else {
first <- 0
plot(cumhazard,type="s",lty=ltys[j,1],col=cols[j,1],lwd=lwds[j,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
xx <- conftype(cumhazard[,2],cumhazard[,3],conf.type=conf.type[1],restrict=restrict[1],conf.int=level)
nl <- cbind(cumhazard[,1],xx$lower); ul <- cbind(cumhazard[,1],xx$upper)
if (!polygon) {
lines(nl,type="s",lty=ltys[j,2],col=cols[j,2],lwd=lwds[i,2],...)
lines(ul,type="s",lty=ltys[j,3],col=cols[j,3],lwd=lwds[j,3],...)
} else plotConfRegion(nl[,1],cbind(nl[,2],ul[,2]),col=cols[j,1])
}
}
}
j <- j+1
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
} else {
if (!add) plot(0,0,ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
}# }}}
###{{{ phreg: basehazplot.phreg predictO.phreg plotO.predictphreg (old)
##' Plotting the baselines of stratified Cox
##'
##' Plotting the baselines of stratified Cox
##' @param x phreg object
##' @param se to include standard errors
##' @param time to plot for specific time variables
##' @param add to add to previous plot
##' @param ylim to give ylim
##' @param xlim to give xlim
##' @param lty to specify lty of components
##' @param col to specify col of components
##' @param lwd to specify lwd of components
##' @param legend to specify col of components
##' @param ylab to specify ylab
##' @param xlab to specify xlab
##' @param polygon to get standard error in shaded form
##' @param level of standard errors
##' @param stratas wich strata to plot
##' @param robust to use robust standard errors if possible
##' @param conf.type "plain" or "log" transformed
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases basehazplot.phreg
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##'
##' par(mfrow=c(2,2))
##' plot(out1)
##' plot(out1,stratas=c(0,3))
##' plot(out1,stratas=c(0,3),col=2:3,lty=1:2,se=TRUE)
##' plot(out1,stratas=c(0),col=2,lty=2,se=TRUE,polygon=FALSE)
##' plot(out1,stratas=c(0),col=matrix(c(2,1,3),1,3),lty=matrix(c(1,2,3),1,3),se=TRUE,polygon=FALSE)
##' @export
basehazplot.phreg <- function(x,se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,
lwd=NULL,legend=TRUE,ylab=NULL,xlab=NULL,polygon=TRUE,level=0.95,
stratas=NULL,robust=FALSE,conf.type=c("plain","log"),...) {# {{{
if (inherits(x,"phreg") & is.null(ylab)) ylab <- "Cumulative hazard"
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
rr <- range(x$cumhaz[,-1])
strat <- x$strata[x$jumps]
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$cumhaz[,1])
if (se==TRUE) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz)) stop("phreg must be with cumhazard=TRUE\n");
if (conf.type[1]=="plain")
rrse <- range(c(x$cumhaz[,-1]+level*x$se.cumhaz[,-1]))
else { ## type="log"
relse <- exp(level*x$se.cumhaz[,-1]/x$cumhaz[,-1])
rrse <- range(x$cumhaz[,-1]/relse,x$cumhaz[,-1]*relse)
}
if (inherits(x,"km")) rrse <- c(min(x$lower,na.rm=TRUE),1)
if (is.null(ylimo)) ylim <- rrse
}
## all strata
if (is.null(stratas)) stratas <- 0:(x$nstrata-1)
ltys <- lty
cols <- col
lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) lty <- ltys <- 1:length(stratas)
if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) col <- cols <- 1:length(stratas)
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas)) else cols <- col
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwd <- lwds <- rep(1,length(stratas))
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas)) else lwds <- lwd
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
first <- 0
for (i in seq(stratas)) {
j <- stratas[i]
cumhazard <- x$cumhaz[strat==j,,drop=FALSE]
if (!is.null(cumhazard)) {
if (nrow(cumhazard)>1) {
if (add | first==1)
lines(cumhazard,type="s",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1])
else {
first <- 1
plot(cumhazard,type="s",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
if (robust==TRUE) secumhazard <- x$robse.cumhaz[strat==j,,drop=FALSE]
else secumhazard <- x$se.cumhaz[strat==j,,drop=FALSE]
xx <- cumhazard[,2]
std.err <- secumhazard[,2]
if (conf.type[1] == "log") {
temp1 <- exp(log(xx) + level * std.err/xx)
temp2 <- exp(log(xx) - level * std.err/xx)
ul = cbind(cumhazard[,1],temp1);
nl <- cbind(cumhazard[,1],temp2);
}
if (conf.type[1] == "plain") {
ul <-cbind(cumhazard[,1],cumhazard[,2]+level*secumhazard[,2])
nl <-cbind(cumhazard[,1],cumhazard[,2]-level*secumhazard[,2])
}
if (inherits(x,"km")) { ul[,2] <- x$upper[x$strata==j];
nl[,2] <- x$lower[x$strata==j];
wna <- which(is.na(ul[,2]))
ul[wna,2] <- 0
nl[wna,2] <- 0
}
if (!polygon) {
lines(nl,type="s",lty=ltys[i,2],col=cols[i,2],lwd=lwds[i,2],...)
lines(ul,type="s",lty=ltys[i,3],col=cols[i,3],lwd=lwds[i,3],...)
} else plotConfRegion(nl[,1],cbind(nl[,2],ul[,2]),col=cols[j+1])
}
}
}
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
}# }}}
##' @export
predictO.phreg <- function(object,newdata,times=NULL,individual.time=FALSE,tminus=FALSE,se=TRUE,robust=FALSE,conf.type="log",conf.int=0.95,km=FALSE,...)
{# {{{ default is all time-points from the object
### take baseline and strata from object# {{{
ocumhaz <- object$cumhaz
jumptimes <- ocumhaz[,1]
chaz <- ocumhaz[,2]
if (is.null(object$nstrata)) { ## try to make more robust
nstrata <- 1;
strata <- rep(1,length(jumptimes))
} else {
nstrata <- object$nstrata
strata <- object$strata[object$jumps]
}
if (length(jumptimes)==0) se <- FALSE
if (se) {
if (!robust) {
se.chaz <- object$se.cumhaz[,2]
varbeta <- object$ihessian
if (!object$no.opt) Pt <- apply(object$E/c(object$S0),2,cumsumstrata,strata,nstrata)
else Pt <- 0
} else {
if ((object$no.opt) | is.null(object$coef)) fixbeta<- 1 else fixbeta <- 0
IsdM <- squareintHdM(object,ft=NULL,fixbeta=fixbeta,...)
###
se.chaz <- IsdM$varInt[object$jumps]^.5
covv <- IsdM$covv[object$jumps,,drop=FALSE]
varbeta <- IsdM$vbeta
Pt <- IsdM$Ht[object$jumps,,drop=FALSE]
}
} # }}}
### setting up newdata with factors and strata
desX <- readPhreg(object,newdata)
X <- desX$X
strataNew <- desX$strata
if (is.null(times)) times <- sort(unique(c(object$exit)))
if (individual.time & is.null(times)) times <- c(object$exit)
if (individual.time & length(times)==1) times <- rep(times,length(object$exit))
se.cumhaz <- NULL
if (!individual.time) {
pcumhaz <- surv <- matrix(0,nrow(X),length(times))
if (se) se.cumhaz <- matrix(0,nrow(X),length(times))
} else {
pcumhaz <- surv <- matrix(0,nrow(X),1)
if (se) se.cumhaz <- matrix(0,nrow(X),1)
}
hazt <- length(times)
for (j in unique(strataNew)) {
### where <- sindex.prodlim(c(0,jumptimes[strata==j]),times,strict=tminus)
where <- predictCumhaz(c(0,jumptimes[strata==j]),times,type="left",tminus=tminus)
### if (sum(abs(whereO-where))>=1) {
### print(c(0,jumptimes[strata==j]))
### print(times)
### print(cbind(where,whereO,where-whereO,times,c(0,jumptimes[strata==j])[where],c(0,jumptimes[strata==j])[whereO]))
### print("sindex.prodlim - phreg-predict");
### }
plhazt <- hazt <- c(0,chaz[strata==j])
if (km) { plhazt <- suppressWarnings(c(1,exp(cumsum(log(1-diff(hazt)))))); plhazt[is.na(hazt)] <- 0 }
if (se) se.hazt <- c(0,se.chaz[strata==j])
Xs <- X[strataNew==j,,drop=FALSE]
if (object$p==0) RR <- rep(1,nrow(Xs)) else RR <- c(exp( Xs %*% coef(object)))
if (se) { # {{{ based on Hazard's
if (object$p>0) {
Ps <- Pt[strata==j,,drop=FALSE]
Ps <- rbind(0,Ps)[where,,drop=FALSE]
Xbeta <- Xs %*% varbeta
seXbeta <- rowSums(Xbeta*Xs)^.5
cov2 <- cov1 <- Xbeta %*% t(Ps*hazt[where])
if (robust) {
covvs <- covv[strata==j,,drop=FALSE]
covvs <- rbind(0,covvs)[where,,drop=FALSE]
covv1 <- Xs %*% t((covvs*hazt[where]))
cov1 <- cov1-covv1
}
} else cov1 <- 0
}# }}}
haztw <- hazt[where]
if (se) se.haztw <- se.hazt[where]
if (is.null(object$propodds)) {
plhaztw <- plhazt[where]
if (!individual.time) pcumhaz[strataNew==j,] <- RR%o%haztw else pcumhaz[strataNew==j,] <- RR*haztw[strataNew==j]
if (!km) {
if (!individual.time) surv[strataNew==j,] <- exp(- RR%o%haztw)
else surv[strataNew==j,] <- exp(-RR*haztw[strataNew==j])
} else {
if (!individual.time) surv[strataNew==j,] <- exp( RR %o% log(plhaztw))
else surv[strataNew==j,] <- plhaztw[strataNew==j]^RR
}
} else {
if (!individual.time) surv[strataNew==j,] <- 1/(1+RR%o%haztw)
else surv[strataNew==j,] <- 1/(1+RR*haztw[strataNew==j])
}
if (se) {# {{{
if (object$p>0) {
if (!individual.time) se.cumhaz[strataNew==j,] <-
((RR %o% se.haztw)^2+(c(RR*seXbeta) %o% haztw)^2-2*RR^2*cov1)^.5
else se.cumhaz[strataNew==j,] <- RR* (se.haztw^2+(c(seXbeta)*haztw)^2-2*diag(cov1))^.5
} else {
if (!individual.time) se.cumhaz[strataNew==j,] <- RR %o% (se.haztw)
else se.cumhaz[strataNew==j,] <- RR* se.haztw[strataNew==j]
}
}# }}}
}
zval <- qnorm(1 - (1 - conf.int)/2, 0, 1)
std.err <- se.cumhaz
cisurv <- list()
cisurv$upper <- NULL
cisurv$lower <- NULL
### different conf-types for surv
if (se) {# {{{
if (conf.type == "plain") {# {{{
temp1 <- surv + zval * std.err * surv
temp2 <- surv - zval * std.err * surv
cisurv <- list(upper = pmin(temp1, 1), lower = pmax(temp2,
0), conf.type = "plain", conf.int = conf.int)
}
if (conf.type == "log") {
xx <- ifelse(surv == 0, 1, surv)
temp1 <- ifelse(surv == 0, NA, exp(log(xx) + zval * std.err))
temp2 <- ifelse(surv == 0, NA, exp(log(xx) - zval * std.err))
cisurv <- list(upper = pmin(temp1, 1), lower = temp2,
conf.type = "log", conf.int = conf.int)
}
if (conf.type == "log-log") {
who <- (surv == 0 | surv == 1)
temp3 <- ifelse(surv == 0, NA, 1)
xx <- ifelse(who, 0.1, surv)
temp1 <- exp(-exp(log(-log(xx)) + zval * std.err/log(xx)))
temp1 <- ifelse(who, temp3, temp1)
temp2 <- exp(-exp(log(-log(xx)) - zval * std.err/log(xx)))
temp2 <- ifelse(who, temp3, temp2)
cisurv <- list(upper = temp1, lower = temp2,
conf.type = "log-log", conf.int = conf.int)
}# }}}
}# }}}
if (object$p>0) RR <- exp(X %*% coef(object)) else RR <- rep(1,nrow(X))
### non-cox setting
if (!is.null(object$propodds)) pcumhaz <- -log(surv)
out <- list(surv=surv,times=times,
surv.upper=cisurv$upper,surv.lower=cisurv$lower,cumhaz=pcumhaz,se.cumhaz=se.cumhaz,strata=strataNew,X=X, RR=RR)
if (length(class(object))==2 && ( substr(class(object)[2],1,3)=="cif" | substr(class(object)[1],1,3)=="cif")) {
out <- c(out,list(cif=1-out$surv,cif.lower=1-out$surv.upper, cif.upper=1-out$surv.lower))
}
if (length(class(object))==2 && ( substr(class(object)[2],1,3)=="rec" | substr(class(object)[1],1,3)=="rec")) {
out <- c(out,list(mean=-log(out$surv),mean.lower=-log(out$surv.upper),mean.upper=-log(out$surv.lower)))
}
class(out) <- c("predictphreg",class(object)[1])
### class(out) <- c("predictphreg")
### if (length(class(object))==2) class(out) <- c("predictphreg",class(object)[1])
return(out)
}# }}}
##' @export
plotO.predictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,type=c("default","surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (type[1]=="default" & (class(x)[2]=="phreg")) { if (is.null(ylab)) ylab <- "Survival probability"; type <- "surv"}
if (type[1]=="default" & (class(x)[2]=="cifreg")) {if (is.null(ylab)) ylab <- "Cumulative probability"; type <- "cif"}
if (type[1]=="default" & (class(x)[2]=="recreg")) {if (is.null(ylab)) ylab <- "Cumulative mean"; type <- "cumhaz"}
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
if (type[1]=="cif") rr <- c(0,1)
if (type[1]=="surv") rr <- c(0,1)
if (type[1]=="cumhaz") rr <- range(c(0,x$cumhaz))
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
if (se==TRUE) {
if (is.null(x$se.cumhaz)) stop("predict.phreg must be with se=TRUE\n");
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower))
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower))
if (type[1]=="cumhaz") {
cumhaz.upper <- x$cumhaz+level*x$se.cumhaz
cumhaz.lower <- x$cumhaz-level*x$se.cumhaz
rrse <- range(c(cumhaz.upper,cumhaz.lower))
}
if (type[1]=="surv") rrse <- c(0,1)
if (type[1]=="cif") rrse <- c(0,1)
if (type[1]=="cumhaz") rrse <- c(max(0,rrse[1]),rrse[2])
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
recreg <- cifreg <- FALSE
if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="cif")) cifreg <- TRUE
### if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="rec")) recreg <- TRUE
if (type[1]=="surv") {
xx <- x$surv
if (cifreg) xx <- x$cif
if (recreg) xx <- x$mean
} else if (type[1]=="cif") {
xx <- 1-x$surv
} else xx <- x$cumhaz
if (se) {
if (type[1]=="surv") {
upper <- x$surv.upper; lower <- x$surv.lower
if (cifreg) { upper <- x$cif.upper; lower <- x$cif.lower}
if (recreg) { upper <- x$mean.upper; lower <- x$mean.lower}
} else if (type[1]=="cif") {
upper <- 1-x$surv.lower; lower <- 1-x$surv.upper
} else { upper <- cumhaz.upper; lower <- cumhaz.lower}
}
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###}}} plot
##' @export
plotpredictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,
type=c("surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(xlab)) xlab <- "time"
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
ylimo <- ylim
nlower <- paste(type[1],".lower",sep="")
nupper <- paste(type[1],".upper",sep="")
xx <- x[[type[1]]]
if (se==TRUE) {
upper <- x[[nupper]]
lower <- x[[nlower]]
if (is.null(x$se.cumhaz)) stop("predict.phreg/cifreg/recreg must be with se=TRUE\n");
rrse <- range(c(0,x[[nlower]],x[[nupper]]),na.rm=TRUE)
if (is.null(ylimo)) ylim <- rrse
} else {
rrse <- range(c(xx),na.rm=TRUE)
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###{{{ predict.phreg print.predict plot.predict.phreg
##' Predictions from proportional hazards model
##'
##' @param object phreg object
##' @param newdata data.frame
##' @param times Time where to predict variable, default is all time-points from the object sorted
##' @param individual.time to use one (individual) time per subject, and then newdata and times have same length and makes only predictions for these individual times.
##' @param tminus to make predictions in T- that is strictly before given times, useful for IPCW techniques
##' @param se with standard errors and upper and lower confidence intervals.
##' @param robust to get robust se's also default for most functions (uses robse.cumhaz otherwise se.cumhaz).
##' @param conf.type transformation for suvival estimates, default is log
##' @param conf.int significance level
##' @param km to use Kaplan-Meier product-limit for baseline \deqn{S_{s0}(t)= (1 - dA_{s0}(t))}, otherwise take exp of cumulative baseline.
##' @param ... Additional arguments to plot functions
##' @aliases headstrata tailstrata revcumsumstrata revcumsumstratasum cumsumstrata sumstrata covfr covfridstrata covfridstrataCov cumsumidstratasum cumsumidstratasumCov cumsumstratasum revcumsum revcumsumidstratasum revcumsumidstratasumCov robust.basehaz.phreg matdoubleindex mdi cumsum2strata revcumsum2strata revcumsum2stratafdN
##' @export
predict.phreg <- function(object,newdata,times=NULL,individual.time=FALSE,tminus=FALSE,se=TRUE,robust=FALSE,conf.type="log",conf.int=0.95,km=FALSE,...)
{# {{{ default is all time-points from the object
### take baseline and strata from object# {{{
ocumhaz <- object$cumhaz
jumptimes <- ocumhaz[,1]
chaz <- ocumhaz[,2]
if (is.null(object$nstrata)) { ## try to make more robust
nstrata <- 1;
strata <- rep(1,length(jumptimes))
} else {
nstrata <- object$nstrata
strata <- object$strata[object$jumps]
}
if (length(jumptimes)==0) se <- FALSE
if (se) {
if (!robust) {
se.chaz <- object$se.cumhaz[,2]
varbeta <- object$ihessian
if (!object$no.opt) Pt <- apply(object$E/c(object$S0),2,cumsumstrata,strata,nstrata)
else Pt <- 0
} else { ## only relevant for phreg objects
if ((object$no.opt) | is.null(object$coef)) fixbeta<- 1 else fixbeta <- 0
IsdM <- squareintHdM(object,ft=NULL,fixbeta=fixbeta,...)
###
se.chaz <- IsdM$varInt[object$jumps]^.5
covv <- IsdM$covv[object$jumps,,drop=FALSE]
varbeta <- IsdM$vbeta
Pt <- IsdM$Ht[object$jumps,,drop=FALSE]
}
} # }}}
### setting up newdata with factors and strata
desX <- readPhreg(object,newdata)
X <- desX$X
strataNew <- desX$strata
if (is.null(times)) times <- sort(unique(c(object$exit)))
if (individual.time & is.null(times)) times <- c(object$exit)
if (individual.time & length(times)==1) times <- rep(times,length(object$exit))
se.cumhaz <- NULL
if (!individual.time) {
pcumhaz <- surv <- matrix(0,nrow(X),length(times))
if (se) se.cumhaz <- matrix(0,nrow(X),length(times))
} else {
pcumhaz <- surv <- matrix(0,nrow(X),1)
if (se) se.cumhaz <- matrix(0,nrow(X),1)
}
hazt <- length(times)
for (j in unique(strataNew)) {
where <- predictCumhaz(c(0,jumptimes[strata==j]),times,type="left",tminus=tminus)
plhazt <- hazt <- c(0,chaz[strata==j])
if (km) { plhazt <- suppressWarnings(c(1,exp(cumsum(log(1-diff(hazt)))))); plhazt[is.na(hazt)] <- 0 }
if (se) se.hazt <- c(0,se.chaz[strata==j])
Xs <- X[strataNew==j,,drop=FALSE]
if (object$p==0) RR <- rep(1,nrow(Xs)) else RR <- c(exp( Xs %*% coef(object)))
if (se) { # {{{ based on Hazard's
if (object$p>0) {
Ps <- Pt[strata==j,,drop=FALSE]
Ps <- rbind(0,Ps)[where,,drop=FALSE]
Xbeta <- Xs %*% varbeta
seXbeta <- rowSums(Xbeta*Xs)^.5
cov2 <- cov1 <- Xbeta %*% t(Ps*hazt[where])
if (robust) {
covvs <- covv[strata==j,,drop=FALSE]
covvs <- rbind(0,covvs)[where,,drop=FALSE]
covv1 <- Xs %*% t((covvs*hazt[where]))
cov1 <- cov1-covv1
}
} else cov1 <- 0
}# }}}
haztw <- hazt[where]
if (se) se.haztw <- se.hazt[where]
if (is.null(object$propodds)) {
plhaztw <- plhazt[where]
if (!individual.time) pcumhaz[strataNew==j,] <- RR%o%haztw else pcumhaz[strataNew==j,] <- RR*haztw[strataNew==j]
if (!km) {
if (!individual.time) surv[strataNew==j,] <- exp(- RR%o%haztw)
else surv[strataNew==j,] <- exp(-RR*haztw[strataNew==j])
} else {
if (!individual.time) surv[strataNew==j,] <- exp( RR %o% log(plhaztw))
else surv[strataNew==j,] <- plhaztw[strataNew==j]^RR
}
} else {
if (!individual.time) surv[strataNew==j,] <- 1/(1+RR%o%haztw)
else surv[strataNew==j,] <- 1/(1+RR*haztw[strataNew==j])
}
if (se) {# {{{
if (object$p>0) {
if (!individual.time) se.cumhaz[strataNew==j,] <-
((RR %o% se.haztw)^2+(c(RR*seXbeta) %o% haztw)^2-2*RR^2*cov1)^.5
else se.cumhaz[strataNew==j,] <- RR* (se.haztw^2+(c(seXbeta)*haztw)^2-2*diag(cov1))^.5
} else {
if (!individual.time) se.cumhaz[strataNew==j,] <- RR %o% (se.haztw)
else se.cumhaz[strataNew==j,] <- RR* se.haztw[strataNew==j]
}
}# }}}
}
if (se) {
cibase <- conftype(pcumhaz,se.cumhaz,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
cisurv <- conftype(surv,surv*se.cumhaz,conf.type=conf.type[1],restrict="prob",conf.int=conf.int)
} else {
cibase <- list(upper=NULL,lower=NULL,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
cisurv <- list(upper=NULL,lower=NULL,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
}
if (object$p>0) RR <- exp(X %*% coef(object)) else RR <- rep(1,nrow(X))
### non-cox setting
if (!is.null(object$propodds)) pcumhaz <- -log(surv)
out <- list(surv=surv,times=times,
surv.upper=cisurv$upper,surv.lower=cisurv$lower,cumhaz=pcumhaz,se.cumhaz=se.cumhaz,
se.surv=surv*se.cumhaz,se.cif=surv*se.cumhaz,
cif=1-surv,cif.lower=1-cisurv$upper,cif.upper=1-cisurv$lower,
cumhaz.upper=cibase$upper,cumhaz.lower=cibase$lower,strata=strataNew,X=X,RR=RR)
class(out) <- c("predictphreg",class(object)[1])
return(out)
}# }}}
##' @export
summary.predictphreg <- function(object,times=NULL,type=c("cif","cumhaz","surv")[3],np=10,...) {# {{{
ret <- summary.predictrecreg(object,times=times,type=type[1],np=np,...)
return(ret)
}# }}}
##' @export
plot.predictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,type=c("surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (is.null(xlab)) xlab <- "time"
if (type[1]=="cif") rr <- c(0,1)
if (type[1]=="surv") rr <- c(0,1)
if (type[1]=="cumhaz") rr <- range(c(0,x$cumhaz))
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
if (se==TRUE) {
if (is.null(x$se.cumhaz)) stop("predict.phreg must be with se=TRUE\n");
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower,na.rm=TRUE))
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower,na.rm=TRUE))
if (type[1]=="cumhaz") {
cumhaz.upper <- x$cumhaz+level*x$se.cumhaz
cumhaz.lower <- x$cumhaz-level*x$se.cumhaz
rrse <- range(c(cumhaz.upper,cumhaz.lower),na.rm=TRUE)
}
if (type[1]=="surv") rrse <- c(0,1)
if (type[1]=="cif") rrse <- c(0,1)
if (type[1]=="cumhaz") rrse <- c(max(0,rrse[1]),rrse[2])
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
recreg <- cifreg <- FALSE
if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="cif")) cifreg <- TRUE
### if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="rec")) recreg <- TRUE
if (type[1]=="surv") {
xx <- x$surv
if (cifreg) xx <- x$cif
if (recreg) xx <- x$mean
} else if (type[1]=="cif") {
xx <- 1-x$surv
} else xx <- x$cumhaz
if (se) {
if (type[1]=="surv") {
upper <- x$surv.upper; lower <- x$surv.lower
if (cifreg) { upper <- x$cif.upper; lower <- x$cif.lower}
if (recreg) { upper <- x$mean.upper; lower <- x$mean.lower}
} else if (type[1]=="cif") {
upper <- 1-x$surv.lower; lower <- 1-x$surv.upper
} else { upper <- cumhaz.upper; lower <- cumhaz.lower}
}
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###}}} predict
# {{{ Restricted mean for stratified Kaplan-Meier with martingale standard errors
##' Restricted mean for stratified Kaplan-Meier or Cox model with martingale standard errors
##'
##' Restricted mean for stratified Kaplan-Meier or stratified Cox with martingale
##' standard error. Standard error is computed using linear interpolation between
##' standard errors at jump-times. Plots gives restricted mean at all times.
##' Years lost can be computed based on this and decomposed into years lost for
##' different causes using the cif.yearslost function that is based on
##' integrating the cumulative incidence functions.
##' One particular feature of these functions are that the restricted mean and years-lost are
##' computed for all event times as functions and can be plotted/viewed. When times are given and beyond
##' the last event time withn a strata the curves are extrapolated using the estimates of
##' cumulative incidence.
##'
##' @param x phreg object
##' @param times possible times for which to report restricted mean
##' @param covs possible covariate for Cox model
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @examples
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' out1 <- phreg(Surv(time,cause!=0)~strata(tcell,platelet),data=bmt)
##'
##' rm1 <- resmean.phreg(out1,times=10*(1:6))
##' summary(rm1)
##' par(mfrow=c(1,2))
##' plot(rm1,se=1)
##' plot(rm1,years.lost=TRUE,se=1)
##'
##' ## years.lost decomposed into causes
##' drm1 <- cif.yearslost(Event(time,cause)~strata(tcell,platelet),data=bmt,times=10*(1:6))
##' par(mfrow=c(1,2)); plot(drm1,cause=1,se=1); plot(drm1,cause=2,se=1);
##' summary(drm1)
##' @export
##' @aliases cif.yearslost rmst.phreg
resmean.phreg <- function(x,times=NULL,covs=NULL,...)
{# {{{
ii <- invhess <- x$II
if (!is.null(times)) {
tt <- expand.grid(times,0:(x$nstrata-1))
mm <- cbind(x$jumptimes,x$strata.jumps,1)
mm <- rbind(mm,cbind(tt[,1],tt[,2],0))
ord <- order(mm[,1])
mm <- mm[ord,]
phd <- which(mm[,3]==1)
newtimes <- which(mm[,3]==0)
S0i <- S0i2 <- rep(0,nrow(mm))
S0i[phd] <- c(1/x$S0)
S0ii2 <- c(1/(x$S0*(x$S0-1)))
S0ii2[x$S0==1] <- 0
S0i2[phd] <- S0ii2
strata.jumps <- mm[,2]
nstrata <- x$nstrata;
jumptimes <- mm[,1]
E <- matrix(0,nrow(mm),x$p)
E[phd,] <- x$E
} else {
strata.jumps <- x$strata.jumps;
nstrata <- x$nstrata;
jumptimes <- x$jumptimes;
S0i <- c(1/x$S0)
S0i2 <- c(1/(x$S0*(x$S0-1)))
S0i2[x$S0==1] <- 0
E <- x$E
}
cumhaz <- cumsumstrata(S0i,strata.jumps,nstrata)
var.cumhazMG <- cumsumstrata(S0i2,strata.jumps,nstrata)
## baseline survival
km <- exp(cumsumstratasum(log(1-S0i),strata.jumps,nstrata,type="lagsum"))
## If covariates compute rr = exp( X beta) and adjust km
if (!is.null(covs)) { rr <- exp(sum(covs * coef(x))) } else rr <- 1
km <- km^rr
## start integral in 0
dtime <- c(diffstrata(jumptimes,strata.jumps,nstrata))
intkm <- cumsumstrata( c(km)*dtime,strata.jumps,nstrata)
### variance of baseline term
var.intkmcumhaz <- cumsumstrata(intkm*S0i2,strata.jumps,nstrata)
var.intkm2cumhaz <- cumsumstrata(intkm^2*S0i2,strata.jumps,nstrata)
var.resmean <- intkm^2*var.cumhazMG+var.intkm2cumhaz-2*intkm*var.intkmcumhaz
if (!is.null(x$coef)) {
intp <- apply(E*S0i,2,cumsumstratasum,strata.jumps,nstrata,type="lagsum")
intpS <- apply(intp*c(km)*dtime,2,cumsumstrata,strata.jumps,nstrata)
Dbeta <- -intpS
if (!is.null(covs)) {
intLam <- cumsumstratasum(S0i,strata.jumps,nstrata,type="lagsum")
intLamS <- cumsumstrata( c(intLam)*km*dtime,strata.jumps,nstrata)
Dbeta <- Dbeta + matrix(covs,nrow=nrow(intLam),ncol=length(covs),byrow=TRUE)*c(intLamS)
}
varbetat <- rowSums((Dbeta %*% x$II)*Dbeta)
var.resmean <- rr^2*(var.resmean+varbetat)
} else {
varbetat <- 0
}
time<- jumptimes
meanm <- cbind(time,intkm)
se.resmean <- var.resmean^.5
se.resmean[var.resmean<0] <- 0
se.mm <- cbind(time,se.resmean)
### make output at specified times
if (!is.null(times)) {
intkmtimes <- meanm[newtimes,,drop=FALSE]
se.intkmtimes <- se.resmean[newtimes]
skmtimes <- mm[newtimes,2]
years.lost <- intkmtimes[,1]-intkmtimes[,2]
intkmtimes <- cbind(skmtimes,intkmtimes,se.intkmtimes,years.lost)
colnames(intkmtimes) <- c("strata","times","rmean","se.rmean","years.lost")
rownames(intkmtimes) <- rep(x$strata.level,length(times));
intkmtimes=data.frame(intkmtimes)
### logintkmtimes=cbind(intkmtimes[,1:2],log(intkmtimes[,3]),se.intkmtimes/intkmtimes[,3])
### colnames(logintkmtimes) <- c("strata","times","log-rmean","log-se.rmean")
} else intkmtimes <- se.intkmtimes <- NULL
rmst <- cbind(meanm[,1],vecAllStrata(meanm[,2],strata.jumps,nstrata))
se.rmst <- cbind(se.mm[,1],vecAllStrata(se.mm[,2],strata.jumps,nstrata))
out <- list(cumhaz=meanm,se.cumhaz=se.mm,covs=covs,
time=time,strata=strata.jumps,nstrata=nstrata,
jumps=1:length(km),strata.name=x$strata.name,
strata.level=x$strata.level,
intkmtimes=intkmtimes,
rmst=rmst,se.rmst=se.rmst,
coef=intkmtimes[,3],var=diag(intkmtimes[,4]^2))
class(out) <- c("resmean_phreg")
return(out)
}# }}}
##' @export
vcov.resmean_phreg <- function(object,cause=1,...)
{# {{{
if (is.na(match("rmean",names(object$intkmtimes)))) name <- paste("se.intF1",cause,sep="") else name <- "se.rmean"
return(diag(object$intkmtimes[,name]^2))
}# }}}
##' @export
coef.resmean_phreg <- function(object,cause=1,...)
{# {{{
if (is.na(match("rmean",names(object$intkmtimes)))) name <- paste("intF1",cause,sep="") else name <- "rmean"
return(object$intkmtimes[,name])
}# }}}
##' @export
rmst.phreg <- function(x,times=NULL,covs=NULL,...)
{# {{{
out <- resmean.phreg(x,times=NULL,covs=NULL,...)
return(out)
}# }}}
##' @export
cif.yearslost <- function(formula,data=data,cens.code=0,times=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
### if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (!inherits(Y,c("Event","Surv"))) stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
x <- phreg(formula,data=data,no.opt=TRUE,no.var=1,Z=as.matrix(status,ncol=1))
causes <- sort(unique(x$cox.prep$Z[,1]))
ccc <- which(causes %in% cens.code)
if (length(ccc)>=1) causes <- causes[-ccc]
if (!is.null(times)) {# {{{
tt <- expand.grid(times,0:(x$nstrata-1))
### cause.jumps <- x$U+x$E
cause.jumps <- x$cox.prep$Z[x$cox.prep$jumps+1,1]
mm <- cbind(x$jumptimes,x$strata.jumps,1,cause.jumps)
mm <- rbind(mm,cbind(tt[,1],tt[,2],0,cens.code))
ord <- order(mm[,1])
mm <- mm[ord,]
phd <- which(mm[,3]==1)
newtimes <- which(mm[,3]==0)
S0i <- S0i2 <- rep(0,nrow(mm))
S0i[phd] <- c(1/x$S0)
S0ii2 <- c(1/(x$S0*(x$S0-1)))
S0ii2[x$S0==1] <- 0
S0i2[phd] <- S0ii2
strata.jumps <- mm[,2]
nstrata <- x$nstrata;
jumptimes <- mm[,1]
cause.jumps <- mm[,4]
} else {
strata.jumps <- x$strata.jumps;
nstrata <- x$nstrata;
jumptimes <- x$jumptimes;
cause.jumps <- x$U+x$E
S0i <- c(1/x$S0)
S0i2 <- c(1/(x$S0*(x$S0-1)))
S0i2[x$S0==1] <- 0
}# }}}
### formula from Pepe-Mori: SIM 93, 737-
pepemori <- 0
### formula from PKA SIM 2013
pka <- 0
years.lostF1 <- se.years.lostF1m <- se.years.lostF1 <- se.years.lostF1pm <- c()
for (i in seq_along(causes)) {
jumpsi <- (cause.jumps==causes[i])*1
jumpsni <- (cause.jumps %in% causes[-i])*1
cumhaz <- cumsumstrata(S0i*jumpsi,strata.jumps,nstrata)
var.cumhazMG <- cumsumstrata(S0i2*jumpsi,strata.jumps,nstrata)
var.cumhazniMG <- cumsumstrata(S0i2*jumpsni,strata.jumps,nstrata)
## baseline survival
km <- exp(cumsumstratasum(log(1-S0i),strata.jumps,nstrata,type="lagsum"))
F1 <- cumsumstratasum(jumpsi*km*S0i,strata.jumps,nstrata,type="lagsum")
### 1 - F2 = S + F1
F1n1 <- km+F1
## start integral in 0
dtime <- c(diffstrata(jumptimes,strata.jumps,nstrata))
intkm <- cumsumstrata( c(km)*dtime,strata.jumps,nstrata)
intF1 <- cumsumstrata( c(F1)*dtime,strata.jumps,nstrata)
years.lostF1 <- cbind(years.lostF1,intF1)
if (pka==1) {
### variance of baseline term \int_0^t 1/Y^2 \int_s^t S(u) du dN^i{{{
var.intkmcumhaz <- cumsumstrata(jumpsi*intkm*S0i2,strata.jumps,nstrata)
var.intkm2cumhaz <- cumsumstrata(jumpsi*intkm^2*S0i2,strata.jumps,nstrata)
var.resmean1 <- intkm^2*var.cumhazMG+var.intkm2cumhaz-2*intkm*var.intkmcumhaz
### variance of baseline term \int_0^t 1/Y^2 \int_s^t F_i(u) du dN^-i
var.intF1cumhaz <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
var.intF12cumhaz <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
var.resmean2 <- intF1^2*var.cumhazniMG+var.intF12cumhaz-2*intF1*var.intF1cumhaz
var.intF1 <- (var.resmean1+var.resmean2)
## possibly negative due to rounding errors
var.intF1[var.intF1<0] <- 0
se.intF1 <- var.intF1^.5
se.years.lostF1 <- cbind(se.years.lostF1,se.intF1) # }}}
}
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s) - (t-s) (1-Fn1(s))) dN_1^i{{{
vars.1 <- cumsumstrata(jumpsi*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazMG+vars.1-2*intF1*vars.2
vars.3 <- cumsumstrata(jumpsi*F1n1^2*S0i2,strata.jumps,nstrata)
vars.4 <- cumsumstrata(jumpsi*F1n1^2*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsi*F1n1^2*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- jumptimes^2*vars.3+vars.4-2*jumptimes*vars.5
vars.6 <- cumsumstrata(jumpsi*F1n1*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsi*F1n1*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsi*F1n1*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsi*F1n1*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7
varsj1 <- vars.11+vars.21-2*vars.31
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s) - (t-s) F1(s)) dN_n1^i
vars.1 <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazniMG+vars.1-2*intF1*vars.2
vars.3 <- cumsumstrata(jumpsni*F1^2*S0i2,strata.jumps,nstrata)
vars.4 <- cumsumstrata(jumpsni*F1^2*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsni*F1^2*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- jumptimes^2*vars.3+vars.4-2*jumptimes*vars.5
vars.6 <- cumsumstrata(jumpsni*F1*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsni*F1*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsni*F1*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsni*F1*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7
varsnj1 <- vars.11+vars.21-2*vars.31
varss <- varsj1+varsnj1
varss[varss<0] <- 0
se.intF1m <- varss^.5
se.years.lostF1m <- cbind(se.years.lostF1m,se.intF1m)
# }}}
if (pepemori==1) {
### variance Pepe-Mori {{{
### variance of dN_1 term \int_0^t 1/Y^2 dN_n1^i
vars.1 <- cumsumstrata(jumpsi*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazMG+vars.1-2*intF1*vars.2
vars.4 <- cumsumstrata(jumpsi*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsi*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- F1n1^2*(jumptimes^2*var.cumhazMG+vars.4-2*jumptimes*vars.5)
vars.6 <- cumsumstrata(jumpsi*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsi*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsi*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- F1n1*(jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7)
varsj1 <- vars.11+vars.21-2*vars.31
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s)) dN_n1^i
vars.1 <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazniMG+vars.1-2*intF1*vars.2
varspm <- vars.11+varsj1
varspm[varspm<0] <- 0
se.intF1pm <- varspm^.5
se.years.lostF1pm <- cbind(se.years.lostF1pm,se.intF1pm)
# }}}
}
}
years.lostF1 <- cbind(jumptimes,years.lostF1)
colnames(years.lostF1) <- c("time",paste("intF_",causes,sep=""))
### make output at specified times
if (!is.null(times)) {
intF1times <- years.lostF1[newtimes,]
years.lost <- apply(intF1times[,-1,drop=FALSE],1,sum)
if (pka==1) se.intF1times <- se.years.lostF1[newtimes,-1]
se.intF1mtimes <- se.years.lostF1m[newtimes,]
stratatimes <- strata.jumps[newtimes]
intF1mtimes <- cbind(stratatimes,intF1times,se.intF1mtimes,years.lost)
colnames(intF1mtimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes),"total-years-lost")
rownames(intF1mtimes) <- rep(x$strata.level,length(times));
intF1mtimes=data.frame(intF1mtimes)
if (pka==1) {
intF1pkatimes <- cbind(stratatimes,intF1times,se.intF1times)
colnames(intF1pkatimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes))
intF1pkatimes=data.frame(intF1times)
} else intF1pkatimes <- NULL
if (pepemori==1) {
se.intF1pmtimes <- se.years.lostF1pm[newtimes,]
intF1pmtimes <- cbind(stratatimes,intF1times,se.intF1pmtimes)
colnames(intF1pmtimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes))
intF1pmtimes=data.frame(intF1pmtimes)
} else intF1pmtimes <- NULL
} else intF1pmtimes <-intF1mtimes <- intF1pkatimes <- NULL
se.years.lostF1 <- cbind(jumptimes,se.years.lostF1m)
colnames(se.years.lostF1) <- c("time",paste("intF_",causes,sep=""))
## name things to make use of other programs
out <- list(cumhaz=years.lostF1,se.cumhaz=se.years.lostF1,
time=jumptimes, strata=strata.jumps,nstrata=nstrata,
jumps=1:length(km),strata.name=x$strata.name,
strata.level=x$strata.level,
intkmtimes=intF1mtimes, intF1times=intF1mtimes,
intF1pmtimes=intF1pmtimes, intF1pkatimes=intF1pkatimes
)
class(out) <- c("resmean_phreg")
return(out)
}# }}}
##' @export
summary.resmean_phreg <- function(object,...)
{# {{{
if (is.null(object$intkmtimes)) return(cbind(object$cumhaz,object$se.cumhaz[,2])) else return(object$intkmtimes)
}# }}}
##' @export
print.resmean_phreg <- function(x,...)
{# {{{
print(summary.resmean_phreg(x,...))
}# }}}
##' @export
plot.resmean_phreg <- function(x, se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,
lty=NULL,col=NULL,lwd=NULL,legend=TRUE,ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,stratas=NULL,robust=FALSE,years.lost=FALSE,cause=1,...) {# {{{
if (inherits(x,"phreg") & is.null(ylab)) ylab <- "Cumulative hazard"
if (inherits(x,"km") & is.null(ylab)) ylab <- "Survival probability"
if (inherits(x,"cif") & is.null(ylab)) ylab <- "Probability"
if (inherits(x,"resmean_phreg") & is.null(ylab)) ylab <- "Restricted residual mean life"
if (inherits(x,"resmean_phreg") & !is.null(x$intF1times)) ylab <- "Years lost up to t: t - E(min(T,t))"
if (years.lost) ylab <- "Years lost up to t: t - E(min(T,t))"
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
if (years.lost) rr <- range(x$cumhaz[,1]-x$cumhaz[,cause+1]) else rr <- range(x$cumhaz[,cause+1])
strat <- x$strata[x$jumps]
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$cumhaz[,1])
if (se==TRUE) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz) )
stop("phreg must be with cumhazard=TRUE\n");
if (years.lost) rrse <- range(c(x$cumhaz[,1]-x$cumhaz[,cause+1]+level*x$se.cumhaz[,cause+1])) else
rrse <- range(c(x$cumhaz[,cause+1]+level*x$se.cumhaz[,cause+1]))
if (is.null(ylimo)) ylim <- rrse
}
## all strata
if (is.null(stratas)) stratas <- 0:(x$nstrata-1)
ltys <- lty
cols <- col
lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(stratas) else if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas))
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwds <- rep(1,length(stratas)) else
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas))
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
if (years.lost) x$cumhaz[,cause+1] <- x$cumhaz[,1]-x$cumhaz[,cause+1]
first <- 0
for (i in seq(stratas)) {
j <- stratas[i]
cumhazard <- x$cumhaz[strat==j,c(1,cause+1),drop=FALSE]
if (!is.null(cumhazard)) {
if (nrow(cumhazard)>1) {
if (add | first==1)
lines(cumhazard,type="l",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1])
else {
first <- 1
plot(cumhazard,type="l",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
if (robust==TRUE) secumhazard <- x$robse.cumhaz[strat==j,c(1,cause+1),drop=FALSE]
else secumhazard <- x$se.cumhaz[strat==j,c(1,cause+1),drop=FALSE]
ul <-cbind(cumhazard[,1],cumhazard[,2]+level*secumhazard[,2])
nl <-cbind(cumhazard[,1],cumhazard[,2]-level*secumhazard[,2])
if (inherits(x,"km")) { ul[,2] <- x$upper[x$strata==j];
nl[,2] <- x$lower[x$strata==j];
wna <- which(is.na(ul[,2]))
ul[wna,2] <- 0
nl[wna,2] <- 0
}
if (!polygon) {
lines(nl,type="l",lty=ltys[i,2],col=cols[i,2],lwd=lwds[i,2])
lines(ul,type="l",lty=ltys[i,3],col=cols[i,3],lwd=lwds[i,3])
} else {
## type="l" confidence regions
ll <- length(nl[,1])
timess <- nl[,1]
tt <- c(timess,rev(timess))
yy <- c(nl[,2],rev(ul[,2]))
col.alpha<-0.1
col.ci<-cols[i,]
col.trans <- sapply(col.ci, FUN=function(x)
do.call(grDevices::rgb,as.list(c(grDevices::col2rgb(x)/255,col.alpha))))
polygon(tt,yy,lty=0,col=col.trans)
}
}
}
}
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
}# }}}
# }}}
##' IPTW Cox, Inverse Probaibilty of Treatment Weighted Cox regression
##'
##' Fits Cox model with treatment weights \deqn{ w(A)= \sum_a I(A=a)/\pi(a|X)}, where
##' \deqn{\pi(a|X)=P(A=a|X)}. Computes
##' standard errors via influence functions that are returned as the IID argument.
##' Propensity scores are fitted using either logistic regression (glm) or the multinomial model (mlogit) when there are
##' than treatment categories. The treatment needs to be a factor and is identified on the rhs
##' of the "treat.model". Recurrent events can be considered with start,stop structure and then cluster(id) must be
##' specified. Robust standard errors are computed in all cases.
##'
##' Time-dependent propensity score weights can also be computed when treat.var is used, it must be 1 at the time
##' of first (A_0) and 2nd treatment (A_1), then uses weights \deqn{w_0(A_0) * w_1(A_1)^{t>T_r}} where \deqn{T_r} is
##' time of 2nd randomization.
##'
##' @param formula for phreg
##' @param data data frame for risk averaging
##' @param treat.model propensity score model (binary or multinomial)
##' @param treat.var a 1/0 variable that indicates when treatment is given and the propensity score is computed
##' @param weights may be given, and then uses weights*w(A) as the weights
##' @param estpr (=1, default) to estimate propensity scores and get infuence function contribution to uncertainty
##' @param pi0 fixed simple weights
##' @param se.cluster to compute GEE type standard errors when additional cluster structure is present
##' @param ... arguments for phreg call
##' @author Thomas Scheike
##' @examples
##' library(mets)
##' data <- mets:::simLT(0.7,100,beta=0.3,betac=0,ce=1,betao=0.3)
##' dfactor(data) <- Z.f~Z
##' out <- phreg_IPTW(Surv(time,status)~Z.f,data=data,treat.model=Z.f~X)
##' summary(out)
##' @export
phreg_IPTW <- function (formula, data,treat.model = NULL, treat.var = NULL,weights = NULL, estpr = 1, pi0 = 0.5,se.cluster=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster", "offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!inherits(Y, c("Event", "Surv")))
stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y) == 2) {
exit <- Y[, 1]
entry <- NULL
status <- Y[, 2]
}
else {
entry <- Y[, 1]
exit <- Y[, 2]
status <- Y[, 3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
}
else pos.cluster <- NULL
if (!is.null(id)) {
orig.id <- id
ids <- sort(unique(id))
nid <- length(ids)
if (is.numeric(id))
id <- fast.approx(ids, id) - 1
else {
id <- as.integer(factor(id, labels = seq(nid))) -
1
}
}
else {
orig.id <- NULL
nid <- length(exit)
id <- 0:(nid - 1)
ids <- NULL
}
if (!is.null(se.cluster)) {
sds <- sort(unique(se.cluster))
sid <- length(sds)
if (is.numeric(se.cluster))
se.cluster <- fast.approx(sds, se.cluster) - 1
else se.cluster <- as.integer(factor(se.cluster, labels = seq(sid))) - 1
}
id <- id + 1
nid <- length(unique(id))
data$id__ <- id
data$cid__ <- cumsumstrata(rep(1, length(id)), id - 1, nid)
treats <- function(treatvar) {
treatvar <- droplevels(treatvar)
nlev <- nlevels(treatvar)
nlevs <- levels(treatvar)
ntreatvar <- as.numeric(treatvar)
return(list(nlev = nlev, nlevs = nlevs, ntreatvar = ntreatvar))
}
fittreat <- function(treat.model, data, id, ntreatvar, nlev) {
if (nlev == 2) {
treat.model <- drop.specials(treat.model, "cluster")
treat <- glm(treat.model, data, family = "binomial")
iidalpha <- lava::iid(treat, id = id)
lpa <- treat$linear.predictors
pal <- expit(lpa)
pal <- cbind(1 - pal, pal)
ppp <- (pal/pal[, 1])
spp <- 1/pal[, 1]
}
else {
treat.modelid <- update.formula(treat.model, . ~
. + cluster(id__))
treat <- mlogit(treat.modelid, data)
iidalpha <- lava::iid(treat)
pal <- predict(treat, data, se = 0, response = FALSE)
ppp <- (pal/pal[, 1])
spp <- 1/pal[, 1]
}
Xtreat <- model.matrix(treat.model, data)
tvg2 <- 1 * (ntreatvar >= 2)
pA <- c(mdi(pal, 1:length(ntreatvar), ntreatvar))
pppy <- c(mdi(ppp, 1:length(ntreatvar), ntreatvar))
Dppy <- (spp * tvg2 - pppy)
Dp <- c()
for (i in seq(nlev - 1)) Dp <- cbind(Dp, Xtreat * ppp[, i + 1] * Dppy/spp^2)
DPai <- -1 * Dp/pA^2
out <- list(iidalpha = iidalpha, pA = pA, Dp = Dp, pal = pal,
ppp = ppp, spp = spp, id = id, DPai = DPai)
return(out)
}
expit <- function(x) 1/(1 + exp(-x))
if (!is.null(treat.var)) {
weightWT <- data[, treat.var]
whereW <- which(weightWT == 1)
CountW <- cumsumstrata(weightWT, id - 1, nid)
dataW <- data[whereW, ]
idW <- id[whereW]
} else {
whereW <- 1:nrow(data)
dataW <- data
idW <- id
CountW <- cumsumstrata(rep(1,nrow(data)), id-1,nid)
}
treat.name <- all.vars(treat.model)[1]
treatvar <- dataW[, treat.name]
if (!is.factor(treatvar))
stop(paste("treatment=", treat.name, " must be coded as factor \n",
sep = ""))
treats <- treats(treatvar)
wlPA <- ww <- rep(1, nrow(data))
idWW <- mystrata2index(cbind(id, CountW))
if (estpr[1] == 1) {
fitt <- fittreat(treat.model, dataW, idW, treats$ntreatvar, treats$nlev)
iidalpha0 <- fitt$iidalpha
wPA <- c(fitt$pA)
DPai <- fitt$DPai
} else {
if (length(pi0)==length(treats$ntreatvar)) wPA <- pi0
else wPA <- 1/ifelse(pi0[1], 1 - pi0[1], treats$ntreatvar == 2)
## pi0 <- rep(pi0, treats$nlev)
DPai <- matrix(0, nrow(data), 1)
}
ww <- rep(1, nrow(data))
ww[whereW] <- wPA
wlPA <- exp(cumsumstrata(log(ww), idWW - 1, attr(idWW, "nlevel")))
wwt <- c(exp(cumsumstrata(log(ww), id - 1, nid)))
## P(t) = P_0 * P_1^(I(t>T1)), time-dependent weights
## DP = P(t) \sum_j P_j I(t> TJ) (-DP_j/P_j^2)
if (estpr[1] == 1) {
DPait <- matrix(0, nrow(data), ncol(DPai))
DPait[whereW, ] <- DPai
DPait <- apply(DPait * c(wlPA), 2, cumsumstrata, id - 1, nid)/wwt
} else DPait <- NULL
if (is.null(weights)) ww <- 1/wwt else ww <- weights/wwt
phw <- phreg(formula, data, weights = ww, Z = DPait, ...)
### check.derivative <- 0
### if (check.derivative == 1) { ## {{{
### ### for checking derivative
### fpar <- glm(treat.model,dataw,family=binomial)
### mm <- model.matrix(treat.model,dataw)
### cpar <- coef(fpar)
### ### library(numderiv)
###
### ff <- function(par,base=0) {
### pa <- expit(mm %*% par)
### www <- ifelse(dataw[,treat.name] == "1", pa, 1 - pa)
### ww <- rep(1, nrow(data))
### ww[wherew] <- www
### wlpa <- exp(cumsumstrata(log(ww), idww - 1, attr(idww, "nlevel")))
### wwwt <- exp(cumsumstrata(log(ww), id - 1, nid))
###
### pp <- phreg(formula,data,weights=1/wwwt,no.opt=true,beta=coef(phw))
### if (base==1) po <- c(pp$cumhaz[,2]) else po <- pp$gradient
### return(po)
### }
###
### print(ff(cpar))
### gf <- jacobian(ff,cpar)
### print(t(gf))
### ###
### print(ff(cpar,base=1))
### gf <- jacobian(ff,cpar,base=1)
### print(gf)
### print("___________________________________");
### } ## }}}
if (estpr[1] == 1) {
xx <- phw$cox.prep
nid <- max(xx$id)
S0i <- rep(0, length(xx$strata))
wPAJ <- xx$weights[xx$jumps+1]*xx$caseweights[xx$jumps+1]
Xt <- xx$X
S0 <- phw$S0 * wPAJ
S0i[xx$jumps + 1] <- 1/S0
U <- E <- matrix(0, nrow(xx$X), phw$p)
U[xx$jumps + 1, ] <- phw$U/wPAJ
E[xx$jumps + 1, ] <- phw$E
if (phw$p>0) {
rr <- c(xx$sign * exp(Xt %*% coef(phw) + xx$offset) * xx$weights)
rrnw <- c(xx$sign * exp(Xt %*% coef(phw) + xx$offset))
} else {
rr <- c(xx$sign * exp(xx$offset) * xx$weights)
rrnw <- c(xx$sign * exp(xx$offset))
}
DWX = .Call("vecMatMat", xx$Z, Xt)$vXZ
S1 = apply(Xt * rr, 2, revcumsumstrata, xx$strata, xx$nstrata)
###S00 = revcumsumstrata( rr, xx$strata, xx$nstrata)
DS1 = apply(DWX * rrnw, 2, revcumsumstrata, xx$strata, xx$nstrata)
DS0 = apply(xx$Z * rrnw, 2, revcumsumstrata, xx$strata, xx$nstrata)
if (phw$p>0) {
DS0S1 = .Call("vecMatMat", DS0[xx$jumps + 1, , drop = FALSE],S1[xx$jumps + 1, , drop = FALSE])$vXZ
DUa2 <- apply(wPAJ * DS1[xx$jumps + 1, , drop = FALSE]/c(S0),2, sum) - apply(wPAJ * DS0S1/c(S0^2), 2, sum)
DUa2 <- matrix(DUa2, ncol(fitt$DPai), phw$p)
DUa1 <- t(xx$Z[xx$jumps + 1, ]) %*% (phw$U/wPAJ)
DUa <- DUa1 - DUa2
iidpal <- iidalpha0 %*% DUa
iidbeta <- lava::iid(phw) + iidpal %*% phw$ihess
phw$DUa <- DUa
phw$IID <- iidbeta
phw$naive.var <- phw$var
phw$var <- crossprod(iidbeta)
} else iidbeta <- NULL
###
DAw <- apply(xx$caseweights[xx$jumps+1]*xx$Z[xx$jumps + 1, ,drop=FALSE]/c(S0),2,cumsumstrata,phw$strata.jumps,xx$nstrata)
DA2 <- apply(wPAJ*DS0[xx$jumps + 1, , drop = FALSE]/c(S0)^2,2,cumsumstrata,phw$strata.jumps,xx$nstrata)
DAt <- 1*(DAw-DA2)
phw <- robust.phreg(phw,beta.iid=iidbeta)
varA <- phw$robse.cumhaz[,2]^2
phw$naive.se.cumhaz <- phw$robse.cumhaz
vtheta <- crossprod(iidalpha0)
varthetat <- rowSums((DAt %*% vtheta)*DAt)
###
ww <- xx$caseweights*xx$weights
S0i2 <- rep(0,length(xx$strata))
S0i2[xx$jumps+1] <- 1/(phw$S0^2*ww[xx$jumps+1])
cumS0i2 <- c(cumsumstrata(S0i2,xx$strata,xx$nstrata))
xxx <- (S0i-rr*cumS0i2)
id <- xx$id
mid <- max(xx$id)+1
thetat <- iidalpha0[id+1,,drop=FALSE]
covk1 <- apply(S0i*thetat,2,cumsumidstratasum,id,mid,xx$strata,xx$nstrata,type="sum")
covk2 <- apply(rr*thetat,2,revcumsumidstratasum,id,mid,xx$strata,xx$nstrata,type="lagsum")
###
covk1 <- apply(S0i*thetat,2,cumsumstrata,xx$strata,xx$nstrata)
covk2 <- apply(rr*thetat,2,revcumsumstrata,xx$strata,xx$nstrata)
###
covk2 <- covk2*cumS0i2
covv <- (covk1-covk2)[xx$jumps+1,,drop=FALSE]
covvt <- 2*apply(covv*DAt,1,sum)
varA <- varA+varthetat+2*apply(covv*DAt,1,sum)
Ht <- NULL
if (phw$p>0) {
covbetatheta <- t(iidalpha0) %*% iidbeta
Ht <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
Ht <- Ht[xx$jumps+1,,drop=FALSE]
covvBT <- 2* rowSums((Ht %*% t(covbetatheta))*DAt)
varA <- varA + covvBT
}
phw$robse.cumhaz[,2] <- varA^.5
phw$se.cumhaz[,2] <- varA^.5
phw$var.cumhaz <- cbind(phw$se.cumhaz[,1],varA)
resAiid <- list(DAt=DAt,Ht=Ht,iidalpha0=iidalpha0,iidbeta=phw$IID)
phw$resAiid <- resAiid
phw$iptw <- ww
} else {
phw$iptw <- ww
phw <- robust.phreg(phw)
phw$naive.se.cumhaz <- phw$se.cumhaz
phw$se.cumhaz <- phw$robse.cumhaz
phw$naive.var <- phw$var
}
if (!is.null(se.cluster)) {
phw$IID.simple <- phw$IID
phw$var.simple <- phw$var
phw$IID <- apply(phw$IID,2,sumstrata,se.cluster,sid)
phw$var <- crossprod(phw$IID)
phw$se.cluster <- se.cluster
}
class(phw) <- c("phreg","IPTW")
return(phw)
}# }}}
##' G-estimator for Cox and Fine-Gray model
##'
##' Computes G-estimator \deqn{ \hat S(t,A=a) = n^{-1} \sum_i \hat S(t,A=a,Z_i) }
##' for the Cox model based on phreg og the Fine-Gray model based on the
##' cifreg function. Gives influence functions of these risk estimates and SE's are
##' based on these. If first covariate is a factor then all contrast are computed,
##' and if continuous then considered covariate values are given by Avalues.
##'
##' @param x phreg or cifreg object
##' @param data data frame for risk averaging
##' @param time for estimate
##' @param Avalues values to compare for first covariate A
##' @param varname if given then averages for this variable, default is first variable
##' @param same.data assumes that same data is used for fitting of survival model and averaging.
##' @param id might be given to link to data to iid decomposition of survival data, must be coded as 1,2,..,
##' @author Thomas Scheike
##' @examples
##'
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' bmt$event <- (bmt$cause!=0)*1
##' dfactor(bmt) <- tcell.f~tcell
##'
##' fg1 <- cifreg(Event(time,cause)~tcell.f+platelet+age,bmt,cause=1,
##' cox.prep=TRUE,propodds=NULL)
##' summary(survivalG(fg1,bmt,50))
##'
##' ss <- phreg(Surv(time,event)~tcell.f+platelet+age,bmt)
##' summary(survivalG(ss,bmt,50))
##'
##' ss <- phreg(Surv(time,event)~strata(tcell.f)+platelet+age,bmt)
##' summary(survivalG(ss,bmt,50))
##'
##' sst <- survivalGtime(ss,bmt,n=50)
##' plot(sst)
##'
##' fg1t <- survivalGtime(fg1,bmt,n=50)
##' plot(fg1t)
##'
##' @export
##' @aliases survivalGtime
survivalG <- function(x,data,time=NULL,Avalues=c(0,1),varname=NULL,same.data=TRUE,id=NULL)
{# {{{
if (is.null(time)) stop("Give time for estimation of survival/cumulative incidence\n")
if (inherits(x,"cifreg"))
Aiid <- IIDbaseline.cifreg(x,time=time) else Aiid <- IIDbaseline.phreg(x,time=time)
### dealing with first variable that is a factor
if (is.null(varname)) {
treat.name <- all.vars(update.formula(x$formula,1~.))[1]
} else treat.name <- varname
treatvar <- data[,treat.name]
if (is.factor(treatvar)) {
###if (!is.factor(treatvar)) stop(paste("treatment=",treat.name,"must be coded as factor \n",sep=""));
## treatvar, 1,2,...,nlev or 1,2
nlev <- nlevels(treatvar)
nlevs <- levels(treatvar)
###treatvar <- as.numeric(treatvar)
ntreatvar <- as.numeric(treatvar)
ytreat <- ntreatvar-1
} else {
nlevs <- Avalues
}
formulaX <- update.formula(x$formula,.~.)
formulaX <- drop.specials(formulaX,"cluster")
datA <- dkeep(data,x=all.vars(formulaX))
xlev <- lapply(datA,levels)
cumhaz.time <- cpred(x$cumhaz,time)[-1,]
k <- 1; risks <- c(); DariskG <- list()
for (a in nlevs) { ## {{{
datA[,treat.name] <- a
pp <- predict(x,datA,time,se=0)
Xbase <- 1*outer(pp$strata,0:(x$nstrata-1),"==")
if (inherits(x,"phreg")) { ps0 <- c(pp$surv); Dma <- -cbind(c(pp$RR)*ps0*Xbase,c(ps0*pp$cumhaz)*pp$X); }
if (inherits(x,"cifreg")) { ps0 <- c(pp$cif); Dma <- cbind(c(pp$RR)*c(1-ps0)*Xbase,c((1-ps0)*pp$cumhaz)*pp$X); }
else if (inherits(x,"recreg")) { ps0 <- pp$cumhaz; Dma <- cbind(c(pp$RR)*Xbase,c(pp$cumhaz)*pp$X) }
risks <- cbind(risks,ps0)
DariskG[[k]] <- apply(Dma,2,sum)
k <- k+1
} ## }}}
predictAiid <- NULL
###
Grisk <- apply(risks,2,mean)
risk.iid <- t(t(risks)-Grisk)
###
nid <- nrow(pp$X)
nidcox <- max(x$id)
mnid <- max(nid,nidcox)
coxiid <- cbind(Aiid$base.iid,Aiid$beta.iid)
if (nid!=nidcox) {
coxiid <- apply(coxiid,2,sumstrata,x$id-1,mnid)
}
if (same.data) {
if (is.null(id)) id <- 1:nrow(pp$X) else id <- data[,id];
risk.iid <- apply(risk.iid,2,sumstrata,id-1,mnid)/nid
for (a in seq_along(nlevs)) risk.iid[,a] <- risk.iid[,a]+ coxiid %*% DariskG[[a]]/nid
vv <- crossprod(risk.iid)
} else {
predictAiid <- matrix(0,nidcox,ncol(risks))
for (a in seq_along(nlevs)) {
risk.iid[,a] <- risk.iid[,a]
predictAiid[,a] <- coxiid %*% DariskG[[a]]/nid
}
vv <- crossprod(risk.iid)+crossprod(predictAiid)
}
###estimate(lava::estimate(coef=theta,vcov=vv,f=function(p) Gf(p,ic=0))
if (inherits(x,"phreg")) {
out <- estimate(coef=1-Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
sout <- estimate(coef=Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
ed <- estimate(coef=Grisk,vcov=vv,f=function(p) (1-p[-1])-(1-p[1]))
rd <- estimate(coef=Grisk,vcov=vv,f=function(p) (1-p[-1])/(1-p[1]),null=1)
srd <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])/(p[1]),null=1)
out <- list(risk.iid=risk.iid,survivalG=sout,risk=out,difference=ed,ratio=rd,survival.ratio=srd,vcov=vv)
}
if (inherits(x,"cifreg") | inherits(x,"recreg")) {
out <- estimate(coef=Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
ed <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])-(p[1]))
rd <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])/(p[1]),null=1)
out <- list(risk.iid=risk.iid,risk=out,difference=ed,ratio=rd,vcov=vv)
}
class(out) <- "survivalG"
return(out)
} ## }}}
##' @export
survivalGtime <- function(x,data,time=NULL,n=100,...)
{# {{{
if (!is.null(time)) if (time=="all") time <- x$cumhaz[,1]
if (is.null(time)) {
rr <- range(x$cumhaz[,1])
time <- seq(rr[1],rr[2],length=n)
}
survivalG <- risk <- difference <- ratio <- survival.ratio <- c()
for (tt in time) {
Gt <- survivalG(x,data,time=tt,...)
strata <- strata(rownames(Gt$risk$coefmat))
survivalG <- rbind(survivalG,cbind(tt,Gt$survivalG$coefmat))
risk <- rbind(risk,cbind(tt,Gt$risk$coefmat))
difference <- rbind(difference,cbind(tt,Gt$difference$coefmat))
ratio <- rbind(ratio,cbind(tt,Gt$ratio$coefmat))
survival.ratio <- rbind(survival.ratio,cbind(tt,Gt$survival.ratio$coefmat))
}
colnames(survivalG)[1] <- "time"
colnames(risk)[1] <- "time"
colnames(difference)[1] <- "time"
colnames(ratio)[1] <- "time"
colnames(survival.ratio)[1] <- "time"
strata <- strata(rownames(risk))
out <- list(time=time,survivalG=survivalG,risk=risk,difference=difference,
ratio=ratio,survival.ratio=survival.ratio,strata=strata)
class(out) <- "survivalGtime"
return(out)
} ## }}}
##' @export
plot.survivalGtime <- function(x,type=c("survival","risk","survival.ratio","difference","ratio"),ylim=NULL,legend=NULL,...) {# {{{
## to deal with fine-gray based things, that do not contain survival estimates
if ((ncol(x$survivalG)==1) & type[1]=="survival") type <- "risk"
us <- unique(x$strata)
cols <- 1:length(us)
ltys <- cols
ss0 <- x$strata==us[1]
if (type[1]=="survival") {
if (is.null(ylim)) ylim <- range(x$survivalG[,c(4,5)])
plot(x$time,x$survivalG[ss0,2],type="s",xlab="time",ylab="Survival",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$survivalG[ss0,c(4,5)],col=cols[1])
k <- 2
for (ss in us[-1]) {
ss0 <- x$strata==ss
lines(x$time,x$survivalG[ss0,2],type="s",ylim=c(0,1),col=cols[k],lty=ltys[k])
plotConfRegion(x$time,x$survivalG[ss0,c(4,5)],col=cols[k])
k <- k+1
}
}
if (type[1]=="risk") {
if (is.null(ylim)) ylim <- range(x$risk[,c(4,5)])
plot(x$time,x$risk[ss0,2],type="s",xlab="time",ylab="risk",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$risk[ss0,c(4,5)],col=cols[1])
k <- 2
for (ss in us[-1]) {
ss0 <- x$strata==ss
lines(x$time,x$risk[ss0,2],type="s",ylim=c(0,1),col=cols[k],lty=ltys[k])
plotConfRegion(x$time,x$risk[ss0,c(4,5)],col=cols[k])
k <- k+1
}
}
if (type[1]=="difference") {
if (is.null(ylim)) ylim <- range(x$risk[,c(4,5)])
plot(x$time,x$difference[,2],type="s",xlab="time",ylab="difference in risk",ylim=range(x$difference[,2]),col=cols[1],lty=ltys[1],...)
plotConfRegion(x$time,x$difference[,c(4,5)],col=cols[1])
}
if (type[1]=="ratio") {
if (is.null(ylim)) ylim <- range(x$ratio[,c(4,5)])
plot(x$time,x$ratio[,2],type="s",ylim=ylim,xlab="time",ylab="ratio",col=cols[1],lty=ltys[1],...)
plotConfRegion(x$time,x$ratio[,c(4,5)],col=cols[1])
}
if (type[1]=="survival.ratio") {
if (is.null(ylim)) ylim <- range(x$survival.ratio[,c(4,5)])
plot(x$time,x$survival.ratio[,2],type="s",xlab="time",ylab="risk",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$survival.ratio[,c(4,5)],col=cols[1])
}
if (is.null(legend)) legend("topleft",levels(x$strata),col=cols,lty=ltys)
}
# }}}
###{{{ summary
##' @export
summary.survivalG <- function(object,...) {
res <- list(risk=object$risk,difference=object$difference,ratio=object$ratio,survival.ratio=object$survival.ratio)
class(res) <- "summary.survivalG"
res
}
##' @export
print.summary.survivalG <- function(x,...) {
cat("risk:\n")
print(x$risk,...)
cat("\n")
cat("Average Treatment effects (G-estimator) :\n")
print(x$difference,...)
cat("\n")
cat("Average Treatment effect risk-ratio (G-estimator) :\n")
print(x$ratio$coefmat,...)
cat("\n")
cat("Average Treatment effect (1-risk=survival)-ratio (G-estimator) :\n")
print(x$survival.ratio$coefmat,...)
cat("\n")
}
###}}} summary
##' Fast additive hazards model with robust standard errors
##'
##' Fast Lin-Ying additive hazards model with a possibly stratified baseline.
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param no.baseline to fit model without baseline hazard
##' @param ... Additional arguments to phreg
##' @author Thomas Scheike
##' @examples
##'
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' out <- aalenMets(Surv(time,cause==1)~tcell+platelet+age,data=bmt)
##' summary(out)
##'
##' ## out2 <- timereg::aalen(Surv(time,cause==1)~const(tcell)+const(platelet)+const(age),data=bmt)
##' ## summary(out2)
##'
##' @export
aalenMets <- function(formula,data=data,no.baseline=FALSE,...)
{# {{{
formula.call <- formula
x <- phreg(formula,data=data,no.opt=TRUE,...)
xx <- x$cox.prep
### computation of intZHZ matrix, and gamma and baseline ##################
# {{{
eXb <- c(xx$sign) * c(xx$weights)
S0 = c(revcumsumstrata(eXb,xx$strata,xx$nstrata))
S0[S0==0] <- 1
E=apply(eXb*xx$X,2,revcumsumstrata,xx$strata,xx$nstrata)/S0;
if (no.baseline) E <- 0*E
###if (!no.int) E <- cbind(1,E)
###if (no.int) X <- xx$X else X <- cbind(1,xx$X)
###if (no.int) XX <- xx$XX else { XX <- .Call("vecCPMat",X)$XX }
X <- xx$X; XX <- xx$XX
###
S2=apply(eXb*XX,2,revcumsumstrata,xx$strata,xx$nstrata)
E2 <- .Call("vecCPMat",E)$XX
###
dts <- c(diffstrata(xx$time,xx$strata,xx$nstrata))
dt <- diff(c(0,xx$time))
###
intZbar <- apply(E*dts,2,cumsumstrata,xx$strata,xx$nstrata)
intZHZt <- apply((S2-S0*E2)*dts,2,cumsum)
p <- ncol(E)
intZHZ <- matrix(.Call("XXMatFULL",tail(intZHZt,1),p,PACKAGE="mets")$XXf,p,p)
IintZHZ <- solve(intZHZ)
intZHdN <- matrix(x$gradient,ncol(E),1)
XJ <- X[xx$jumps+1,]
if (no.baseline) intZHdN <- matrix(apply(XJ,2,sum),ncol(E),1)
gamma <- IintZHZ %*% intZHdN
###if (!no.int) nn <- c("int",colnames(x$X)) else
nn <- colnames(x$X)
rownames(gamma) <- nn
x$cumhaz[,2] <- x$cumhaz[,2]- intZbar[xx$jumps+1,] %*% gamma
# }}}
### iid gamma #########################################
# {{{
id <- xx$id
if (no.baseline==FALSE) {
mm <- X * c(X %*% gamma) * c(xx$time)+ apply( E* c(E %*% gamma)*dts,2,cumsumstrata,xx$strata,xx$nstrata) - X* c(intZbar %*% gamma) - c(X %*% gamma)* intZbar
mm <- c(xx$weights*xx$sign) * mm
mm <- apply(mm,2,sumstrata,id,max(id)+1)
###
MGt <- t(x$hessian %*% t(lava::iid(x))) + mm
XJ2l <- .Call("vecCPMat",x$U)$XX
XJ2l <- matrix(apply(XJ2l,2,sum),nrow=1)
varmg <- matrix(.Call("XXMatFULL",XJ2l,p,PACKAGE="mets")$XXf,p,p)
varmg <- IintZHZ %*% varmg %*% IintZHZ
} else {
mm <- X * c(X %*% gamma) * c(xx$time)
mm <- c(xx$weights*xx$sign) * mm
mm <- apply(mm,2,sumstrata,id,max(id)+1)
XJ2l <- .Call("vecCPMat",XJ)$XX
XJ2l <- matrix(apply(XJ2l,2,sum),nrow=1)
varmg <- matrix(.Call("XXMatFULL",XJ2l,p,PACKAGE="mets")$XXf,p,p)
varmg <- IintZHZ %*% varmg %*% IintZHZ
XdN <- apply(XJ,2,sumstrata,id[xx$jumps+1],max(id)+1)
MGt <- XdN-mm
}
iid <- MGt %*% IintZHZ
# }}}
### output #########################################
# {{{
coef <- c(gamma)
names(coef) <- nn
x$coef <- coef
x$var <- crossprod(iid)
x$varmg <- varmg
x$iid <- iid
x$intZHdN <- intZHdN
x$intZHZ <- intZHZ
x$formula <- formula.call
x$ihessian <- IintZHZ
## score of gamma
x$gradient <- c(intZHdN-intZHZ %*% gamma)
x$no.opt <- FALSE
class(x) <- c(class(x),"aalenMets")
# }}}
return(x)
}# }}}
aalenMetsOld <- function(formula,data=data,...)
{# {{{
formula.call <- formula
x <- phreg(formula,data=data,no.opt=TRUE,...)
xx <- x$cox.prep
###ii <- solve(x$hessian)
###S0i <- rep(0,length(xx$strata))
###S0i[xx$jumps+1] <- 1/x$S0
###Z <- xx$X
###U <- E <- matrix(0,nrow(xx$X),x$p)
###E[xx$jumps+1,] <- x$E
###U[xx$jumps+1,] <- x$U
###cumhaz <- cbind(xx$time,cumsumstrata(S0i,xx$strata,xx$nstrata))
###EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### computation of intZHZ matrix, and gamma and baseline ##################
# {{{
eXb <- c(xx$sign) * c(xx$weights)
S0 = c(revcumsumstrata(eXb,xx$strata,xx$nstrata))
E=apply(eXb*xx$X,2,revcumsumstrata,xx$strata,xx$nstrata)/S0;
S2=apply(eXb*xx$XX,2,revcumsumstrata,xx$strata,xx$nstrata)
###
###E2=.Call("vecMatMat",E,E)$vXZ;
E2 <- .Call("vecCPMat",E)$XX
###
dts <- c(diffstrata(xx$time,xx$strata,xx$nstrata))
dt <- diff(c(0,xx$time))
###
intZbar <- apply(E*dts,2,cumsumstrata,xx$strata,xx$nstrata)
intZHZt <- apply((S2-S0*E2)*dts,2,cumsum)
intZHZ <- matrix(0,ncol(E),ncol(E));
intZHZ[lower.tri(intZHZ,diag=TRUE)] <- tail(intZHZt,1)
intZHZ<- intZHZ+t(intZHZ)
diag(intZHZ) <- diag(intZHZ)/2
###intZHZ <- matrix(tail(intZHZt,1),ncol(E), ncol(E))
IintZHZ <- solve(intZHZ)
intZHdN <- matrix(x$gradient,ncol(E),1)
gamma <- IintZHZ %*% intZHdN
rownames(gamma) <- colnames(x$X)
x$cumhaz[,2] <- x$cumhaz[,2]- intZbar[xx$jumps+1,] %*% gamma
# }}}
### iid gamma #########################################
# {{{
mm <- xx$X * c(xx$X %*% gamma) * c(xx$time)+ apply( E* c(E %*% gamma)*dts,2,cumsumstrata,xx$strata,xx$nstrata) - xx$X* c(intZbar %*% gamma) - c(xx$X %*% gamma)* intZbar
mm <- c(xx$weights) * mm
id <- xx$id
mm <- apply(mm,2,sumstrata,id,max(id)+1)
MGt <- t(x$hessian %*% t(iid(x))) + mm
iid <- MGt %*% IintZHZ
# }}}
coef <- c(gamma)
names(coef) <- rownames(gamma)
x$coef <- coef
x$var <- crossprod(iid)
x$iid <- iid
x$intZHdN <- intZHdN
x$intZHZ <- intZHZ
x$formula <- formula.call
x$ihessian <- IintZHZ
## score of gamma
x$gradient <- c(intZHdN-intZHZ %*% gamma)
x$no.opt <- FALSE
class(x) <- c(class(x),"aalenMets")
return(x)
}# }}}
##' Kaplan-Meier with robust standard errors
##'
##' Kaplan-Meier with robust standard errors
##' Robust variance is default variance and obtained from the predict call
##' @param formula formula with 'Surv' 'Event' outcome
##' @param data data frame
##' @param ... Additional arguments to phreg
##' @author Thomas Scheike
##' @examples
##' library(mets)
##' data(sTRACE)
##' sTRACE$cluster <- sample(1:100,500,replace=TRUE)
##' out1 <- km(Surv(time,status==9)~strata(vf,chf),data=sTRACE)
##' out2 <- km(Surv(time,status==9)~strata(vf,chf)+cluster(cluster),data=sTRACE)
##'
##' summary(out1,times=1:3)
##' summary(out2,times=1:3)
##'
##' par(mfrow=c(1,2))
##' plot(out1,se=TRUE)
##' plot(out2,se=TRUE)
##' @export
km <- function(formula,data=data,...)
{# {{{
### coxo <- phreg(formula,data=data,...)
### coxo <- robust.phreg(coxo)
### chaz <- coxo$cumhaz[,2]
### time <- coxo$cumhaz[,1]
### if (robust) std.err <- coxo$robse.cumhaz[,2] else std.err <- coxo$se.cumhaz[,2]
### strat <- coxo$strata[coxo$jumps]
### S0i <- rep(0,length(coxo$S0))
### S0i[coxo$S0>0] <- 1/coxo$S0[coxo$S0>0]
### kmt <- exp(cumsumstrata(log(1-S0i),strat,coxo$nstrata))
### ### to use basehazplot.phreg
### res <- list(cumhaz=cbind(time,kmt),se.cumhaz=cbind(time,kmt*std.err),time=time,surv=kmt,
### strata=strat,nstrata=coxo$nstrata,jumps=1:length(kmt),strata.name=coxo$strata.name,strata.level=coxo$strata.level,
### model.frame=coxo$model.frame,formula=coxo$formula)
res <- phreg(formula,data=data,...)
rhs <- update(formula,-1~.)
varss <- all.vars(rhs)
## find all strata
first <- c(headstrata(res$strata.call,res$nstrata))
ddf <- data[first,varss]
pres <- predict(res,ddf,robust=TRUE,...)
pres$formula <- formula
pres$call <- match.call()
attr(pres,"data") <- ddf
class(pres) <- c("km","predictphreg")
return(pres)
}# }}}
##' @export
summary.km <- function(object,times=NULL,type=c("cif","cumhaz","surv")[3],...) { ## {{{
out <- summary.predictrecreg(object,times=times,type=type[1],...)
return(out)
} ## }}}
##' @export
plot.km <- function(x,...) { ## {{{
plot.predictphreg(x,...)
}# }}}
###predict.km <- function(object,newdata,...) { ## {{{
## take strata after readPhreg
### take relevant parts of prediction that is only for each strata
## out <- predict.phreg(object,newdata,se=se,conf.type=conf.type[1],...)
###}# }}}
##' Cumulative incidence with robust standard errors
##'
##' Cumulative incidence with robust standard errors
##' @param formula formula with 'Event' outcome and strata (only!)
##' @param data data frame
##' @param cause NULL looks at all, otherwise specify which cause to consider
##' @param cens.code censoring code "0" is default, and death is cens.code!=0
##' @param death.code alternative to cens.code give codes of death
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @examples
##' data(bmt)
##' bmt$cluster <- sample(1:100,408,replace=TRUE)
##' out1 <- cif(Event(time,cause)~+1,data=bmt,cause=1)
##' out2 <- cif(Event(time,cause)~+1+cluster(cluster),data=bmt,cause=1)
##'
##' par(mfrow=c(1,2))
##' plot(out1,se=TRUE)
##' plot(out2,se=TRUE)
##' @export
cif <- function(formula,data=data,cause=1,cens.code=0,death.code=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!inherits(Y,"Event")) stop("Expected a 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
}
if (!is.null(stratapos <- attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else strata.name <- NULL
if (!is.null(offsetpos <- attributes(Terms)$specials$offset)) {
ts <- survival::untangle.specials(Terms, "offset")
Terms <- Terms[-ts$terms]
offset <- m[[ts$vars]]
}
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
id.orig <- id;
if (!is.null(id)) {
ids <- sort(unique(id))
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(exit))-1;
statusE <- 1*(status %in% cause)
if (is.null(death.code)) statusD <- 1*(!(status %in% cens.code)) else statusD <- 1*(status %in% death.code)
data$statusE__ <- statusE
data$statusD__ <- statusD
data$strata__ <- strata
### setting up formulae for the two phreg (cause of interest and death)
if (is.null(id.orig)) {
formid <- update.formula(formula,~.+cluster(id))
data$id <- id
} else formid <- formula
tt <- terms(formid)
tt <- delete.response(tt)
formid <- formula(tt)
if (ncol(Y)==3) {
formE <- as.formula(paste("Surv(entry,exit,statusE__)~+1"))
formD <- as.formula(paste("Surv(entry,exit,statusD__)~+1"))
} else {
formE <- as.formula(paste("Surv(exit,statusE__)~+1"))
formD <- as.formula(paste("Surv(exit,statusD__)~+1"))
}
formE <- update.formula(formE,formid)
formD <- update.formula(formD,formid)
if (sum(statusE)==0) warning("No events of type 1\n");
coxE <- phreg(formE,data=data,...)
coxS <- phreg(formD,data=data,...)
### cif
if (sum(statusE)>0) cifo <- recurrentMarginalPhreg(coxE,coxS) else cifo <- coxE
## to work with predict function
## cifo$no.opt <- TRUE
### to use basehazplot.phreg
class(cifo) <- c("cif","phreg")
attr(cifo,"cause") <- cause
attr(cifo,"cens.code") <- cens.code
attr(cifo,"death.code") <- death.code
return(cifo)
}# }}}
##' @export
plot.cif <- function(x,se=FALSE,ylab=NULL,ylim=c(0,1),conf.type=c("log","plain"),...) { ## {{{
if (inherits(x,"cif") & is.null(ylab)) ylab <- "Probability"
baseplot(x,se=se,ylab=ylab,ylim=ylim,restrict="prob",conf.type=conf.type[1],...)
} ## }}}
##' @export
summary.cif <- function(object,se=FALSE,ylab=NULL,times=NULL,conf.type=c("log","plain"),...) { ## {{{
if (inherits(object,"cif") & is.null(ylab)) ylab <- "Probability"
out <- summaryRecurrentobject(object,name="probability",times=times,conf.type=conf.type[1],restrict="prob",...)
return(out)
} ## }}}
##' Proportional odds survival model
##'
##' Semiparametric Proportional odds model, that has the advantage that
##' \deqn{
##' logit(S(t|x)) = \log(\Lambda(t)) + x \beta
##' }
##' so covariate effects give OR of survival.
##'
##' This is equivalent to using a hazards model
##' \deqn{
##' Z \lambda(t) \exp(x \beta)
##' }
##' where Z is gamma distributed with mean and variance 1.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for exp(x beta) terms
##' @param weights weights for score equations
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @references
##'
##' The proportional odds cumulative incidence model for competing risks,
##' Eriksson, Frank and Li, Jianing and Scheike, Thomas and Zhang, Mei-Jie,
##' Biometrics, 2015, 3, 687--695, 71,
##'
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- logitSurv(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##' summary(out1)
##' gof(out1)
##' plot(out1)
##' @export
logitSurv <- function(formula,data,offset=NULL,weights=NULL,...)
{# {{{
out <- phreg(formula,data,offset=offset,weights=weights,propodds=1,...)
out$se.cumhaz <- NULL
return(out)
}# }}}
## {{{ Utility functions, cumsumstrata ....
##' @export
tailstrata <- function(strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("tailstrataR",length(strata),strata,nstrata,PACKAGE="mets")
if (any(res$found<0.5)) { warning("Not all strata found"); cat((1:nstrata)[res$found>0.5]); }
return(res$where)
}# }}}
##' @export
headstrata <- function(strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("headstrataR",length(strata),strata,nstrata,PACKAGE="mets")
if (any(res$found<0.5)) { warning("Not all strata found"); cat((1:nstrata)[res$found>0.5]); }
return(res$where)
}# }}}
##' @export
sumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("sumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
cumsumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("cumsumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
diffstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("diffstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("revcumsumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsum2strata <- function(x,strata,nstrata,strata2,nstrata2,lag=FALSE)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
res <- .Call("revcumsum2strataR",as.double(x),strata,nstrata,strata2,nstrata2,PACKAGE="mets")
return(res)
}# }}}
##' @export
revcumsum2stratafdN <- function(x,y,strata,nstrata,strata2,nstrata2,startx)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
if (length(x)!=length(y)) stop("length of x and y must be same\n");
res <- .Call("revcumsum2stratafdNR",as.double(x),as.double(y),strata,nstrata,strata2,nstrata2,as.double(startx),PACKAGE="mets")
return(res)
}# }}}
##' @export
cumsum2strata <- function(x,y,strata,nstrata,strata2,nstrata2,startx)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
res <- .Call("cumsum2strataR",as.double(x),as.double(y),strata,nstrata,strata2,nstrata2,as.double(startx),PACKAGE="mets")
return(res)
}# }}}
##' @export
vecAllStrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("vecAllStrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsum <- function(x)
{# {{{
res <- .Call("revcumsumR",x,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsumstratasum <- function(x,strata,nstrata,type="all")
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (type=="sum") res <- .Call("revcumsumstratasumR",x,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumstratasumR",x,strata,nstrata)$lagsum
if (type=="all") res <- .Call("revcumsumstratasumR",x,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumstratasum <- function(x,strata,nstrata,type="all")
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (type=="sum") res <- .Call("cumsumstratasumR",x,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("cumsumstratasumR",x,strata,nstrata)$lagsum
if (type=="all") res <- .Call("cumsumstratasumR",x,strata,nstrata)
return(res)
}# }}}
##' @export
matdoubleindex <- function(x,rows,cols,xvec=NULL)
{# {{{
if (!is.matrix(x)) stop("x must be matrix")
ncols <- ncol(x); nrows <- nrow(x)
## to avoid warnings when going to C, get rid of Inf
cols[cols==Inf] <- ncol(x)+1;
rows[rows==Inf] <- nrow(x)+1;
if (length(rows)==1) rows <- rep(rows,length(cols))
if (length(cols)==1) cols <- rep(cols,length(rows))
if (length(cols)!=length(rows)) stop("rows and cols different lengths\n");
if (is.null(xvec)) { assign <- 0; xvec <- 1} else {
assign <- 1;
if (length(cols)!=length(xvec)) stop("rows and cols and xvec differ \n");
}
res <- .Call("Matdoubleindex",x,rows-1,cols-1,length(cols),assign,xvec)$mat
return(res)
}# }}}
##' @export
mdi <- function(x,...) matdoubleindex(x,...)
##' @export
covfr <- function(x,y,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfR",x,y,strata,nstrata)
return(res)
}# }}}
##' @export
revcumsumidstratasum <- function(x,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$lagsum
if (type=="lagsumsquare") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$lagsumsquare
if (type=="all") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
revcumsumidstratasumCov <- function(x,y,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$lagsum
if (type=="lagsumsquare") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$lagsumsquare
if (type=="all") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumidstratasumCov <- function(x,y,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("cumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$sum
else res <- .Call("cumsumidstratasumCovR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumidstratasum <- function(x,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("cumsumidstratasumR",x,id,nid,strata,nstrata)$sum
else res <- .Call("cumsumidstratasumR",x,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
covfridstrata <- function(x,y,id,nid,strata,nstrata)
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfstrataR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
covfridstrataCov <- function(x,y,x1,y1,id,nid,strata,nstrata)
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfstrataCovR",x,y,x1,y1,id,nid,strata,nstrata)
return(res)
}# }}}
## }}}
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Defines functions phreg phreg01
Documented in phreg
###{{{ phreg01
phreg01 <- function(X,entry,exit,status,id=NULL,strata=NULL, offset=NULL,weights=NULL,strata.name=NULL,cumhaz=TRUE,
beta,stderr=TRUE,method="NR",no.opt=FALSE,Z=NULL,propodds=NULL,AddGam=NULL,
case.weights=NULL,no.var=0,augmentation=0,...) {
p <- ncol(X)
if (missing(beta)) beta <- rep(0,p)
if (p==0) X <- cbind(rep(0,length(exit)))
if (is.null(strata)) { strata <- rep(0,length(exit)); nstrata <- 1; strata.level <- NULL; } else {
strata.level <- levels(strata)
ustrata <- sort(unique(strata))
nstrata <- length(ustrata)
strata.values <- ustrata
if (is.numeric(strata)) strata <- fast.approx(ustrata,strata)-1 else {
strata <- as.integer(factor(strata,labels=seq(nstrata)))-1
}
}
if (is.null(offset)) offset <- rep(0,length(exit))
if (is.null(weights)) weights <- rep(1,length(exit))
strata.call <- strata
Zcall <- matrix(1,1,1) ## to not use for ZX products when Z is not given
if (!is.null(Z)) Zcall <- Z
## possible casewights to use for bootstrapping and other things
if (is.null(case.weights)) case.weights <- rep(1,length(exit))
trunc <- (!is.null(entry))
if (!trunc) entry <- rep(0,length(exit))
call.id <- id
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(entry))-1;
## orginal id coding into integers
id.orig <- id+1;
dd <- .Call("FastCoxPrepStrata", entry,exit,status,X,id,trunc,strata,weights,offset,Zcall,case.weights,PACKAGE="mets")
dd$nstrata <- nstrata
obj <- function(pp,U=FALSE,all=FALSE) {# {{{
if (length(dd$jumps) >0) {
if (is.null(propodds) & is.null(AddGam)) {
val <- with(dd, .Call("FastCoxPLstrata",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,caseweights,PACKAGE="mets"))
} else if (is.null(AddGam))
val <- with(dd, .Call("FastCoxPLstrataPO",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,propodds,PACKAGE="mets"))
else val <- with(dd, .Call("FastCoxPLstrataAddGam",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,
AddGam$theta,AddGam$dimthetades,AddGam$thetades,AddGam$ags,AddGam$varlink,AddGam$dimjumprv,AddGam$jumprv,
AddGam$JumpsCauses,PACKAGE="mets"))
val$gradient <- val$gradient+augmentation
} else {
val <- list(jumps=NULL,ploglik=NULL,U=NULL,gradient=NULL,hessian=NULL,hessiantime=NULL,S2S0=NULL,E=NULL,S0=NULL)
}
if (all) {
val$time <- dd$time
### plus 1 for R index
val$ord <- dd$ord+1
val$jumps <- dd$jumps+1
val$jumptimes <- val$time[val$jumps]
val$weightsJ <- dd$weights[val$jumps]
val$case.weights <- dd$case.weights[val$jumps]
val$nevent <- length(val$S0)
val$nstrata <- dd$nstrata
val$strata <- dd$strata
val$strata.jumps <- val$strata[val$jumps]
return(val)
}
n <- length(dd$time)
with(val,structure(-ploglik/n,gradient=-gradient/n,hessian=-hessian/n))
}# }}}
opt <- NULL
if (p>0) {
if (no.opt==FALSE) {
if (tolower(method)=="nr") {
tim <- system.time(opt <- lava::NR(beta,obj,...))
opt$timing <- tim
opt$estimate <- opt$par
} else {
opt <- nlm(obj,beta,...)
opt$method <- "nlm"
}
cc <- opt$estimate; names(cc) <- colnames(X)
if (!stderr) return(cc)
val <- c(list(coef=cc), obj(opt$estimate,all=TRUE))
} else val <- c(list(coef=beta), obj(beta,all=TRUE))
} else {
val <- obj(0,all=TRUE)
}
se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL
II <- NULL
if (no.opt==FALSE & p!=0) {
II <- - tryCatch(solve(val$hessian),error=function(e) matrix(0,nrow(val$hessian),ncol(val$hessian)) )
} else II <- matrix(0,p,p)
## Brewslow estimator, to handle also possible weights, caseweights that are 0
ww <- val$caseweightsJ * val$weightsJ
val$S0[abs(ww)<.00000001] <- 0
### computes Breslow estimator
if (cumhaz==TRUE & (length(val$jumps)>0)) { # {{{
strata <- val$strata[val$jumps]
nstrata <- val$nstrata
jumptimes <- val$jumptimes
## Brewslow estimator, to handle also possible weights/case-weights, and caseweights that are 0
S0i2 <- S0i <- rep(0,length(val$S0))
wwJ <- val$caseweightsJ*val$weightsJ
S0i[val$S0>0] <- 1/val$S0[val$S0>0]
S0i2[val$S0>0] <- 1/(val$S0[val$S0>0]^2*wwJ[val$S0>0])
cumhaz <- cbind(jumptimes,cumsumstrata(S0i,strata,nstrata))
if ((no.opt==FALSE & p!=0)) {
DLambeta.t <- apply(val$E*S0i,2,cumsumstrata,strata,nstrata)
varbetat <- rowSums((DLambeta.t %*% II)*DLambeta.t)
### covv <- apply(covv*DLambeta.t,1,sum) Covariance is "0" by construction
} else varbetat <- 0
var.cumhaz <- cumsumstrata(S0i2,strata,nstrata)+varbetat
se.cumhaz <- cbind(jumptimes,(var.cumhaz)^.5)
colnames(cumhaz) <- c("time","cumhaz")
colnames(se.cumhaz) <- c("time","se.cumhaz")
} # }}}
else {cumhaz <- se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL}
res <- c(val,
list(cox.prep=dd,
strata.call=strata.call, strata.level=strata.level,
entry=entry,
exit=exit,
status=status,
p=p,
X=X,
offsets=offset,
weights=weights,
id=id.orig, call.id=call.id,
opt=opt,
no.opt=no.opt,
cumhaz=cumhaz, se.cumhaz=se.cumhaz,
lcumhaz=lcumhaz, lse.cumhaz=lse.cumhaz,
ihessian=II,
II=II,strata.name=strata.name,propodds=propodds))
class(res) <- "phreg"
## also computing robust variance
if (p>0 & no.var==0) {
beta.iid <- iid(res)
phvar <- crossprod(beta.iid)
colnames(phvar) <- rownames(phvar) <- names(res$coef)
res$var <- phvar
res$beta.iid <- beta.iid
} else res$var <- 0
return(res)
}
###}}} phreg0
###{{{ phreg
##' Fast Cox PH regression
##'
##' Fast Cox PH regression
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for Cox model
##' @param weights weights for Cox score equations
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases phreg phreg.par robust.phreg readPhreg IIDbaseline.phreg conftype plotO.predictphreg plotpredictphreg predictO.phreg predictrecreg summarybase.phreg
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##' ## robust standard errors default
##' summary(out1)
##'
##' par(mfrow=c(1,2))
##' plot(out1)
##'
##' ## computing robust variance for baseline
##' rob1 <- robust.phreg(out1)
##' plot(rob1,se=TRUE,robust=TRUE)
##'
##' ## taking iid decomposition of regression parameters
##' betaiiid <- lava::iid(out1)
##'
##' ## making iid decomposition of baseline at a specific time-point
##' Aiiid <- mets::IIDbaseline.phreg(out1,time=30)
##'
##' @export
phreg <- function(formula,data,offset=NULL,weights=NULL,...) {# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
### if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (!inherits(Y,c("Event","Surv"))) stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
} else pos.cluster <- NULL
if (!is.null(attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
pos.strata <- ts$terms
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else { strata.name <- NULL; pos.strata <- NULL}
### if (!is.null(attributes(Terms)$specials$offset)) {
### ts <- survival::untangle.specials(Terms, "offset")
### pos.offset <- ts$terms
### Terms <- Terms[-ts$terms]
### offset <- m[[ts$vars]]
### } else pos.offset <- NULL
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
res <- c(phreg01(X,entry,exit,status,id,strata,offset,weights,strata.name,...),
list(call=cl,model.frame=m,formula=formula,strata.pos=pos.strata,
cluster.pos=pos.cluster,n=length(exit)))
class(res) <- "phreg"
res
}# }}}
##' @export
readPhreg <- function (object, newdata, nr=TRUE, ...)
{# {{{
exit <- entry <- status <- clusters <- NULL
if (missing(newdata)) { # {{{
X <- object$X
strataNew <- object$strata
if (!nr) {
exit <- object$exit; entry <- object$entry; status <- object$status;
clusters <- object$id
}
} else { ## make design for newdata
xlev <- lapply(object$model.frame,levels)
ff <- unlist(lapply(object$model.frame,is.factor))
upf <- update(object$formula,~.)
tt <- terms(upf)
if (nr) tt <- delete.response(tt)
X <- model.matrix(tt,data=newdata,xlev=xlev)[,-1,drop=FALSE]
if (!nr) {
allvar <- all.vars(tt)
pr <- length(allvar)-ncol(object$model.frame)+1
if (pr==2) {
exit <- newdata[,allvar[1]]
status <- newdata[,allvar[2]]
} else {
entry <- newdata[,allvar[1]]
exit <- newdata[,allvar[2]]
status <- newdata[,allvar[3]]
}
}
clusterTerm<- grep("^cluster[(][A-z0-9._:]*",colnames(X),perl=TRUE)
## remove clusterTerm from design
if (length(clusterTerm)==1) {
clusters <- X[,clusterTerm]
X <- X[,-clusterTerm,drop=FALSE]
id <- clusters
id.orig <- id;
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
clusters <- id
} else clusters <- (1:nrow(newdata))-1
}
strataTerm<- grep("^strata[(][A-z0-9._:]*",colnames(X),perl=TRUE)
## remove strataTerm from design, and construct numeric version of strata
if (length(strataTerm)>=1) {
strataNew <- X[,strataTerm,drop=FALSE]
whichstrata <- paste(object$strata.name,object$strata.level,sep="")
if (length(strataTerm)>=1) { ## construct strata levels numeric
mm <- match(colnames(X)[strataTerm], whichstrata)-1
strataNew <- c(strataNew %*% mm )
}
X <- X[,-strataTerm,drop=FALSE]
} else strataNew <- rep(0,nrow(X))
}# }}}
return(list(X=X,strata=strataNew,entry=entry,exit=exit,status=status,clusters=clusters))
}# }}}
###}}} phreg
###{{{ phregR
##' Fast Cox PH regression and calculations done in R to make play and adjustments easy
##'
##' Fast Cox PH regression with R implementation to play and adjust in R function: FastCoxPLstrataR
##'
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for cox model
##' @param weights weights for Cox score equations
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases FastCoxPLstrataR
##'
##' @export
phregR <- function(formula,data,offset=NULL,weights=NULL,...) {# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
} else pos.cluster <- NULL
if (!is.null(attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
pos.strata <- ts$terms
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else { strata.name <- NULL; pos.strata <- NULL}
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
res <- c(phreg01R(X,entry,exit,status,id,strata,offset,weights,strata.name,...),
list(call=cl,model.frame=m,formula=formula,strata.pos=pos.strata,cluster.pos=pos.cluster,
n=length(exit)))
class(res) <- "phreg"
res
}# }}}
phreg01R <- function(X,entry,exit,status,id=NULL,strata=NULL,offset=NULL,weights=NULL,
strata.name=NULL,cumhaz=TRUE,
beta,stderr=TRUE,method="NR",no.opt=FALSE,Z=NULL,propodds=NULL,AddGam=NULL,
case.weights=NULL,...) {# {{{
p <- ncol(X)
if (missing(beta)) beta <- rep(0,p)
if (p==0) X <- cbind(rep(0,length(exit)))
if (is.null(strata)) { strata <- rep(0,length(exit)); nstrata <- 1; strata.level <- NULL; } else {
strata.level <- levels(strata)
ustrata <- sort(unique(strata))
nstrata <- length(ustrata)
strata.values <- ustrata
if (is.numeric(strata)) strata <- fast.approx(ustrata,strata)-1 else {
strata <- as.integer(factor(strata,labels=seq(nstrata)))-1
}
}
if (is.null(offset)) offset <- rep(0,length(exit))
if (is.null(weights)) weights <- rep(1,length(exit))
strata.call <- strata
Zcall <- matrix(1,1,1) ## to not use for ZX products when Z is not given
if (!is.null(Z)) Zcall <- Z
## possible casewights to use for bootstrapping and other things
if (is.null(case.weights)) case.weights <- rep(1,length(exit))
trunc <- (!is.null(entry))
if (!trunc) entry <- rep(0,length(exit))
if (!is.null(id)) {
ids <- unique(id)
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(entry))-1;
## orginal id coding into integers
id.orig <- id+1;
dd <- .Call("FastCoxPrepStrata", entry,exit,status,X, id,trunc,strata,weights,offset,Zcall,case.weights,PACKAGE="mets")
dd$nstrata <- nstrata
obj <- function(pp,U=FALSE,all=FALSE) {# {{{
if (is.null(propodds) & is.null(AddGam))
cc <- system.time(
val <- with(dd, FastCoxPLstrataR(pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,caseweights))
)
else if (is.null(AddGam))
val <- with(dd, .Call("FastCoxPLstrataPO",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,propodds,PACKAGE="mets"))
else val <- with(dd, .Call("FastCoxPLstrataAddGam",pp,X,XX,sign,jumps, strata,nstrata,weights,offset,ZX,
AddGam$theta,AddGam$dimthetades,AddGam$thetades,AddGam$ags,AddGam$varlink,AddGam$dimjumprv,AddGam$jumprv,AddGam$JumpsCauses,PACKAGE="mets"))
if (all) {
val$time <- dd$time
val$ord <- dd$ord+1
val$jumps <- dd$jumps+1
val$jumptimes <- val$time[val$jumps]
val$weightsJ <- dd$weights[val$jumps]
val$case.weights <- dd$case.weights[val$jumps]
val$strata.jumps <- val$strata[val$jumps]
val$nevent <- length(val$S0)
val$nstrata <- dd$nstrata
val$strata <- dd$strata
return(val)
}
with(val,structure(-ploglik,gradient=-gradient,hessian=-hessian))
}# }}}
opt <- NULL
if (p>0) {
if (no.opt==FALSE) {
if (tolower(method)=="nr") {
tim <- system.time(opt <- lava::NR(beta,obj,...))
opt$timing <- tim
opt$estimate <- opt$par
} else {
opt <- nlm(obj,beta,...)
opt$method <- "nlm"
}
cc <- opt$estimate; names(cc) <- colnames(X)
if (!stderr) return(cc)
val <- c(list(coef=cc),obj(opt$estimate,all=TRUE))
} else val <- c(list(coef=beta),obj(beta,all=TRUE))
} else {
val <- obj(0,all=TRUE)
}
se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL
II <- NULL
### computes Breslow estimator
if (cumhaz==TRUE) { # {{{
if (no.opt==FALSE & p!=0) {
II <- - tryCatch(solve(val$hessian),error=
function(e) matrix(0,nrow(val$hessian),ncol(val$hessian)) )
} else II <- matrix(0,p,p)
strata <- val$strata[val$jumps]
nstrata <- val$nstrata
jumptimes <- val$jumptimes
## Brewslow estimator
cumhaz <- cbind(jumptimes,cumsumstrata(1/val$S0,strata,nstrata))
if ((no.opt==FALSE & p!=0)) {
DLambeta.t <- apply(val$E/c(val$S0),2,cumsumstrata,strata,nstrata)
varbetat <- rowSums((DLambeta.t %*% II)*DLambeta.t)
### covv <- apply(covv*DLambeta.t,1,sum) Covariance is "0" by construction
} else varbetat <- 0
var.cumhaz <- cumsumstrata(1/val$S0^2,strata,nstrata)+varbetat
se.cumhaz <- cbind(jumptimes,(var.cumhaz)^.5)
colnames(cumhaz) <- c("time","cumhaz")
colnames(se.cumhaz) <- c("time","se.cumhaz")
} # }}}
else {cumhaz <- se.cumhaz <- lcumhaz <- lse.cumhaz <- NULL}
res <- c(val,
list(cox.prep=dd,
strata.call=strata.call, strata.level=strata.level,
entry=entry,
exit=exit,
status=status,
p=p,
X=X,
offsets=offset,
weights=weights,
id=id.orig,
opt=opt,
cumhaz=cumhaz, se.cumhaz=se.cumhaz,
lcumhaz=lcumhaz, lse.cumhaz=lse.cumhaz,
II=II,strata.name=strata.name,propodds=propodds))
class(res) <- "phreg"
## also computing robust variance
if (p>0) {
phvar <- crossprod(iid(res))
colnames(phvar) <- rownames(phvar) <- names(res$coef)
res$var <- phvar
} else res$var <- 0
return(res)
}# }}}
##' @export
FastCoxPLstrataR <- function(beta, X, XX, Sign, Jumps, strata, nstrata, weights, offsets, ZX, caseweights)
{# {{{
p=length(beta)
strata=c(strata)
Xb = c(X %*% beta+offsets)
eXb = c(exp(Xb)*weights);
if (nrow((Sign))==length(eXb)) { ## Truncation
eXb = c(Sign)*eXb;
}
S0 = c(revcumsumstrata(eXb,strata,nstrata))
E=apply(eXb*X,2,revcumsumstrata,strata,nstrata)/S0;
Jumps=Jumps+1
E = E[Jumps,];
E2=.Call("vecMatMat",E,E)$vXZ;
XX2=apply(XX*eXb,2,revcumsumstrata,strata,nstrata)/S0;
## mat XX2=revcumsumstrataMatCols(XX,eXb,S0,strata,nstrata);
XX2 = XX2[Jumps,];
weightsJ=weights[Jumps];
caseweightsJ=caseweights[Jumps];
S0 = S0[Jumps];
grad = (X[Jumps,]-E); ## Score
val = (Xb[Jumps]-log(S0)); ## Partial log-likelihood
## colvec iweightsJ=1/weightsJ;
S02 = S0/(caseweightsJ*weightsJ); ## S0 with weights to estimate baseline
grad2= grad*(caseweightsJ*weightsJ); ## score with weights
gradient=apply(grad2,2,sum)
val2 = caseweightsJ*weightsJ*val; ## Partial log-likelihood with weights
hesst = -(XX2-E2); ## hessian contributions in jump times
hesst2 = hesst*(caseweightsJ*weightsJ); ## hessian over time with weights
hess2 = matrix(apply(hesst2,2,sum),p,p); ## hessian with weights
out=list(jumps=Jumps, ploglik=sum(val2),U=grad2,
gradient=matrix(gradient,1,p), hessian=hess2, hessianttime=hesst2, S2S0=XX2, E=E, S0=S02 )
return(out)
}# }}}
###}}}
###{{{ iid & Robust variances
##' @export
IC.phreg <- function(x,type="robust",all=FALSE,baseline=FALSE,...) {# {{{
if (baseline) {
if (inherits(x, "cifreg")) {
res <- IIDbaseline.cifreg(x, ...)$base.iid
} else {
res <- IIDbaseline.phreg(x, ...)$base.iid
}
tryCatch(rownames(res) <- rownames(x$X), error=function(...) NULL)
return(res*NROW(res))
}
classes1 <- "mlogit"
if ((length(class(x))==1) || inherits(x, classes1)) {
invhess <- -solve(x$hessian)
orig.order <- FALSE
if (is.null(x$propodds)) {
if (type=="robust") { # {{{ cox model
xx <- x$cox.prep
ii <- invhess
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
cumhaz <- cbind(xx$time,cumsumstrata(S0i,xx$strata,xx$nstrata))
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz[,2]-EdLam0)*rr*c(xx$weights)
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of iid variable
MGt <- MGt[oo,,drop=FALSE] ## sum after id later so not needed
id <- xx$id[oo]
} else id <- xx$id
} else {
MGt <- x$U; MG.base <- 1/x$S0;
}# }}}
} else { # {{{ prop-odds model logitSurv
xx <- x$cox.prep
ii <- invhess
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
cumhazA <- cumsumstratasum(S0i,xx$strata,xx$nstrata,type="all")
cumhaz <- c(cumhazA$sum)
cumhazm <- cumhazA$lagsum
###
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
rro <- c(exp(Z %*% coef(x) + xx$offset))
S0star <- revcumsumstrata(rr/(1+rro*cumhazm),xx$strata,xx$nstrata)
S0 <- revcumsumstrata(rr,xx$strata,xx$nstrata)
S1 <- apply(Z*rr,2,revcumsumstrata,xx$strata,xx$nstrata)
Et <- S1/c(S0)
lt <- apply((Z-Et)*c(rr*rro/(1+rro*cumhazm)),2,revcumsumstrata,xx$strata,xx$nstrata)
Estar <- S0star/S0
EstardLam <- cumsumstrata(Estar*S0i,xx$strata,xx$nstrata)
k <- exp(-EstardLam)
basecor <- apply(lt*c(k*S0i),2,revcumsumstrata,xx$strata,xx$nstrata)
basecor <- basecor/c(k*S0)
www <- x$propoddsW*x$weightsJ
U[xx$jumps+1,] <- U[xx$jumps+1,]-c(www)*basecor[xx$jumps+1,]
MGt <- U;
if (type=="robust") {
baseDLam0 <- apply(basecor*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz-EdLam0-baseDLam0)*rr*c(xx$weights) ### -baseIII
} else MGt <- MGt[xx$jumps+1,]
MG.base <- 1/x$S0;
id <- xx$id
}# }}}
ncluster <- NULL
if (type == "robust" & (!is.null(x$id) | any(x$entry > 0))) {
if (type == "martingale") id <- x$id[x$jumps]
### ii <- mets::cluster.index(id)
UU <- apply(MGt, 2, sumstrata, id, max(id) + 1)
### names of clusters given in call
ncluster <- nrow(UU)
} else {
UU <- MGt
}
res <- structure(UU %*% invhess, invhess = invhess, ncluster = ncluster)
if (is.null(colnames(res)))
colnames(res) <- names(coef(x))
tryCatch(rownames(res) <- rownames(x$X), error=function(...) NULL)
res <- res*NROW(res)
return(res)
} else if (inherits(x,c("cifreg","recreg","IPTW"))) {
if (inherits(x,c("IPTW"))) res <- x$IID else res <- x$iid
if (is.null(colnames(res)))
colnames(res) <- names(coef(x))
res <- res*NROW(res)
return(res)
}
} # }}}
##' @export IIDbaseline.phreg
IIDbaseline.phreg <- function(x,time=NULL,ft=NULL,fixbeta=NULL,beta.iid=NULL,...)
{# {{{
### sum_i int_0^t f(s)/S_0(s) dM_{ki}(s) - P(t) \beta_k
### with possible strata and cluster "k", and i in clusters
if (!inherits(x,"phreg")) stop("Must be phreg object\n");
if (is.null(time)) stop("Must give time for iid of baseline")
if (!is.null(x$propodds)) stop("Only for Cox model")
### sets fixbeta based on wheter xr has been optimized in beta (so cox case)
if (is.null(fixbeta))
if ((x$no.opt) | is.null(x$coef)) fixbeta<- 1 else fixbeta <- 0
xx <- x$cox.prep
btimexx <- c(1*(xx$time < time))
S0i2 <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
ww <- xx$caseweights*xx$weights
S0i2[xx$jumps+1] <- 1/(x$S0^2*ww[xx$jump+1])
Z <- xx$X
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
### only up to time t for A
if (is.null(ft)) ft <- rep(1,length(xx$time))
if (is.matrix(ft)) ft <- c(ft)
cumhaz <- c(cumsumstrata(ft*S0i,xx$strata,xx$nstrata))
cumS0i2 <- c(cumsumstrata(ft*S0i2*btimexx,xx$strata,xx$nstrata))
if (fixbeta==0) {
EdLam0 <- apply(ft*E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
Ht <- apply(ft*E*S0i*btimexx,2,cumsumstrata,xx$strata,xx$nstrata)
} else Ht <- NULL
if (fixbeta==0) rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset)) else rr <- c(xx$sign*exp(xx$offset))
id <- xx$id
mid <- max(id)+1
MGAiid <- ft*S0i*btimexx-cumS0i2*rr*c(xx$weights)
MGtiid <- NULL
if (fixbeta==0) {# {{{
if (!is.null(beta.iid)) MGtiid <- beta.iid else {
invhess <- -solve(x$hessian)
MGt <- ft*U[,drop=FALSE]-(Z*cumhaz-EdLam0)*rr*c(xx$weights)
MGt <- MGt %*% invhess
MGtiid <- apply(MGt,2,sumstrata,id,mid)
}
## Ht efter strata
Htlast <- tailstrata(xx$strata,xx$nstrata)
HtS <- Ht[Htlast,,drop=FALSE]
}# }}}
### \hat beta - \beta = \sum_i \beta_i (iid)
### iid after baseline:
### \hat A_s-A_s=\sum_{i clusters} \sum_{j: i(j)=i, s(j)=s} \int_0^t 1/S_0 dM^s_{i,j} - P^s(t) \sum_i \beta_i
### = \sum_{i clusters} ( \sum_{j \in i(j)=i, s(j)=s} \int_0^t 1/S_0 dM^s_j - P^s(t) \beta_i )
## sum after id's within strata and order
MGAiids <- c()
sus <- sort(unique(xx$strata))
for (i in sus) {
wi <- which(xx$strata==i)
MGAiidl <- sumstrata(MGAiid[xx$strata==i],xx$id[xx$strata==i],mid)
if (fixbeta==0) {
UU <- apply(HtS[i+1,]*t(MGtiid),2,sum)
MGAiidl <- MGAiidl - UU
}
MGAiids <- cbind(MGAiids,MGAiidl)
}
MGAiid <- MGAiids
colnames(MGAiid) <- paste("strata",sus,sep="")
return(list(time=time,base.iid=MGAiid,strata=xx$strata,nstrata=xx$nstrata,
id=id,beta.iid=MGtiid,model.frame=x$model.frame,formula=x$formula))
} # }}}
##' @export
residuals.phreg <- function(object,cumsum=FALSE,...) {# {{{
orig.order <- FALSE
x <- object
if (is.null(x$propodds)) { # {{{ cox model
xx <- x$cox.prep
dN <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
dN[xx$jumps+1] <- 1
cumhaz <- cumsumstrata(S0i,xx$strata,xx$nstrata)
Z <- xx$X
if (is.null(coef(x)))
rr <- c(xx$sign*exp(xx$offset))
else
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
### dMartingale as a function of time and for all subjects to handle strata
Lamt <- (cumhaz)*rr*c(xx$weights)
dMGt <- dN-Lamt
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of iid variable
dMGt <- dMGt[oo,,drop=FALSE] ## sum after id later so not needed
id <- xx$id[oo]
} else id <- xx$id
} else { ## }}}
# {{{ prop-odds model logitSurv
xx <- x$cox.prep
dN <- S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
dN[xx$jumps+1] <- 1
U <- E <- matrix(0,nrow(xx$X),x$p)
E[xx$jumps+1,] <- x$E
U[xx$jumps+1,] <- x$U
S0i <- rep(0,length(xx$strata))
S0i[xx$jumps+1] <- 1/x$S0
cumhazA <- cumsumstratasum(S0i,xx$strata,xx$nstrata,type="all")
cumhaz <- c(cumhazA$sum)
cumhazm <- cumhazA$lagsum
###
EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
rr <- c(xx$sign*exp(Z %*% coef(x) + xx$offset))
rro <- c(exp(Z %*% coef(x) + xx$offset))
S0star <- revcumsumstrata(rr/(1+rro*cumhazm),xx$strata,xx$nstrata)
S0 <- revcumsumstrata(rr,xx$strata,xx$nstrata)
S1 <- apply(Z*rr,2,revcumsumstrata,xx$strata,xx$nstrata)
Et <- S1/c(S0)
lt <- apply((Z-Et)*c(rr*rro/(1+rro*cumhazm)),2,revcumsumstrata,xx$strata,xx$nstrata)
Estar <- S0star/S0
EstardLam <- cumsumstrata(Estar*S0i,xx$strata,xx$nstrata)
k <- exp(-EstardLam)
basecor <- apply(lt*c(k*S0i),2,revcumsumstrata,xx$strata,xx$nstrata)
basecor <- basecor/c(k*S0)
www <- x$propoddsW*x$weightsJ
U[xx$jumps+1,] <- U[xx$jumps+1,] - c(www)* basecor[xx$jumps+1,]
baseDLam0 <- apply(basecor*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### Martingale as a function of time and for all subjects to handle strata
MGt <- U[,drop=FALSE]-(Z*cumhaz-EdLam0-baseDLam0)*rr*c(xx$weights)
if (orig.order) {
oo <- (1:nrow(xx$X))[xx$ord+1]
oo <- order(oo)
### back to order of data-set
MGt <- MGt[oo,,drop=FALSE]
id <- xx$id[oo]
} else id <- xx$id
}# }}}
ncluster <- NULL
if (!cumsum) {
mid <- max(id)+1
Mt <- sumstrata(dMGt,id,mid)
cumhaz <- sumstrata(Lamt,id,mid)
out <- list(residuals=c(Mt),cumhaz=c(cumhaz))
} else {
mid <- max(id)+1
out <- data.frame(dMGt=c(dMGt),Lamt=Lamt,status=dN,
time=c(xx$time),id=c(xx$id)+1,sign=xx$sign)
dsort(out) <- ~time+status+id-sign
Mt <- cumsumstrata(out$dMGt,out$id-1,mid)
cumhaz <- cumsumstrata(out$Lamt,out$id-1,mid)
out <- cbind(out,Mt,cumhaz)
out <- subset(out,sign==1)
ddrop(out) <- ~sign+dMGt+Lamt
}
return(out)
} # }}}
##' @export
robust.basehaz.phreg <- function(x,type="robust",fixbeta=NULL,...) {# {{{
IsdM <- squareintHdM(x,ft=NULL,fixbeta=fixbeta,...)
varA <- IsdM$varInt[x$jumps]
strata <- x$strata[x$jumps]
cumhaz <- x$cumhaz
se.cumhaz <- cbind(cumhaz[,1],varA^.5)
colnames(se.cumhaz) <- c("time","se.cumhaz")
return(list(cumhaz=cumhaz,se.cumhaz=se.cumhaz,strata=strata))
} # }}}
##' @export robust.phreg
robust.phreg <- function(x,fixbeta=NULL,...) {
if (is.null(fixbeta))
if ((x$no.opt) | is.null(x$coef)) fixbeta<- 1 else fixbeta <- 0
if (fixbeta==0) {
beta.iid <- iid(x)
robvar <- crossprod(beta.iid)
} else robvar <- beta.iid <- NULL
baseline <- robust.basehaz.phreg(x,fixbeta=fixbeta,...);
## add arguments so that we can call basehazplot.phreg
res <- c(x,list(beta.iid=beta.iid,robvar=robvar,robse.cumhaz=baseline$se.cumhaz))
class(res) <- "phreg"
return(res)
}
###}}}
###{{{ phreg: coef vcov print summary print.summary plot lines
##' @export
coef.phreg <- function(object,...) { ## {{{
object$coef
} ## }}}
##' @export
vcov.phreg <- function(object,...) { ## {{{
if ((length(class(object))==1) & inherits(object,"phreg")) {
res <- as.matrix(object$var) ### objectcrossprod(ii <- iid(object,...))
### attributes(res)$ncluster <- attributes(ii)$ncluster
### attributes(res)$invhess <- attributes(ii)$invhess
colnames(res) <- rownames(res) <- names(coef(object))
} else { ##if ((length(class(object))==2) & class(object)[2]=="cifreg") {
res <- as.matrix(object$var)
colnames(res) <- rownames(res) <- names(coef(object))
}
res
} ## }}}
##' @export
summary.phreg <- function(object,type=c("robust","martingale"),augment.type=c("var.augment.times","var.augment"),...) { ## {{{
expC <- cc <- ncluster <- V <- NULL
if (length(object$p)>0 & object$p>0 & (!object$no.opt)) {
I <- -solve(object$hessian)
if ( (length(class(object))==2) && ( inherits(object,c("cifreg","recreg")))) {
V <- object$var
ncluster <- object$ncluster ## nrow(object$Uiid)
if (!is.null(object$augmentation)) { V <- object[[augment.type[1]]]; }
} else { ## phreg
V <- vcov(object,type=type[1])
ncluster <- object$n
}
cc <- cbind(coef(object),diag(V)^0.5,diag(I)^0.5)
cc <- cbind(cc,2*(pnorm(abs(cc[,1]/cc[,2]),lower.tail=FALSE)))
colnames(cc) <- c("Estimate","S.E.","dU^-1/2","P-value")
if (length(class(object))==1) if (!is.null(ncluster <- attributes(V)$ncluster))
rownames(cc) <- names(coef(object))
expC <- exp(lava::estimate(coef=coef(object),vcov=V)$coefmat[,c(1,3,4),drop=FALSE])
}
Strata <- levels(object$strata)
n <- object$n
res <- list(coef=cc,n=n,nevent=object$nevent,strata=Strata,ncluster=ncluster,var=V,exp.coef=expC)
class(res) <- "summary.phreg"
res
} ## }}}
##' @export
summarybase.phreg <- function(object,robust=FALSE,...) { ## {{{
out <- summaryRecurrentobject(object,robust=robust,...)
class(out) <- "summary.recurrent"
return(out)
}# }}}
##' @export
print.phreg <- function(x,...) { ## {{{
cat("Call:\n")
dput(x$call)
print(summary(x),...)
} ## }}}
##' Plotting the baselines of stratified Cox
##'
##' Plotting the baselines of stratified Cox
##' @param x phreg object
##' @param ... Additional arguments to baseplot funtion
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases basehazplotO.phreg baseplot bplot basecumhaz plotConfRegion plotConfRegionSE plotstrata kmplot plotConfregion
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##'
##' par(mfrow=c(2,2))
##' plot(out1)
##' plot(out1,stratas=c(0,3))
##' plot(out1,stratas=c(0,3),col=2:3,lty=1:2,se=TRUE)
##' plot(out1,stratas=c(0),col=2,lty=2,se=TRUE,polygon=FALSE)
##' plot(out1,stratas=c(0),col=matrix(c(2,1,3),1,3),lty=matrix(c(1,2,3),1,3),se=TRUE,polygon=FALSE)
##' @aliases plotConfRegion plotConfRegionSE plotstrata kmplot plotConfregion
##' @export
plot.phreg <- function(x,...) baseplot(x,...)
##' @export
lines.phreg <- function(x,...,add=TRUE) plot(x,...,add=add)
##' @export
bplot <- function(x,...,add=TRUE) plot(x,...,add=add)
##' @export
print.summary.phreg <- function(x,max.strata=5,...) { ## {{{
if (length(class(x))==2 & inherits(x,"cifreg")) cat("Competing risks regression \n");
if (!is.null(x$propodds)) {
cat("Proportional odds model, log-OR regression \n");
} else cat("\n")
nn <- cbind(x$n, x$nevent)
rownames(nn) <- levels(x$strata); colnames(nn) <- c("n","events")
if (is.null(rownames(nn))) rownames(nn) <- rep("",NROW(nn))
if (length(x$strata)>max.strata) {
nn <- rbind(c(colSums(nn),length(x$strata)));
colnames(nn) <- c("n","events","stratas")
rownames(nn) <- ""
}
print(nn,quote=FALSE)
if (!is.null(x$ncluster)) cat("\n ", x$ncluster, " clusters\n",sep="")
if (!is.null(x$coef)) {
cat("coeffients:\n")
printCoefmat(x$coef,...)
cat("\n")
cat("exp(coeffients):\n")
printCoefmat(x$exp.coef,...)
}
cat("\n")
## for binreg ATE
if (!is.null(x$ateDR)) {
cat("Average Treatment effects (G-formula) :\n")
printCoefmat(x$ateG,...)
cat("\n")
cat("Average Treatment effects (double robust) :\n")
printCoefmat(x$ateDR,...)
cat("\n")
### if (!is.null(x$attc)) {
### cat("Average Treatment effects on Treated/Non-Treated (DR) :\n")
### printCoefmat(x$attc,...)
### cat("\n")
### }
}
cat("\n")
} ## }}}
###}}}
##' @export
conftype <- function(x,std.err,conf.type=c("log","plain"),restrict=c("positive","prob","none"),conf.int=0.95)
{ ## {{{
zval <- qnorm(1 - (1 - conf.int)/2, 0, 1)
if (conf.type[1] == "plain") {# {{{
temp1 <- x + zval * std.err
temp2 <- x - zval * std.err
if (restrict[1]=="prob") cix <- list(upper = pmin(temp1, 1), lower = pmax(temp2, 0), conf.type = "plain", conf.int = conf.int)
if (restrict[1]=="positive") cix <- list(upper = pmax(temp1, 0), lower = pmax(temp2, 0), conf.type = "plain", conf.int = conf.int)
if (restrict[1]=="none") cix <- list(upper = temp1, lower = temp2, conf.type = "plain", conf.int = conf.int)
}
if (conf.type[1] == "log") {
xx <- ifelse(x <= 0, NA, x)
temp1 <- ifelse(x <= 0, NA, exp(log(xx) + zval * std.err/xx))
temp2 <- ifelse(x <= 0, NA, exp(log(xx) - zval * std.err/xx))
if (restrict[1]=="prob") cix <- list(upper = pmin(temp1, 1), lower = temp2, conf.type = "log", conf.int = conf.int)
else cix <- list(upper = temp1, lower = temp2, conf.type = "log", conf.int = conf.int)
}
### if (conf.type[1] == "log-log") {
### who <- (x == 0 | x == 1)
### xx <- ifelse(who, NA, x)
### temp1 <- exp(-exp(log(-log(xx)) + zval * std.err/log(xx)))
### temp2 <- exp(-exp(log(-log(xx)) - zval * std.err/log(xx)))
### if (restrict[1]=="prob") {
### temp3 <- ifelse(x == 0, NA, 1)
### temp1 <- ifelse(who, temp3, temp1)
### temp2 <- ifelse(who, temp3, temp2)
### } else {
### cix <- list(upper = temp1, lower = temp2, conf.type = "log-log", conf.int = conf.int)
### }
### }# }}}
return(cix)
}# }}}
##' @export
basecumhaz <- function(x,type=c("list"),only=0,joint=0,cumhaz="cumhaz",
se.cumhaz="se.cumhaz",robust=FALSE,...) {# {{{
## all strata
stratobs <- x$strata[x$jumps]
ustratobs <- sort(unique(stratobs))
stratas <- 0:(x$nstrata-1)
se.cum <- cum <- c()
se.cum <- cum <- x[[cumhaz]]
if (robust==TRUE) {
## take robse if there otherwise stay with se.cumhaz
secum <- x$robse.cumhaz
if (is.null(secum)) secum <- x[[se.cumhaz]]
} else secum <- x[[se.cumhaz]]
if (is.null(secum)) nose <- TRUE else nose <- FALSE
out <- rep(list(NULL),x$nstrata)
if (length(ustratobs)>0)
for (i in ustratobs) {
if (!is.null(x[[cumhaz]])) {
cumhazard <- x[[cumhaz]][stratobs==i,,drop=FALSE]
nr <- nrow(cumhazard)
if (nr>=1) {
if (!nose) se.cum <- secum[stratobs==i,,drop=FALSE] else se.cum <- NULL
if (only==0) {
if (joint==0) out[[i+1]] <- list(cumhaz=cumhazard,se.cumhaz=se.cum,strata=i) else
out[[i+1]] <- list(cumhaz=cbind(cumhazard,se.cum[,2],i))
} else out[[i+1]] <- cumhazard
}
}
}
attr(out,"stratobs") <- ustratobs
return(out)
}# }}}
###
###basecumhaz <- function(x,type=c("list"),only=0,joint=0,robust=FALSE,...) {# {{{
### ## all strata
### stratobs <- x$strata[x$jumps]
### ustratobs <- sort(unique(stratobs))
### stratas <- 0:(x$nstrata-1)
###
### se.cum <- cum <- c()
### se.cum <- cum <- x$cumhaz
### if (robust==TRUE) {
### ## take robse if there otherwise stay with se.cumhaz
### secum <- x$robse.cumhaz
### if (is.null(secum)) secum <- x$se.cumhaz
### } else secum <- x$se.cumhaz
### if (is.null(secum)) nose <- TRUE else nose <- FALSE
###
### out <- rep(list(NULL),x$nstrata)
### if (length(ustratobs)>0)
### for (i in ustratobs) {
### if (!is.null(x$cumhaz)) {
### cumhazard <- x$cumhaz[stratobs==i,,drop=FALSE]
### nr <- nrow(cumhazard)
### if (nr>=1) {
### if (!nose) se.cum <- secum[stratobs==i,,drop=FALSE] else se.cum <- NULL
### if (only==0) {
### if (joint==0) out[[i+1]] <- list(cumhaz=cumhazard,se.cumhaz=se.cum,strata=i) else
### out[[i+1]] <- list(cumhaz=cbind(cumhazard,se.cum[,2],i))
### } else out[[i+1]] <- cumhazard
### }
### }
### }
###
### attr(out,"stratobs") <- ustratobs
### return(out)
###}# }}}
###
##' @export
baseplot <- function(x,se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,
lty=NULL,col=NULL,lwd=NULL,legend=TRUE,ylab="Cumulative hazard",xlab="time",
polygon=TRUE,level=0.95,stratas=NULL,robust=FALSE,cumhaz="cumhaz",se.cumhaz="se.cumhaz",
conf.type=c("log","plain"),restrict = c("positive","prob", "none"),...) {# {{{
base <- basecumhaz(x,joint=1,robust=robust,cumhaz=cumhaz,se.cumhaz=se.cumhaz)
nstrata <- x$nstrata
stratobs <- attr(base,"stratobs")
###
if (is.null(stratas)) stratas <- stratobs else {
wm <- match(stratas,stratobs)
wm <- wm[!is.na(wm)]
if (length(wm)==0) stratas <- rep(0,0) else stratas <- stratobs[wm]
}
## all confidence intervals for relevant strata to make ylim
if (length(stratobs)>0) {
xx <- conftype(x$cumhaz[,2],x$se.cumhaz[,2],conf.type=conf.type[1],restrict=restrict[1],conf.int=level)
if (is.null(xlim)) {
xlim <- range(x$cumhaz[,1],na.rm=TRUE)
}
if (se) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz)) stop("phreg must be with cumhazard=TRUE\n");
rrse <- range(c(xx$lower,xx$upper),na.rm=TRUE)
if (is.null(ylim))
{
if (Inf %in% abs(rrse)) ylim <- range(x$cumhaz[,2],na.rm=TRUE) else ylim <- rrse
}
} else {
if (is.null(ylim)) ylim <- range(x$cumhaz[,2],na.rm=TRUE)
}
## all strata
## {{{
ltys <- lty; cols <- col; lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) lty <- ltys <- 1:length(stratas)
if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) col <- cols <- 1:length(stratas)
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas)) else cols <- col
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwd <- lwds <- rep(1,length(stratas))
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas)) else lwds <- lwd
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
## }}}
first <- 1
j <- 1
for (i in stratas) {
if (!is.null(base[[i+1]])) {
cumhazard <- base[[i+1]]$cumhaz
if (nrow(cumhazard)>1) {
if (add | first==0) lines(cumhazard,type="s",lty=ltys[j,1],col=cols[j,1],lwd=lwds[j,1])
else {
first <- 0
plot(cumhazard,type="s",lty=ltys[j,1],col=cols[j,1],lwd=lwds[j,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
xx <- conftype(cumhazard[,2],cumhazard[,3],conf.type=conf.type[1],restrict=restrict[1],conf.int=level)
nl <- cbind(cumhazard[,1],xx$lower); ul <- cbind(cumhazard[,1],xx$upper)
if (!polygon) {
lines(nl,type="s",lty=ltys[j,2],col=cols[j,2],lwd=lwds[i,2],...)
lines(ul,type="s",lty=ltys[j,3],col=cols[j,3],lwd=lwds[j,3],...)
} else plotConfRegion(nl[,1],cbind(nl[,2],ul[,2]),col=cols[j,1])
}
}
}
j <- j+1
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
} else {
if (!add) plot(0,0,ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
}# }}}
###{{{ phreg: basehazplot.phreg predictO.phreg plotO.predictphreg (old)
##' Plotting the baselines of stratified Cox
##'
##' Plotting the baselines of stratified Cox
##' @param x phreg object
##' @param se to include standard errors
##' @param time to plot for specific time variables
##' @param add to add to previous plot
##' @param ylim to give ylim
##' @param xlim to give xlim
##' @param lty to specify lty of components
##' @param col to specify col of components
##' @param lwd to specify lwd of components
##' @param legend to specify col of components
##' @param ylab to specify ylab
##' @param xlab to specify xlab
##' @param polygon to get standard error in shaded form
##' @param level of standard errors
##' @param stratas wich strata to plot
##' @param robust to use robust standard errors if possible
##' @param conf.type "plain" or "log" transformed
##' @param ... Additional arguments to lower level funtions
##' @author Klaus K. Holst, Thomas Scheike
##' @aliases basehazplot.phreg
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- phreg(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##'
##' par(mfrow=c(2,2))
##' plot(out1)
##' plot(out1,stratas=c(0,3))
##' plot(out1,stratas=c(0,3),col=2:3,lty=1:2,se=TRUE)
##' plot(out1,stratas=c(0),col=2,lty=2,se=TRUE,polygon=FALSE)
##' plot(out1,stratas=c(0),col=matrix(c(2,1,3),1,3),lty=matrix(c(1,2,3),1,3),se=TRUE,polygon=FALSE)
##' @export
basehazplot.phreg <- function(x,se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,
lwd=NULL,legend=TRUE,ylab=NULL,xlab=NULL,polygon=TRUE,level=0.95,
stratas=NULL,robust=FALSE,conf.type=c("plain","log"),...) {# {{{
if (inherits(x,"phreg") & is.null(ylab)) ylab <- "Cumulative hazard"
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
rr <- range(x$cumhaz[,-1])
strat <- x$strata[x$jumps]
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$cumhaz[,1])
if (se==TRUE) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz)) stop("phreg must be with cumhazard=TRUE\n");
if (conf.type[1]=="plain")
rrse <- range(c(x$cumhaz[,-1]+level*x$se.cumhaz[,-1]))
else { ## type="log"
relse <- exp(level*x$se.cumhaz[,-1]/x$cumhaz[,-1])
rrse <- range(x$cumhaz[,-1]/relse,x$cumhaz[,-1]*relse)
}
if (inherits(x,"km")) rrse <- c(min(x$lower,na.rm=TRUE),1)
if (is.null(ylimo)) ylim <- rrse
}
## all strata
if (is.null(stratas)) stratas <- 0:(x$nstrata-1)
ltys <- lty
cols <- col
lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) lty <- ltys <- 1:length(stratas)
if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) col <- cols <- 1:length(stratas)
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas)) else cols <- col
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwd <- lwds <- rep(1,length(stratas))
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas)) else lwds <- lwd
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
first <- 0
for (i in seq(stratas)) {
j <- stratas[i]
cumhazard <- x$cumhaz[strat==j,,drop=FALSE]
if (!is.null(cumhazard)) {
if (nrow(cumhazard)>1) {
if (add | first==1)
lines(cumhazard,type="s",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1])
else {
first <- 1
plot(cumhazard,type="s",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
if (robust==TRUE) secumhazard <- x$robse.cumhaz[strat==j,,drop=FALSE]
else secumhazard <- x$se.cumhaz[strat==j,,drop=FALSE]
xx <- cumhazard[,2]
std.err <- secumhazard[,2]
if (conf.type[1] == "log") {
temp1 <- exp(log(xx) + level * std.err/xx)
temp2 <- exp(log(xx) - level * std.err/xx)
ul = cbind(cumhazard[,1],temp1);
nl <- cbind(cumhazard[,1],temp2);
}
if (conf.type[1] == "plain") {
ul <-cbind(cumhazard[,1],cumhazard[,2]+level*secumhazard[,2])
nl <-cbind(cumhazard[,1],cumhazard[,2]-level*secumhazard[,2])
}
if (inherits(x,"km")) { ul[,2] <- x$upper[x$strata==j];
nl[,2] <- x$lower[x$strata==j];
wna <- which(is.na(ul[,2]))
ul[wna,2] <- 0
nl[wna,2] <- 0
}
if (!polygon) {
lines(nl,type="s",lty=ltys[i,2],col=cols[i,2],lwd=lwds[i,2],...)
lines(ul,type="s",lty=ltys[i,3],col=cols[i,3],lwd=lwds[i,3],...)
} else plotConfRegion(nl[,1],cbind(nl[,2],ul[,2]),col=cols[j+1])
}
}
}
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
}# }}}
##' @export
predictO.phreg <- function(object,newdata,times=NULL,individual.time=FALSE,tminus=FALSE,se=TRUE,robust=FALSE,conf.type="log",conf.int=0.95,km=FALSE,...)
{# {{{ default is all time-points from the object
### take baseline and strata from object# {{{
ocumhaz <- object$cumhaz
jumptimes <- ocumhaz[,1]
chaz <- ocumhaz[,2]
if (is.null(object$nstrata)) { ## try to make more robust
nstrata <- 1;
strata <- rep(1,length(jumptimes))
} else {
nstrata <- object$nstrata
strata <- object$strata[object$jumps]
}
if (length(jumptimes)==0) se <- FALSE
if (se) {
if (!robust) {
se.chaz <- object$se.cumhaz[,2]
varbeta <- object$ihessian
if (!object$no.opt) Pt <- apply(object$E/c(object$S0),2,cumsumstrata,strata,nstrata)
else Pt <- 0
} else {
if ((object$no.opt) | is.null(object$coef)) fixbeta<- 1 else fixbeta <- 0
IsdM <- squareintHdM(object,ft=NULL,fixbeta=fixbeta,...)
###
se.chaz <- IsdM$varInt[object$jumps]^.5
covv <- IsdM$covv[object$jumps,,drop=FALSE]
varbeta <- IsdM$vbeta
Pt <- IsdM$Ht[object$jumps,,drop=FALSE]
}
} # }}}
### setting up newdata with factors and strata
desX <- readPhreg(object,newdata)
X <- desX$X
strataNew <- desX$strata
if (is.null(times)) times <- sort(unique(c(object$exit)))
if (individual.time & is.null(times)) times <- c(object$exit)
if (individual.time & length(times)==1) times <- rep(times,length(object$exit))
se.cumhaz <- NULL
if (!individual.time) {
pcumhaz <- surv <- matrix(0,nrow(X),length(times))
if (se) se.cumhaz <- matrix(0,nrow(X),length(times))
} else {
pcumhaz <- surv <- matrix(0,nrow(X),1)
if (se) se.cumhaz <- matrix(0,nrow(X),1)
}
hazt <- length(times)
for (j in unique(strataNew)) {
### where <- sindex.prodlim(c(0,jumptimes[strata==j]),times,strict=tminus)
where <- predictCumhaz(c(0,jumptimes[strata==j]),times,type="left",tminus=tminus)
### if (sum(abs(whereO-where))>=1) {
### print(c(0,jumptimes[strata==j]))
### print(times)
### print(cbind(where,whereO,where-whereO,times,c(0,jumptimes[strata==j])[where],c(0,jumptimes[strata==j])[whereO]))
### print("sindex.prodlim - phreg-predict");
### }
plhazt <- hazt <- c(0,chaz[strata==j])
if (km) { plhazt <- suppressWarnings(c(1,exp(cumsum(log(1-diff(hazt)))))); plhazt[is.na(hazt)] <- 0 }
if (se) se.hazt <- c(0,se.chaz[strata==j])
Xs <- X[strataNew==j,,drop=FALSE]
if (object$p==0) RR <- rep(1,nrow(Xs)) else RR <- c(exp( Xs %*% coef(object)))
if (se) { # {{{ based on Hazard's
if (object$p>0) {
Ps <- Pt[strata==j,,drop=FALSE]
Ps <- rbind(0,Ps)[where,,drop=FALSE]
Xbeta <- Xs %*% varbeta
seXbeta <- rowSums(Xbeta*Xs)^.5
cov2 <- cov1 <- Xbeta %*% t(Ps*hazt[where])
if (robust) {
covvs <- covv[strata==j,,drop=FALSE]
covvs <- rbind(0,covvs)[where,,drop=FALSE]
covv1 <- Xs %*% t((covvs*hazt[where]))
cov1 <- cov1-covv1
}
} else cov1 <- 0
}# }}}
haztw <- hazt[where]
if (se) se.haztw <- se.hazt[where]
if (is.null(object$propodds)) {
plhaztw <- plhazt[where]
if (!individual.time) pcumhaz[strataNew==j,] <- RR%o%haztw else pcumhaz[strataNew==j,] <- RR*haztw[strataNew==j]
if (!km) {
if (!individual.time) surv[strataNew==j,] <- exp(- RR%o%haztw)
else surv[strataNew==j,] <- exp(-RR*haztw[strataNew==j])
} else {
if (!individual.time) surv[strataNew==j,] <- exp( RR %o% log(plhaztw))
else surv[strataNew==j,] <- plhaztw[strataNew==j]^RR
}
} else {
if (!individual.time) surv[strataNew==j,] <- 1/(1+RR%o%haztw)
else surv[strataNew==j,] <- 1/(1+RR*haztw[strataNew==j])
}
if (se) {# {{{
if (object$p>0) {
if (!individual.time) se.cumhaz[strataNew==j,] <-
((RR %o% se.haztw)^2+(c(RR*seXbeta) %o% haztw)^2-2*RR^2*cov1)^.5
else se.cumhaz[strataNew==j,] <- RR* (se.haztw^2+(c(seXbeta)*haztw)^2-2*diag(cov1))^.5
} else {
if (!individual.time) se.cumhaz[strataNew==j,] <- RR %o% (se.haztw)
else se.cumhaz[strataNew==j,] <- RR* se.haztw[strataNew==j]
}
}# }}}
}
zval <- qnorm(1 - (1 - conf.int)/2, 0, 1)
std.err <- se.cumhaz
cisurv <- list()
cisurv$upper <- NULL
cisurv$lower <- NULL
### different conf-types for surv
if (se) {# {{{
if (conf.type == "plain") {# {{{
temp1 <- surv + zval * std.err * surv
temp2 <- surv - zval * std.err * surv
cisurv <- list(upper = pmin(temp1, 1), lower = pmax(temp2,
0), conf.type = "plain", conf.int = conf.int)
}
if (conf.type == "log") {
xx <- ifelse(surv == 0, 1, surv)
temp1 <- ifelse(surv == 0, NA, exp(log(xx) + zval * std.err))
temp2 <- ifelse(surv == 0, NA, exp(log(xx) - zval * std.err))
cisurv <- list(upper = pmin(temp1, 1), lower = temp2,
conf.type = "log", conf.int = conf.int)
}
if (conf.type == "log-log") {
who <- (surv == 0 | surv == 1)
temp3 <- ifelse(surv == 0, NA, 1)
xx <- ifelse(who, 0.1, surv)
temp1 <- exp(-exp(log(-log(xx)) + zval * std.err/log(xx)))
temp1 <- ifelse(who, temp3, temp1)
temp2 <- exp(-exp(log(-log(xx)) - zval * std.err/log(xx)))
temp2 <- ifelse(who, temp3, temp2)
cisurv <- list(upper = temp1, lower = temp2,
conf.type = "log-log", conf.int = conf.int)
}# }}}
}# }}}
if (object$p>0) RR <- exp(X %*% coef(object)) else RR <- rep(1,nrow(X))
### non-cox setting
if (!is.null(object$propodds)) pcumhaz <- -log(surv)
out <- list(surv=surv,times=times,
surv.upper=cisurv$upper,surv.lower=cisurv$lower,cumhaz=pcumhaz,se.cumhaz=se.cumhaz,strata=strataNew,X=X, RR=RR)
if (length(class(object))==2 && ( substr(class(object)[2],1,3)=="cif" | substr(class(object)[1],1,3)=="cif")) {
out <- c(out,list(cif=1-out$surv,cif.lower=1-out$surv.upper, cif.upper=1-out$surv.lower))
}
if (length(class(object))==2 && ( substr(class(object)[2],1,3)=="rec" | substr(class(object)[1],1,3)=="rec")) {
out <- c(out,list(mean=-log(out$surv),mean.lower=-log(out$surv.upper),mean.upper=-log(out$surv.lower)))
}
class(out) <- c("predictphreg",class(object)[1])
### class(out) <- c("predictphreg")
### if (length(class(object))==2) class(out) <- c("predictphreg",class(object)[1])
return(out)
}# }}}
##' @export
plotO.predictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,type=c("default","surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (type[1]=="default" & (class(x)[2]=="phreg")) { if (is.null(ylab)) ylab <- "Survival probability"; type <- "surv"}
if (type[1]=="default" & (class(x)[2]=="cifreg")) {if (is.null(ylab)) ylab <- "Cumulative probability"; type <- "cif"}
if (type[1]=="default" & (class(x)[2]=="recreg")) {if (is.null(ylab)) ylab <- "Cumulative mean"; type <- "cumhaz"}
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
if (type[1]=="cif") rr <- c(0,1)
if (type[1]=="surv") rr <- c(0,1)
if (type[1]=="cumhaz") rr <- range(c(0,x$cumhaz))
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
if (se==TRUE) {
if (is.null(x$se.cumhaz)) stop("predict.phreg must be with se=TRUE\n");
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower))
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower))
if (type[1]=="cumhaz") {
cumhaz.upper <- x$cumhaz+level*x$se.cumhaz
cumhaz.lower <- x$cumhaz-level*x$se.cumhaz
rrse <- range(c(cumhaz.upper,cumhaz.lower))
}
if (type[1]=="surv") rrse <- c(0,1)
if (type[1]=="cif") rrse <- c(0,1)
if (type[1]=="cumhaz") rrse <- c(max(0,rrse[1]),rrse[2])
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
recreg <- cifreg <- FALSE
if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="cif")) cifreg <- TRUE
### if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="rec")) recreg <- TRUE
if (type[1]=="surv") {
xx <- x$surv
if (cifreg) xx <- x$cif
if (recreg) xx <- x$mean
} else if (type[1]=="cif") {
xx <- 1-x$surv
} else xx <- x$cumhaz
if (se) {
if (type[1]=="surv") {
upper <- x$surv.upper; lower <- x$surv.lower
if (cifreg) { upper <- x$cif.upper; lower <- x$cif.lower}
if (recreg) { upper <- x$mean.upper; lower <- x$mean.lower}
} else if (type[1]=="cif") {
upper <- 1-x$surv.lower; lower <- 1-x$surv.upper
} else { upper <- cumhaz.upper; lower <- cumhaz.lower}
}
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###}}} plot
##' @export
plotpredictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,
type=c("surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(xlab)) xlab <- "time"
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
ylimo <- ylim
nlower <- paste(type[1],".lower",sep="")
nupper <- paste(type[1],".upper",sep="")
xx <- x[[type[1]]]
if (se==TRUE) {
upper <- x[[nupper]]
lower <- x[[nlower]]
if (is.null(x$se.cumhaz)) stop("predict.phreg/cifreg/recreg must be with se=TRUE\n");
rrse <- range(c(0,x[[nlower]],x[[nupper]]),na.rm=TRUE)
if (is.null(ylimo)) ylim <- rrse
} else {
rrse <- range(c(xx),na.rm=TRUE)
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###{{{ predict.phreg print.predict plot.predict.phreg
##' Predictions from proportional hazards model
##'
##' @param object phreg object
##' @param newdata data.frame
##' @param times Time where to predict variable, default is all time-points from the object sorted
##' @param individual.time to use one (individual) time per subject, and then newdata and times have same length and makes only predictions for these individual times.
##' @param tminus to make predictions in T- that is strictly before given times, useful for IPCW techniques
##' @param se with standard errors and upper and lower confidence intervals.
##' @param robust to get robust se's also default for most functions (uses robse.cumhaz otherwise se.cumhaz).
##' @param conf.type transformation for suvival estimates, default is log
##' @param conf.int significance level
##' @param km to use Kaplan-Meier product-limit for baseline \deqn{S_{s0}(t)= (1 - dA_{s0}(t))}, otherwise take exp of cumulative baseline.
##' @param ... Additional arguments to plot functions
##' @aliases headstrata tailstrata revcumsumstrata revcumsumstratasum cumsumstrata sumstrata covfr covfridstrata covfridstrataCov cumsumidstratasum cumsumidstratasumCov cumsumstratasum revcumsum revcumsumidstratasum revcumsumidstratasumCov robust.basehaz.phreg matdoubleindex mdi cumsum2strata revcumsum2strata revcumsum2stratafdN
##' @export
predict.phreg <- function(object,newdata,times=NULL,individual.time=FALSE,tminus=FALSE,se=TRUE,robust=FALSE,conf.type="log",conf.int=0.95,km=FALSE,...)
{# {{{ default is all time-points from the object
### take baseline and strata from object# {{{
ocumhaz <- object$cumhaz
jumptimes <- ocumhaz[,1]
chaz <- ocumhaz[,2]
if (is.null(object$nstrata)) { ## try to make more robust
nstrata <- 1;
strata <- rep(1,length(jumptimes))
} else {
nstrata <- object$nstrata
strata <- object$strata[object$jumps]
}
if (length(jumptimes)==0) se <- FALSE
if (se) {
if (!robust) {
se.chaz <- object$se.cumhaz[,2]
varbeta <- object$ihessian
if (!object$no.opt) Pt <- apply(object$E/c(object$S0),2,cumsumstrata,strata,nstrata)
else Pt <- 0
} else { ## only relevant for phreg objects
if ((object$no.opt) | is.null(object$coef)) fixbeta<- 1 else fixbeta <- 0
IsdM <- squareintHdM(object,ft=NULL,fixbeta=fixbeta,...)
###
se.chaz <- IsdM$varInt[object$jumps]^.5
covv <- IsdM$covv[object$jumps,,drop=FALSE]
varbeta <- IsdM$vbeta
Pt <- IsdM$Ht[object$jumps,,drop=FALSE]
}
} # }}}
### setting up newdata with factors and strata
desX <- readPhreg(object,newdata)
X <- desX$X
strataNew <- desX$strata
if (is.null(times)) times <- sort(unique(c(object$exit)))
if (individual.time & is.null(times)) times <- c(object$exit)
if (individual.time & length(times)==1) times <- rep(times,length(object$exit))
se.cumhaz <- NULL
if (!individual.time) {
pcumhaz <- surv <- matrix(0,nrow(X),length(times))
if (se) se.cumhaz <- matrix(0,nrow(X),length(times))
} else {
pcumhaz <- surv <- matrix(0,nrow(X),1)
if (se) se.cumhaz <- matrix(0,nrow(X),1)
}
hazt <- length(times)
for (j in unique(strataNew)) {
where <- predictCumhaz(c(0,jumptimes[strata==j]),times,type="left",tminus=tminus)
plhazt <- hazt <- c(0,chaz[strata==j])
if (km) { plhazt <- suppressWarnings(c(1,exp(cumsum(log(1-diff(hazt)))))); plhazt[is.na(hazt)] <- 0 }
if (se) se.hazt <- c(0,se.chaz[strata==j])
Xs <- X[strataNew==j,,drop=FALSE]
if (object$p==0) RR <- rep(1,nrow(Xs)) else RR <- c(exp( Xs %*% coef(object)))
if (se) { # {{{ based on Hazard's
if (object$p>0) {
Ps <- Pt[strata==j,,drop=FALSE]
Ps <- rbind(0,Ps)[where,,drop=FALSE]
Xbeta <- Xs %*% varbeta
seXbeta <- rowSums(Xbeta*Xs)^.5
cov2 <- cov1 <- Xbeta %*% t(Ps*hazt[where])
if (robust) {
covvs <- covv[strata==j,,drop=FALSE]
covvs <- rbind(0,covvs)[where,,drop=FALSE]
covv1 <- Xs %*% t((covvs*hazt[where]))
cov1 <- cov1-covv1
}
} else cov1 <- 0
}# }}}
haztw <- hazt[where]
if (se) se.haztw <- se.hazt[where]
if (is.null(object$propodds)) {
plhaztw <- plhazt[where]
if (!individual.time) pcumhaz[strataNew==j,] <- RR%o%haztw else pcumhaz[strataNew==j,] <- RR*haztw[strataNew==j]
if (!km) {
if (!individual.time) surv[strataNew==j,] <- exp(- RR%o%haztw)
else surv[strataNew==j,] <- exp(-RR*haztw[strataNew==j])
} else {
if (!individual.time) surv[strataNew==j,] <- exp( RR %o% log(plhaztw))
else surv[strataNew==j,] <- plhaztw[strataNew==j]^RR
}
} else {
if (!individual.time) surv[strataNew==j,] <- 1/(1+RR%o%haztw)
else surv[strataNew==j,] <- 1/(1+RR*haztw[strataNew==j])
}
if (se) {# {{{
if (object$p>0) {
if (!individual.time) se.cumhaz[strataNew==j,] <-
((RR %o% se.haztw)^2+(c(RR*seXbeta) %o% haztw)^2-2*RR^2*cov1)^.5
else se.cumhaz[strataNew==j,] <- RR* (se.haztw^2+(c(seXbeta)*haztw)^2-2*diag(cov1))^.5
} else {
if (!individual.time) se.cumhaz[strataNew==j,] <- RR %o% (se.haztw)
else se.cumhaz[strataNew==j,] <- RR* se.haztw[strataNew==j]
}
}# }}}
}
if (se) {
cibase <- conftype(pcumhaz,se.cumhaz,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
cisurv <- conftype(surv,surv*se.cumhaz,conf.type=conf.type[1],restrict="prob",conf.int=conf.int)
} else {
cibase <- list(upper=NULL,lower=NULL,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
cisurv <- list(upper=NULL,lower=NULL,conf.type=conf.type[1],restrict="positive",conf.int=conf.int)
}
if (object$p>0) RR <- exp(X %*% coef(object)) else RR <- rep(1,nrow(X))
### non-cox setting
if (!is.null(object$propodds)) pcumhaz <- -log(surv)
out <- list(surv=surv,times=times,
surv.upper=cisurv$upper,surv.lower=cisurv$lower,cumhaz=pcumhaz,se.cumhaz=se.cumhaz,
se.surv=surv*se.cumhaz,se.cif=surv*se.cumhaz,
cif=1-surv,cif.lower=1-cisurv$upper,cif.upper=1-cisurv$lower,
cumhaz.upper=cibase$upper,cumhaz.lower=cibase$lower,strata=strataNew,X=X,RR=RR)
class(out) <- c("predictphreg",class(object)[1])
return(out)
}# }}}
##' @export
summary.predictphreg <- function(object,times=NULL,type=c("cif","cumhaz","surv")[3],np=10,...) {# {{{
ret <- summary.predictrecreg(object,times=times,type=type[1],np=np,...)
return(ret)
}# }}}
##' @export
plot.predictphreg <- function(x,se=FALSE,add=FALSE,ylim=NULL,xlim=NULL,lty=NULL,col=NULL,type=c("surv","cumhaz","cif"),ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,whichx=NULL,robust=FALSE,...) {# {{{
if (type[1]=="cumhaz" & is.null(ylab)) ylab <- "Cumulative hazard"
if (type[1]=="cif" & is.null(ylab)) ylab <- "Cumulative probability"
if (type[1]=="surv" & is.null(ylab)) ylab <- "Surival probability"
if (is.null(xlab)) xlab <- "time"
if (type[1]=="cif") rr <- c(0,1)
if (type[1]=="surv") rr <- c(0,1)
if (type[1]=="cumhaz") rr <- range(c(0,x$cumhaz))
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$times)
if (is.null(x$se.cumhaz) & se==TRUE) {
warning("predict.phreg must be with se=TRUE\n");
se <- FALSE
}
if (se==TRUE) {
if (is.null(x$se.cumhaz)) stop("predict.phreg must be with se=TRUE\n");
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower,na.rm=TRUE))
if (type[1]=="surv") rrse <- range(c(x$surv.upper,x$surv.lower,na.rm=TRUE))
if (type[1]=="cumhaz") {
cumhaz.upper <- x$cumhaz+level*x$se.cumhaz
cumhaz.lower <- x$cumhaz-level*x$se.cumhaz
rrse <- range(c(cumhaz.upper,cumhaz.lower),na.rm=TRUE)
}
if (type[1]=="surv") rrse <- c(0,1)
if (type[1]=="cif") rrse <- c(0,1)
if (type[1]=="cumhaz") rrse <- c(max(0,rrse[1]),rrse[2])
if (is.null(ylimo)) ylim <- rrse
}
## all covriates
nx <- nrow(x$surv)
if (is.null(whichx)) whichx <- 1:nx
stratas <- whichx
ltys <- lty
cols <- col
if (length(whichx)>0 ) { ## with X
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(whichx) else
if (length(lty)!=length(whichx)) ltys <- rep(lty[1],length(whichx)) else ltys <- lty
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
} else {
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
i <- 1
j <- whichx[i]
recreg <- cifreg <- FALSE
if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="cif")) cifreg <- TRUE
### if ((length(class(x))==2) && (substr(class(x)[2],1,3)=="rec")) recreg <- TRUE
if (type[1]=="surv") {
xx <- x$surv
if (cifreg) xx <- x$cif
if (recreg) xx <- x$mean
} else if (type[1]=="cif") {
xx <- 1-x$surv
} else xx <- x$cumhaz
if (se) {
if (type[1]=="surv") {
upper <- x$surv.upper; lower <- x$surv.lower
if (cifreg) { upper <- x$cif.upper; lower <- x$cif.lower}
if (recreg) { upper <- x$mean.upper; lower <- x$mean.lower}
} else if (type[1]=="cif") {
upper <- 1-x$surv.lower; lower <- 1-x$surv.upper
} else { upper <- cumhaz.upper; lower <- cumhaz.lower}
}
if (!add)
plot(x$times,xx[j,],type="s",lty=ltys[i,1],col=cols[i,1],ylim=ylim,ylab=ylab,xlim=xlim,xlab=xlab,...)
else lines(x$times,xx[j,],type="s", lty=ltys[i,1],col=cols[i,1],...)
if (length(whichx)>1)
for (i in seq(2,length(whichx))) lines(x$times,xx[whichx[i],],type="s",lty=ltys[i,1],col=cols[i,1],...)
if (se==TRUE) {
for (i in seq(1,length(whichx))) {
j <- whichx[i]
ul <- upper[j,]; nl <- lower[j,];
if (!polygon) {
lines(x$times,nl,type="s",lty=ltys[i,2],col=cols[i,2])
lines(x$times,ul,type="s",lty=ltys[i,3],col=cols[i,3])
} else plotConfRegion(x$times,cbind(nl,ul),col=cols[i,1])
}
}
where <- "topleft";
if (type[1]=="surv") where <- "topright"
}# }}}
###}}} predict
# {{{ Restricted mean for stratified Kaplan-Meier with martingale standard errors
##' Restricted mean for stratified Kaplan-Meier or Cox model with martingale standard errors
##'
##' Restricted mean for stratified Kaplan-Meier or stratified Cox with martingale
##' standard error. Standard error is computed using linear interpolation between
##' standard errors at jump-times. Plots gives restricted mean at all times.
##' Years lost can be computed based on this and decomposed into years lost for
##' different causes using the cif.yearslost function that is based on
##' integrating the cumulative incidence functions.
##' One particular feature of these functions are that the restricted mean and years-lost are
##' computed for all event times as functions and can be plotted/viewed. When times are given and beyond
##' the last event time withn a strata the curves are extrapolated using the estimates of
##' cumulative incidence.
##'
##' @param x phreg object
##' @param times possible times for which to report restricted mean
##' @param covs possible covariate for Cox model
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @examples
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' out1 <- phreg(Surv(time,cause!=0)~strata(tcell,platelet),data=bmt)
##'
##' rm1 <- resmean.phreg(out1,times=10*(1:6))
##' summary(rm1)
##' par(mfrow=c(1,2))
##' plot(rm1,se=1)
##' plot(rm1,years.lost=TRUE,se=1)
##'
##' ## years.lost decomposed into causes
##' drm1 <- cif.yearslost(Event(time,cause)~strata(tcell,platelet),data=bmt,times=10*(1:6))
##' par(mfrow=c(1,2)); plot(drm1,cause=1,se=1); plot(drm1,cause=2,se=1);
##' summary(drm1)
##' @export
##' @aliases cif.yearslost rmst.phreg
resmean.phreg <- function(x,times=NULL,covs=NULL,...)
{# {{{
ii <- invhess <- x$II
if (!is.null(times)) {
tt <- expand.grid(times,0:(x$nstrata-1))
mm <- cbind(x$jumptimes,x$strata.jumps,1)
mm <- rbind(mm,cbind(tt[,1],tt[,2],0))
ord <- order(mm[,1])
mm <- mm[ord,]
phd <- which(mm[,3]==1)
newtimes <- which(mm[,3]==0)
S0i <- S0i2 <- rep(0,nrow(mm))
S0i[phd] <- c(1/x$S0)
S0ii2 <- c(1/(x$S0*(x$S0-1)))
S0ii2[x$S0==1] <- 0
S0i2[phd] <- S0ii2
strata.jumps <- mm[,2]
nstrata <- x$nstrata;
jumptimes <- mm[,1]
E <- matrix(0,nrow(mm),x$p)
E[phd,] <- x$E
} else {
strata.jumps <- x$strata.jumps;
nstrata <- x$nstrata;
jumptimes <- x$jumptimes;
S0i <- c(1/x$S0)
S0i2 <- c(1/(x$S0*(x$S0-1)))
S0i2[x$S0==1] <- 0
E <- x$E
}
cumhaz <- cumsumstrata(S0i,strata.jumps,nstrata)
var.cumhazMG <- cumsumstrata(S0i2,strata.jumps,nstrata)
## baseline survival
km <- exp(cumsumstratasum(log(1-S0i),strata.jumps,nstrata,type="lagsum"))
## If covariates compute rr = exp( X beta) and adjust km
if (!is.null(covs)) { rr <- exp(sum(covs * coef(x))) } else rr <- 1
km <- km^rr
## start integral in 0
dtime <- c(diffstrata(jumptimes,strata.jumps,nstrata))
intkm <- cumsumstrata( c(km)*dtime,strata.jumps,nstrata)
### variance of baseline term
var.intkmcumhaz <- cumsumstrata(intkm*S0i2,strata.jumps,nstrata)
var.intkm2cumhaz <- cumsumstrata(intkm^2*S0i2,strata.jumps,nstrata)
var.resmean <- intkm^2*var.cumhazMG+var.intkm2cumhaz-2*intkm*var.intkmcumhaz
if (!is.null(x$coef)) {
intp <- apply(E*S0i,2,cumsumstratasum,strata.jumps,nstrata,type="lagsum")
intpS <- apply(intp*c(km)*dtime,2,cumsumstrata,strata.jumps,nstrata)
Dbeta <- -intpS
if (!is.null(covs)) {
intLam <- cumsumstratasum(S0i,strata.jumps,nstrata,type="lagsum")
intLamS <- cumsumstrata( c(intLam)*km*dtime,strata.jumps,nstrata)
Dbeta <- Dbeta + matrix(covs,nrow=nrow(intLam),ncol=length(covs),byrow=TRUE)*c(intLamS)
}
varbetat <- rowSums((Dbeta %*% x$II)*Dbeta)
var.resmean <- rr^2*(var.resmean+varbetat)
} else {
varbetat <- 0
}
time<- jumptimes
meanm <- cbind(time,intkm)
se.resmean <- var.resmean^.5
se.resmean[var.resmean<0] <- 0
se.mm <- cbind(time,se.resmean)
### make output at specified times
if (!is.null(times)) {
intkmtimes <- meanm[newtimes,,drop=FALSE]
se.intkmtimes <- se.resmean[newtimes]
skmtimes <- mm[newtimes,2]
years.lost <- intkmtimes[,1]-intkmtimes[,2]
intkmtimes <- cbind(skmtimes,intkmtimes,se.intkmtimes,years.lost)
colnames(intkmtimes) <- c("strata","times","rmean","se.rmean","years.lost")
rownames(intkmtimes) <- rep(x$strata.level,length(times));
intkmtimes=data.frame(intkmtimes)
### logintkmtimes=cbind(intkmtimes[,1:2],log(intkmtimes[,3]),se.intkmtimes/intkmtimes[,3])
### colnames(logintkmtimes) <- c("strata","times","log-rmean","log-se.rmean")
} else intkmtimes <- se.intkmtimes <- NULL
rmst <- cbind(meanm[,1],vecAllStrata(meanm[,2],strata.jumps,nstrata))
se.rmst <- cbind(se.mm[,1],vecAllStrata(se.mm[,2],strata.jumps,nstrata))
out <- list(cumhaz=meanm,se.cumhaz=se.mm,covs=covs,
time=time,strata=strata.jumps,nstrata=nstrata,
jumps=1:length(km),strata.name=x$strata.name,
strata.level=x$strata.level,
intkmtimes=intkmtimes,
rmst=rmst,se.rmst=se.rmst,
coef=intkmtimes[,3],var=diag(intkmtimes[,4]^2))
class(out) <- c("resmean_phreg")
return(out)
}# }}}
##' @export
vcov.resmean_phreg <- function(object,cause=1,...)
{# {{{
if (is.na(match("rmean",names(object$intkmtimes)))) name <- paste("se.intF1",cause,sep="") else name <- "se.rmean"
return(diag(object$intkmtimes[,name]^2))
}# }}}
##' @export
coef.resmean_phreg <- function(object,cause=1,...)
{# {{{
if (is.na(match("rmean",names(object$intkmtimes)))) name <- paste("intF1",cause,sep="") else name <- "rmean"
return(object$intkmtimes[,name])
}# }}}
##' @export
rmst.phreg <- function(x,times=NULL,covs=NULL,...)
{# {{{
out <- resmean.phreg(x,times=NULL,covs=NULL,...)
return(out)
}# }}}
##' @export
cif.yearslost <- function(formula,data=data,cens.code=0,times=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
### if (!is.Surv(Y)) stop("Expected a 'Surv'-object")
if (!inherits(Y,c("Event","Surv"))) stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
x <- phreg(formula,data=data,no.opt=TRUE,no.var=1,Z=as.matrix(status,ncol=1))
causes <- sort(unique(x$cox.prep$Z[,1]))
ccc <- which(causes %in% cens.code)
if (length(ccc)>=1) causes <- causes[-ccc]
if (!is.null(times)) {# {{{
tt <- expand.grid(times,0:(x$nstrata-1))
### cause.jumps <- x$U+x$E
cause.jumps <- x$cox.prep$Z[x$cox.prep$jumps+1,1]
mm <- cbind(x$jumptimes,x$strata.jumps,1,cause.jumps)
mm <- rbind(mm,cbind(tt[,1],tt[,2],0,cens.code))
ord <- order(mm[,1])
mm <- mm[ord,]
phd <- which(mm[,3]==1)
newtimes <- which(mm[,3]==0)
S0i <- S0i2 <- rep(0,nrow(mm))
S0i[phd] <- c(1/x$S0)
S0ii2 <- c(1/(x$S0*(x$S0-1)))
S0ii2[x$S0==1] <- 0
S0i2[phd] <- S0ii2
strata.jumps <- mm[,2]
nstrata <- x$nstrata;
jumptimes <- mm[,1]
cause.jumps <- mm[,4]
} else {
strata.jumps <- x$strata.jumps;
nstrata <- x$nstrata;
jumptimes <- x$jumptimes;
cause.jumps <- x$U+x$E
S0i <- c(1/x$S0)
S0i2 <- c(1/(x$S0*(x$S0-1)))
S0i2[x$S0==1] <- 0
}# }}}
### formula from Pepe-Mori: SIM 93, 737-
pepemori <- 0
### formula from PKA SIM 2013
pka <- 0
years.lostF1 <- se.years.lostF1m <- se.years.lostF1 <- se.years.lostF1pm <- c()
for (i in seq_along(causes)) {
jumpsi <- (cause.jumps==causes[i])*1
jumpsni <- (cause.jumps %in% causes[-i])*1
cumhaz <- cumsumstrata(S0i*jumpsi,strata.jumps,nstrata)
var.cumhazMG <- cumsumstrata(S0i2*jumpsi,strata.jumps,nstrata)
var.cumhazniMG <- cumsumstrata(S0i2*jumpsni,strata.jumps,nstrata)
## baseline survival
km <- exp(cumsumstratasum(log(1-S0i),strata.jumps,nstrata,type="lagsum"))
F1 <- cumsumstratasum(jumpsi*km*S0i,strata.jumps,nstrata,type="lagsum")
### 1 - F2 = S + F1
F1n1 <- km+F1
## start integral in 0
dtime <- c(diffstrata(jumptimes,strata.jumps,nstrata))
intkm <- cumsumstrata( c(km)*dtime,strata.jumps,nstrata)
intF1 <- cumsumstrata( c(F1)*dtime,strata.jumps,nstrata)
years.lostF1 <- cbind(years.lostF1,intF1)
if (pka==1) {
### variance of baseline term \int_0^t 1/Y^2 \int_s^t S(u) du dN^i{{{
var.intkmcumhaz <- cumsumstrata(jumpsi*intkm*S0i2,strata.jumps,nstrata)
var.intkm2cumhaz <- cumsumstrata(jumpsi*intkm^2*S0i2,strata.jumps,nstrata)
var.resmean1 <- intkm^2*var.cumhazMG+var.intkm2cumhaz-2*intkm*var.intkmcumhaz
### variance of baseline term \int_0^t 1/Y^2 \int_s^t F_i(u) du dN^-i
var.intF1cumhaz <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
var.intF12cumhaz <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
var.resmean2 <- intF1^2*var.cumhazniMG+var.intF12cumhaz-2*intF1*var.intF1cumhaz
var.intF1 <- (var.resmean1+var.resmean2)
## possibly negative due to rounding errors
var.intF1[var.intF1<0] <- 0
se.intF1 <- var.intF1^.5
se.years.lostF1 <- cbind(se.years.lostF1,se.intF1) # }}}
}
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s) - (t-s) (1-Fn1(s))) dN_1^i{{{
vars.1 <- cumsumstrata(jumpsi*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazMG+vars.1-2*intF1*vars.2
vars.3 <- cumsumstrata(jumpsi*F1n1^2*S0i2,strata.jumps,nstrata)
vars.4 <- cumsumstrata(jumpsi*F1n1^2*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsi*F1n1^2*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- jumptimes^2*vars.3+vars.4-2*jumptimes*vars.5
vars.6 <- cumsumstrata(jumpsi*F1n1*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsi*F1n1*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsi*F1n1*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsi*F1n1*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7
varsj1 <- vars.11+vars.21-2*vars.31
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s) - (t-s) F1(s)) dN_n1^i
vars.1 <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazniMG+vars.1-2*intF1*vars.2
vars.3 <- cumsumstrata(jumpsni*F1^2*S0i2,strata.jumps,nstrata)
vars.4 <- cumsumstrata(jumpsni*F1^2*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsni*F1^2*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- jumptimes^2*vars.3+vars.4-2*jumptimes*vars.5
vars.6 <- cumsumstrata(jumpsni*F1*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsni*F1*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsni*F1*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsni*F1*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7
varsnj1 <- vars.11+vars.21-2*vars.31
varss <- varsj1+varsnj1
varss[varss<0] <- 0
se.intF1m <- varss^.5
se.years.lostF1m <- cbind(se.years.lostF1m,se.intF1m)
# }}}
if (pepemori==1) {
### variance Pepe-Mori {{{
### variance of dN_1 term \int_0^t 1/Y^2 dN_n1^i
vars.1 <- cumsumstrata(jumpsi*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazMG+vars.1-2*intF1*vars.2
vars.4 <- cumsumstrata(jumpsi*jumptimes^2*S0i2,strata.jumps,nstrata)
vars.5 <- cumsumstrata(jumpsi*jumptimes*S0i2,strata.jumps,nstrata)
vars.21 <- F1n1^2*(jumptimes^2*var.cumhazMG+vars.4-2*jumptimes*vars.5)
vars.6 <- cumsumstrata(jumpsi*S0i2,strata.jumps,nstrata)
vars.7 <- cumsumstrata(jumpsi*intF1*S0i2,strata.jumps,nstrata)
vars.8 <- cumsumstrata(jumpsi*jumptimes*S0i2,strata.jumps,nstrata)
vars.9 <- cumsumstrata(jumpsi*intF1*jumptimes*S0i2,strata.jumps,nstrata)
vars.31 <- F1n1*(jumptimes*intF1*vars.6+vars.9-intF1*vars.8-jumptimes*vars.7)
varsj1 <- vars.11+vars.21-2*vars.31
### variance of baseline term \int_0^t 1/Y^2 ( IF(t)-IF(s)) dN_n1^i
vars.1 <- cumsumstrata(jumpsni*intF1^2*S0i2,strata.jumps,nstrata)
vars.2 <- cumsumstrata(jumpsni*intF1*S0i2,strata.jumps,nstrata)
vars.11 <- intF1^2*var.cumhazniMG+vars.1-2*intF1*vars.2
varspm <- vars.11+varsj1
varspm[varspm<0] <- 0
se.intF1pm <- varspm^.5
se.years.lostF1pm <- cbind(se.years.lostF1pm,se.intF1pm)
# }}}
}
}
years.lostF1 <- cbind(jumptimes,years.lostF1)
colnames(years.lostF1) <- c("time",paste("intF_",causes,sep=""))
### make output at specified times
if (!is.null(times)) {
intF1times <- years.lostF1[newtimes,]
years.lost <- apply(intF1times[,-1,drop=FALSE],1,sum)
if (pka==1) se.intF1times <- se.years.lostF1[newtimes,-1]
se.intF1mtimes <- se.years.lostF1m[newtimes,]
stratatimes <- strata.jumps[newtimes]
intF1mtimes <- cbind(stratatimes,intF1times,se.intF1mtimes,years.lost)
colnames(intF1mtimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes),"total-years-lost")
rownames(intF1mtimes) <- rep(x$strata.level,length(times));
intF1mtimes=data.frame(intF1mtimes)
if (pka==1) {
intF1pkatimes <- cbind(stratatimes,intF1times,se.intF1times)
colnames(intF1pkatimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes))
intF1pkatimes=data.frame(intF1times)
} else intF1pkatimes <- NULL
if (pepemori==1) {
se.intF1pmtimes <- se.years.lostF1pm[newtimes,]
intF1pmtimes <- cbind(stratatimes,intF1times,se.intF1pmtimes)
colnames(intF1pmtimes) <- c("strata","times",
paste0("intF1",causes),paste0("se.intF1",causes))
intF1pmtimes=data.frame(intF1pmtimes)
} else intF1pmtimes <- NULL
} else intF1pmtimes <-intF1mtimes <- intF1pkatimes <- NULL
se.years.lostF1 <- cbind(jumptimes,se.years.lostF1m)
colnames(se.years.lostF1) <- c("time",paste("intF_",causes,sep=""))
## name things to make use of other programs
out <- list(cumhaz=years.lostF1,se.cumhaz=se.years.lostF1,
time=jumptimes, strata=strata.jumps,nstrata=nstrata,
jumps=1:length(km),strata.name=x$strata.name,
strata.level=x$strata.level,
intkmtimes=intF1mtimes, intF1times=intF1mtimes,
intF1pmtimes=intF1pmtimes, intF1pkatimes=intF1pkatimes
)
class(out) <- c("resmean_phreg")
return(out)
}# }}}
##' @export
summary.resmean_phreg <- function(object,...)
{# {{{
if (is.null(object$intkmtimes)) return(cbind(object$cumhaz,object$se.cumhaz[,2])) else return(object$intkmtimes)
}# }}}
##' @export
print.resmean_phreg <- function(x,...)
{# {{{
print(summary.resmean_phreg(x,...))
}# }}}
##' @export
plot.resmean_phreg <- function(x, se=FALSE,time=NULL,add=FALSE,ylim=NULL,xlim=NULL,
lty=NULL,col=NULL,lwd=NULL,legend=TRUE,ylab=NULL,xlab=NULL,
polygon=TRUE,level=0.95,stratas=NULL,robust=FALSE,years.lost=FALSE,cause=1,...) {# {{{
if (inherits(x,"phreg") & is.null(ylab)) ylab <- "Cumulative hazard"
if (inherits(x,"km") & is.null(ylab)) ylab <- "Survival probability"
if (inherits(x,"cif") & is.null(ylab)) ylab <- "Probability"
if (inherits(x,"resmean_phreg") & is.null(ylab)) ylab <- "Restricted residual mean life"
if (inherits(x,"resmean_phreg") & !is.null(x$intF1times)) ylab <- "Years lost up to t: t - E(min(T,t))"
if (years.lost) ylab <- "Years lost up to t: t - E(min(T,t))"
if (is.null(xlab)) xlab <- "time"
level <- -qnorm((1-level)/2)
if (years.lost) rr <- range(x$cumhaz[,1]-x$cumhaz[,cause+1]) else rr <- range(x$cumhaz[,cause+1])
strat <- x$strata[x$jumps]
ylimo <- ylim
if (is.null(ylim)) ylim <- rr
if (is.null(xlim)) xlim <- range(x$cumhaz[,1])
if (se==TRUE) {
if (is.null(x$se.cumhaz) & is.null(x$robse.cumhaz) )
stop("phreg must be with cumhazard=TRUE\n");
if (years.lost) rrse <- range(c(x$cumhaz[,1]-x$cumhaz[,cause+1]+level*x$se.cumhaz[,cause+1])) else
rrse <- range(c(x$cumhaz[,cause+1]+level*x$se.cumhaz[,cause+1]))
if (is.null(ylimo)) ylim <- rrse
}
## all strata
if (is.null(stratas)) stratas <- 0:(x$nstrata-1)
ltys <- lty
cols <- col
lwds <- lwd
if (length(stratas)>0 & x$nstrata>1) { ## with strata
lstrata <- x$strata.level[(stratas+1)]
stratn <- substring(x$strata.name,8,nchar(x$strata.name)-1)
stratnames <- paste(stratn,lstrata,sep=":")
if (!is.matrix(lty)) {
if (is.null(lty)) ltys <- 1:length(stratas) else if (length(lty)!=length(stratas)) ltys <- rep(lty[1],length(stratas))
} else ltys <- lty
if (!is.matrix(col)) {
if (is.null(col)) cols <- 1:length(stratas) else
if (length(col)!=length(stratas)) cols <- rep(col[1],length(stratas))
} else cols <- col
if (!is.matrix(lwd)) {
if (is.null(lwd)) lwds <- rep(1,length(stratas)) else
if (length(lwd)!=length(stratas)) lwds <- rep(lwd[1],length(stratas))
} else lwds <- lwd
} else {
stratnames <- "Baseline"
if (is.matrix(col)) cols <- col
if (is.null(col)) cols <- 1 else cols <- col[1]
if (is.matrix(lty)) ltys <- lty
if (is.null(lty)) ltys <- 1 else ltys <- lty[1]
if (is.matrix(lwd)) lwds <- lwd
if (is.null(lwd)) lwds <- 1 else lwds <- lwd[1]
}
if (!is.matrix(ltys)) ltys <- cbind(ltys,ltys,ltys)
if (!is.matrix(cols)) cols <- cbind(cols,cols,cols)
if (!is.matrix(lwds)) lwds <- cbind(lwds,lwds,lwds)
if (years.lost) x$cumhaz[,cause+1] <- x$cumhaz[,1]-x$cumhaz[,cause+1]
first <- 0
for (i in seq(stratas)) {
j <- stratas[i]
cumhazard <- x$cumhaz[strat==j,c(1,cause+1),drop=FALSE]
if (!is.null(cumhazard)) {
if (nrow(cumhazard)>1) {
if (add | first==1)
lines(cumhazard,type="l",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1])
else {
first <- 1
plot(cumhazard,type="l",lty=ltys[i,1],col=cols[i,1],lwd=lwds[i,1],ylim=ylim,ylab=ylab,xlab=xlab,xlim=xlim,...)
}
if (se==TRUE) {
if (robust==TRUE) secumhazard <- x$robse.cumhaz[strat==j,c(1,cause+1),drop=FALSE]
else secumhazard <- x$se.cumhaz[strat==j,c(1,cause+1),drop=FALSE]
ul <-cbind(cumhazard[,1],cumhazard[,2]+level*secumhazard[,2])
nl <-cbind(cumhazard[,1],cumhazard[,2]-level*secumhazard[,2])
if (inherits(x,"km")) { ul[,2] <- x$upper[x$strata==j];
nl[,2] <- x$lower[x$strata==j];
wna <- which(is.na(ul[,2]))
ul[wna,2] <- 0
nl[wna,2] <- 0
}
if (!polygon) {
lines(nl,type="l",lty=ltys[i,2],col=cols[i,2],lwd=lwds[i,2])
lines(ul,type="l",lty=ltys[i,3],col=cols[i,3],lwd=lwds[i,3])
} else {
## type="l" confidence regions
ll <- length(nl[,1])
timess <- nl[,1]
tt <- c(timess,rev(timess))
yy <- c(nl[,2],rev(ul[,2]))
col.alpha<-0.1
col.ci<-cols[i,]
col.trans <- sapply(col.ci, FUN=function(x)
do.call(grDevices::rgb,as.list(c(grDevices::col2rgb(x)/255,col.alpha))))
polygon(tt,yy,lty=0,col=col.trans)
}
}
}
}
}
where <- "topleft";
if (inherits(x,"km")) where <- "topright"
if (legend & (!add))
graphics::legend(where,legend=stratnames,col=cols[,1],lty=ltys[,1])
}# }}}
# }}}
##' IPTW Cox, Inverse Probaibilty of Treatment Weighted Cox regression
##'
##' Fits Cox model with treatment weights \deqn{ w(A)= \sum_a I(A=a)/\pi(a|X)}, where
##' \deqn{\pi(a|X)=P(A=a|X)}. Computes
##' standard errors via influence functions that are returned as the IID argument.
##' Propensity scores are fitted using either logistic regression (glm) or the multinomial model (mlogit) when there are
##' than treatment categories. The treatment needs to be a factor and is identified on the rhs
##' of the "treat.model". Recurrent events can be considered with start,stop structure and then cluster(id) must be
##' specified. Robust standard errors are computed in all cases.
##'
##' Time-dependent propensity score weights can also be computed when treat.var is used, it must be 1 at the time
##' of first (A_0) and 2nd treatment (A_1), then uses weights \deqn{w_0(A_0) * w_1(A_1)^{t>T_r}} where \deqn{T_r} is
##' time of 2nd randomization.
##'
##' @param formula for phreg
##' @param data data frame for risk averaging
##' @param treat.model propensity score model (binary or multinomial)
##' @param treat.var a 1/0 variable that indicates when treatment is given and the propensity score is computed
##' @param weights may be given, and then uses weights*w(A) as the weights
##' @param estpr (=1, default) to estimate propensity scores and get infuence function contribution to uncertainty
##' @param pi0 fixed simple weights
##' @param se.cluster to compute GEE type standard errors when additional cluster structure is present
##' @param ... arguments for phreg call
##' @author Thomas Scheike
##' @examples
##' library(mets)
##' data <- mets:::simLT(0.7,100,beta=0.3,betac=0,ce=1,betao=0.3)
##' dfactor(data) <- Z.f~Z
##' out <- phreg_IPTW(Surv(time,status)~Z.f,data=data,treat.model=Z.f~X)
##' summary(out)
##' @export
phreg_IPTW <- function (formula, data,treat.model = NULL, treat.var = NULL,weights = NULL, estpr = 1, pi0 = 0.5,se.cluster=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster", "offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!inherits(Y, c("Event", "Surv")))
stop("Expected a 'Surv' or 'Event'-object")
if (ncol(Y) == 2) {
exit <- Y[, 1]
entry <- NULL
status <- Y[, 2]
}
else {
entry <- Y[, 1]
exit <- Y[, 2]
status <- Y[, 3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
pos.cluster <- ts$terms
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
}
else pos.cluster <- NULL
if (!is.null(id)) {
orig.id <- id
ids <- sort(unique(id))
nid <- length(ids)
if (is.numeric(id))
id <- fast.approx(ids, id) - 1
else {
id <- as.integer(factor(id, labels = seq(nid))) -
1
}
}
else {
orig.id <- NULL
nid <- length(exit)
id <- 0:(nid - 1)
ids <- NULL
}
if (!is.null(se.cluster)) {
sds <- sort(unique(se.cluster))
sid <- length(sds)
if (is.numeric(se.cluster))
se.cluster <- fast.approx(sds, se.cluster) - 1
else se.cluster <- as.integer(factor(se.cluster, labels = seq(sid))) - 1
}
id <- id + 1
nid <- length(unique(id))
data$id__ <- id
data$cid__ <- cumsumstrata(rep(1, length(id)), id - 1, nid)
treats <- function(treatvar) {
treatvar <- droplevels(treatvar)
nlev <- nlevels(treatvar)
nlevs <- levels(treatvar)
ntreatvar <- as.numeric(treatvar)
return(list(nlev = nlev, nlevs = nlevs, ntreatvar = ntreatvar))
}
fittreat <- function(treat.model, data, id, ntreatvar, nlev) {
if (nlev == 2) {
treat.model <- drop.specials(treat.model, "cluster")
treat <- glm(treat.model, data, family = "binomial")
iidalpha <- lava::iid(treat, id = id)
lpa <- treat$linear.predictors
pal <- expit(lpa)
pal <- cbind(1 - pal, pal)
ppp <- (pal/pal[, 1])
spp <- 1/pal[, 1]
}
else {
treat.modelid <- update.formula(treat.model, . ~
. + cluster(id__))
treat <- mlogit(treat.modelid, data)
iidalpha <- lava::iid(treat)
pal <- predict(treat, data, se = 0, response = FALSE)
ppp <- (pal/pal[, 1])
spp <- 1/pal[, 1]
}
Xtreat <- model.matrix(treat.model, data)
tvg2 <- 1 * (ntreatvar >= 2)
pA <- c(mdi(pal, 1:length(ntreatvar), ntreatvar))
pppy <- c(mdi(ppp, 1:length(ntreatvar), ntreatvar))
Dppy <- (spp * tvg2 - pppy)
Dp <- c()
for (i in seq(nlev - 1)) Dp <- cbind(Dp, Xtreat * ppp[, i + 1] * Dppy/spp^2)
DPai <- -1 * Dp/pA^2
out <- list(iidalpha = iidalpha, pA = pA, Dp = Dp, pal = pal,
ppp = ppp, spp = spp, id = id, DPai = DPai)
return(out)
}
expit <- function(x) 1/(1 + exp(-x))
if (!is.null(treat.var)) {
weightWT <- data[, treat.var]
whereW <- which(weightWT == 1)
CountW <- cumsumstrata(weightWT, id - 1, nid)
dataW <- data[whereW, ]
idW <- id[whereW]
} else {
whereW <- 1:nrow(data)
dataW <- data
idW <- id
CountW <- cumsumstrata(rep(1,nrow(data)), id-1,nid)
}
treat.name <- all.vars(treat.model)[1]
treatvar <- dataW[, treat.name]
if (!is.factor(treatvar))
stop(paste("treatment=", treat.name, " must be coded as factor \n",
sep = ""))
treats <- treats(treatvar)
wlPA <- ww <- rep(1, nrow(data))
idWW <- mystrata2index(cbind(id, CountW))
if (estpr[1] == 1) {
fitt <- fittreat(treat.model, dataW, idW, treats$ntreatvar, treats$nlev)
iidalpha0 <- fitt$iidalpha
wPA <- c(fitt$pA)
DPai <- fitt$DPai
} else {
if (length(pi0)==length(treats$ntreatvar)) wPA <- pi0
else wPA <- 1/ifelse(pi0[1], 1 - pi0[1], treats$ntreatvar == 2)
## pi0 <- rep(pi0, treats$nlev)
DPai <- matrix(0, nrow(data), 1)
}
ww <- rep(1, nrow(data))
ww[whereW] <- wPA
wlPA <- exp(cumsumstrata(log(ww), idWW - 1, attr(idWW, "nlevel")))
wwt <- c(exp(cumsumstrata(log(ww), id - 1, nid)))
## P(t) = P_0 * P_1^(I(t>T1)), time-dependent weights
## DP = P(t) \sum_j P_j I(t> TJ) (-DP_j/P_j^2)
if (estpr[1] == 1) {
DPait <- matrix(0, nrow(data), ncol(DPai))
DPait[whereW, ] <- DPai
DPait <- apply(DPait * c(wlPA), 2, cumsumstrata, id - 1, nid)/wwt
} else DPait <- NULL
if (is.null(weights)) ww <- 1/wwt else ww <- weights/wwt
phw <- phreg(formula, data, weights = ww, Z = DPait, ...)
### check.derivative <- 0
### if (check.derivative == 1) { ## {{{
### ### for checking derivative
### fpar <- glm(treat.model,dataw,family=binomial)
### mm <- model.matrix(treat.model,dataw)
### cpar <- coef(fpar)
### ### library(numderiv)
###
### ff <- function(par,base=0) {
### pa <- expit(mm %*% par)
### www <- ifelse(dataw[,treat.name] == "1", pa, 1 - pa)
### ww <- rep(1, nrow(data))
### ww[wherew] <- www
### wlpa <- exp(cumsumstrata(log(ww), idww - 1, attr(idww, "nlevel")))
### wwwt <- exp(cumsumstrata(log(ww), id - 1, nid))
###
### pp <- phreg(formula,data,weights=1/wwwt,no.opt=true,beta=coef(phw))
### if (base==1) po <- c(pp$cumhaz[,2]) else po <- pp$gradient
### return(po)
### }
###
### print(ff(cpar))
### gf <- jacobian(ff,cpar)
### print(t(gf))
### ###
### print(ff(cpar,base=1))
### gf <- jacobian(ff,cpar,base=1)
### print(gf)
### print("___________________________________");
### } ## }}}
if (estpr[1] == 1) {
xx <- phw$cox.prep
nid <- max(xx$id)
S0i <- rep(0, length(xx$strata))
wPAJ <- xx$weights[xx$jumps+1]*xx$caseweights[xx$jumps+1]
Xt <- xx$X
S0 <- phw$S0 * wPAJ
S0i[xx$jumps + 1] <- 1/S0
U <- E <- matrix(0, nrow(xx$X), phw$p)
U[xx$jumps + 1, ] <- phw$U/wPAJ
E[xx$jumps + 1, ] <- phw$E
if (phw$p>0) {
rr <- c(xx$sign * exp(Xt %*% coef(phw) + xx$offset) * xx$weights)
rrnw <- c(xx$sign * exp(Xt %*% coef(phw) + xx$offset))
} else {
rr <- c(xx$sign * exp(xx$offset) * xx$weights)
rrnw <- c(xx$sign * exp(xx$offset))
}
DWX = .Call("vecMatMat", xx$Z, Xt)$vXZ
S1 = apply(Xt * rr, 2, revcumsumstrata, xx$strata, xx$nstrata)
###S00 = revcumsumstrata( rr, xx$strata, xx$nstrata)
DS1 = apply(DWX * rrnw, 2, revcumsumstrata, xx$strata, xx$nstrata)
DS0 = apply(xx$Z * rrnw, 2, revcumsumstrata, xx$strata, xx$nstrata)
if (phw$p>0) {
DS0S1 = .Call("vecMatMat", DS0[xx$jumps + 1, , drop = FALSE],S1[xx$jumps + 1, , drop = FALSE])$vXZ
DUa2 <- apply(wPAJ * DS1[xx$jumps + 1, , drop = FALSE]/c(S0),2, sum) - apply(wPAJ * DS0S1/c(S0^2), 2, sum)
DUa2 <- matrix(DUa2, ncol(fitt$DPai), phw$p)
DUa1 <- t(xx$Z[xx$jumps + 1, ]) %*% (phw$U/wPAJ)
DUa <- DUa1 - DUa2
iidpal <- iidalpha0 %*% DUa
iidbeta <- lava::iid(phw) + iidpal %*% phw$ihess
phw$DUa <- DUa
phw$IID <- iidbeta
phw$naive.var <- phw$var
phw$var <- crossprod(iidbeta)
} else iidbeta <- NULL
###
DAw <- apply(xx$caseweights[xx$jumps+1]*xx$Z[xx$jumps + 1, ,drop=FALSE]/c(S0),2,cumsumstrata,phw$strata.jumps,xx$nstrata)
DA2 <- apply(wPAJ*DS0[xx$jumps + 1, , drop = FALSE]/c(S0)^2,2,cumsumstrata,phw$strata.jumps,xx$nstrata)
DAt <- 1*(DAw-DA2)
phw <- robust.phreg(phw,beta.iid=iidbeta)
varA <- phw$robse.cumhaz[,2]^2
phw$naive.se.cumhaz <- phw$robse.cumhaz
vtheta <- crossprod(iidalpha0)
varthetat <- rowSums((DAt %*% vtheta)*DAt)
###
ww <- xx$caseweights*xx$weights
S0i2 <- rep(0,length(xx$strata))
S0i2[xx$jumps+1] <- 1/(phw$S0^2*ww[xx$jumps+1])
cumS0i2 <- c(cumsumstrata(S0i2,xx$strata,xx$nstrata))
xxx <- (S0i-rr*cumS0i2)
id <- xx$id
mid <- max(xx$id)+1
thetat <- iidalpha0[id+1,,drop=FALSE]
covk1 <- apply(S0i*thetat,2,cumsumidstratasum,id,mid,xx$strata,xx$nstrata,type="sum")
covk2 <- apply(rr*thetat,2,revcumsumidstratasum,id,mid,xx$strata,xx$nstrata,type="lagsum")
###
covk1 <- apply(S0i*thetat,2,cumsumstrata,xx$strata,xx$nstrata)
covk2 <- apply(rr*thetat,2,revcumsumstrata,xx$strata,xx$nstrata)
###
covk2 <- covk2*cumS0i2
covv <- (covk1-covk2)[xx$jumps+1,,drop=FALSE]
covvt <- 2*apply(covv*DAt,1,sum)
varA <- varA+varthetat+2*apply(covv*DAt,1,sum)
Ht <- NULL
if (phw$p>0) {
covbetatheta <- t(iidalpha0) %*% iidbeta
Ht <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
Ht <- Ht[xx$jumps+1,,drop=FALSE]
covvBT <- 2* rowSums((Ht %*% t(covbetatheta))*DAt)
varA <- varA + covvBT
}
phw$robse.cumhaz[,2] <- varA^.5
phw$se.cumhaz[,2] <- varA^.5
phw$var.cumhaz <- cbind(phw$se.cumhaz[,1],varA)
resAiid <- list(DAt=DAt,Ht=Ht,iidalpha0=iidalpha0,iidbeta=phw$IID)
phw$resAiid <- resAiid
phw$iptw <- ww
} else {
phw$iptw <- ww
phw <- robust.phreg(phw)
phw$naive.se.cumhaz <- phw$se.cumhaz
phw$se.cumhaz <- phw$robse.cumhaz
phw$naive.var <- phw$var
}
if (!is.null(se.cluster)) {
phw$IID.simple <- phw$IID
phw$var.simple <- phw$var
phw$IID <- apply(phw$IID,2,sumstrata,se.cluster,sid)
phw$var <- crossprod(phw$IID)
phw$se.cluster <- se.cluster
}
class(phw) <- c("phreg","IPTW")
return(phw)
}# }}}
##' G-estimator for Cox and Fine-Gray model
##'
##' Computes G-estimator \deqn{ \hat S(t,A=a) = n^{-1} \sum_i \hat S(t,A=a,Z_i) }
##' for the Cox model based on phreg og the Fine-Gray model based on the
##' cifreg function. Gives influence functions of these risk estimates and SE's are
##' based on these. If first covariate is a factor then all contrast are computed,
##' and if continuous then considered covariate values are given by Avalues.
##'
##' @param x phreg or cifreg object
##' @param data data frame for risk averaging
##' @param time for estimate
##' @param Avalues values to compare for first covariate A
##' @param varname if given then averages for this variable, default is first variable
##' @param same.data assumes that same data is used for fitting of survival model and averaging.
##' @param id might be given to link to data to iid decomposition of survival data, must be coded as 1,2,..,
##' @author Thomas Scheike
##' @examples
##'
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' bmt$event <- (bmt$cause!=0)*1
##' dfactor(bmt) <- tcell.f~tcell
##'
##' fg1 <- cifreg(Event(time,cause)~tcell.f+platelet+age,bmt,cause=1,
##' cox.prep=TRUE,propodds=NULL)
##' summary(survivalG(fg1,bmt,50))
##'
##' ss <- phreg(Surv(time,event)~tcell.f+platelet+age,bmt)
##' summary(survivalG(ss,bmt,50))
##'
##' ss <- phreg(Surv(time,event)~strata(tcell.f)+platelet+age,bmt)
##' summary(survivalG(ss,bmt,50))
##'
##' sst <- survivalGtime(ss,bmt,n=50)
##' plot(sst)
##'
##' fg1t <- survivalGtime(fg1,bmt,n=50)
##' plot(fg1t)
##'
##' @export
##' @aliases survivalGtime
survivalG <- function(x,data,time=NULL,Avalues=c(0,1),varname=NULL,same.data=TRUE,id=NULL)
{# {{{
if (is.null(time)) stop("Give time for estimation of survival/cumulative incidence\n")
if (inherits(x,"cifreg"))
Aiid <- IIDbaseline.cifreg(x,time=time) else Aiid <- IIDbaseline.phreg(x,time=time)
### dealing with first variable that is a factor
if (is.null(varname)) {
treat.name <- all.vars(update.formula(x$formula,1~.))[1]
} else treat.name <- varname
treatvar <- data[,treat.name]
if (is.factor(treatvar)) {
###if (!is.factor(treatvar)) stop(paste("treatment=",treat.name,"must be coded as factor \n",sep=""));
## treatvar, 1,2,...,nlev or 1,2
nlev <- nlevels(treatvar)
nlevs <- levels(treatvar)
###treatvar <- as.numeric(treatvar)
ntreatvar <- as.numeric(treatvar)
ytreat <- ntreatvar-1
} else {
nlevs <- Avalues
}
formulaX <- update.formula(x$formula,.~.)
formulaX <- drop.specials(formulaX,"cluster")
datA <- dkeep(data,x=all.vars(formulaX))
xlev <- lapply(datA,levels)
cumhaz.time <- cpred(x$cumhaz,time)[-1,]
k <- 1; risks <- c(); DariskG <- list()
for (a in nlevs) { ## {{{
datA[,treat.name] <- a
pp <- predict(x,datA,time,se=0)
Xbase <- 1*outer(pp$strata,0:(x$nstrata-1),"==")
if (inherits(x,"phreg")) { ps0 <- c(pp$surv); Dma <- -cbind(c(pp$RR)*ps0*Xbase,c(ps0*pp$cumhaz)*pp$X); }
if (inherits(x,"cifreg")) { ps0 <- c(pp$cif); Dma <- cbind(c(pp$RR)*c(1-ps0)*Xbase,c((1-ps0)*pp$cumhaz)*pp$X); }
else if (inherits(x,"recreg")) { ps0 <- pp$cumhaz; Dma <- cbind(c(pp$RR)*Xbase,c(pp$cumhaz)*pp$X) }
risks <- cbind(risks,ps0)
DariskG[[k]] <- apply(Dma,2,sum)
k <- k+1
} ## }}}
predictAiid <- NULL
###
Grisk <- apply(risks,2,mean)
risk.iid <- t(t(risks)-Grisk)
###
nid <- nrow(pp$X)
nidcox <- max(x$id)
mnid <- max(nid,nidcox)
coxiid <- cbind(Aiid$base.iid,Aiid$beta.iid)
if (nid!=nidcox) {
coxiid <- apply(coxiid,2,sumstrata,x$id-1,mnid)
}
if (same.data) {
if (is.null(id)) id <- 1:nrow(pp$X) else id <- data[,id];
risk.iid <- apply(risk.iid,2,sumstrata,id-1,mnid)/nid
for (a in seq_along(nlevs)) risk.iid[,a] <- risk.iid[,a]+ coxiid %*% DariskG[[a]]/nid
vv <- crossprod(risk.iid)
} else {
predictAiid <- matrix(0,nidcox,ncol(risks))
for (a in seq_along(nlevs)) {
risk.iid[,a] <- risk.iid[,a]
predictAiid[,a] <- coxiid %*% DariskG[[a]]/nid
}
vv <- crossprod(risk.iid)+crossprod(predictAiid)
}
###estimate(lava::estimate(coef=theta,vcov=vv,f=function(p) Gf(p,ic=0))
if (inherits(x,"phreg")) {
out <- estimate(coef=1-Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
sout <- estimate(coef=Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
ed <- estimate(coef=Grisk,vcov=vv,f=function(p) (1-p[-1])-(1-p[1]))
rd <- estimate(coef=Grisk,vcov=vv,f=function(p) (1-p[-1])/(1-p[1]),null=1)
srd <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])/(p[1]),null=1)
out <- list(risk.iid=risk.iid,survivalG=sout,risk=out,difference=ed,ratio=rd,survival.ratio=srd,vcov=vv)
}
if (inherits(x,"cifreg") | inherits(x,"recreg")) {
out <- estimate(coef=Grisk,vcov=vv,labels=paste("risk",nlevs,sep=""))
ed <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])-(p[1]))
rd <- estimate(coef=Grisk,vcov=vv,f=function(p) (p[-1])/(p[1]),null=1)
out <- list(risk.iid=risk.iid,risk=out,difference=ed,ratio=rd,vcov=vv)
}
class(out) <- "survivalG"
return(out)
} ## }}}
##' @export
survivalGtime <- function(x,data,time=NULL,n=100,...)
{# {{{
if (!is.null(time)) if (time=="all") time <- x$cumhaz[,1]
if (is.null(time)) {
rr <- range(x$cumhaz[,1])
time <- seq(rr[1],rr[2],length=n)
}
survivalG <- risk <- difference <- ratio <- survival.ratio <- c()
for (tt in time) {
Gt <- survivalG(x,data,time=tt,...)
strata <- strata(rownames(Gt$risk$coefmat))
survivalG <- rbind(survivalG,cbind(tt,Gt$survivalG$coefmat))
risk <- rbind(risk,cbind(tt,Gt$risk$coefmat))
difference <- rbind(difference,cbind(tt,Gt$difference$coefmat))
ratio <- rbind(ratio,cbind(tt,Gt$ratio$coefmat))
survival.ratio <- rbind(survival.ratio,cbind(tt,Gt$survival.ratio$coefmat))
}
colnames(survivalG)[1] <- "time"
colnames(risk)[1] <- "time"
colnames(difference)[1] <- "time"
colnames(ratio)[1] <- "time"
colnames(survival.ratio)[1] <- "time"
strata <- strata(rownames(risk))
out <- list(time=time,survivalG=survivalG,risk=risk,difference=difference,
ratio=ratio,survival.ratio=survival.ratio,strata=strata)
class(out) <- "survivalGtime"
return(out)
} ## }}}
##' @export
plot.survivalGtime <- function(x,type=c("survival","risk","survival.ratio","difference","ratio"),ylim=NULL,legend=NULL,...) {# {{{
## to deal with fine-gray based things, that do not contain survival estimates
if ((ncol(x$survivalG)==1) & type[1]=="survival") type <- "risk"
us <- unique(x$strata)
cols <- 1:length(us)
ltys <- cols
ss0 <- x$strata==us[1]
if (type[1]=="survival") {
if (is.null(ylim)) ylim <- range(x$survivalG[,c(4,5)])
plot(x$time,x$survivalG[ss0,2],type="s",xlab="time",ylab="Survival",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$survivalG[ss0,c(4,5)],col=cols[1])
k <- 2
for (ss in us[-1]) {
ss0 <- x$strata==ss
lines(x$time,x$survivalG[ss0,2],type="s",ylim=c(0,1),col=cols[k],lty=ltys[k])
plotConfRegion(x$time,x$survivalG[ss0,c(4,5)],col=cols[k])
k <- k+1
}
}
if (type[1]=="risk") {
if (is.null(ylim)) ylim <- range(x$risk[,c(4,5)])
plot(x$time,x$risk[ss0,2],type="s",xlab="time",ylab="risk",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$risk[ss0,c(4,5)],col=cols[1])
k <- 2
for (ss in us[-1]) {
ss0 <- x$strata==ss
lines(x$time,x$risk[ss0,2],type="s",ylim=c(0,1),col=cols[k],lty=ltys[k])
plotConfRegion(x$time,x$risk[ss0,c(4,5)],col=cols[k])
k <- k+1
}
}
if (type[1]=="difference") {
if (is.null(ylim)) ylim <- range(x$risk[,c(4,5)])
plot(x$time,x$difference[,2],type="s",xlab="time",ylab="difference in risk",ylim=range(x$difference[,2]),col=cols[1],lty=ltys[1],...)
plotConfRegion(x$time,x$difference[,c(4,5)],col=cols[1])
}
if (type[1]=="ratio") {
if (is.null(ylim)) ylim <- range(x$ratio[,c(4,5)])
plot(x$time,x$ratio[,2],type="s",ylim=ylim,xlab="time",ylab="ratio",col=cols[1],lty=ltys[1],...)
plotConfRegion(x$time,x$ratio[,c(4,5)],col=cols[1])
}
if (type[1]=="survival.ratio") {
if (is.null(ylim)) ylim <- range(x$survival.ratio[,c(4,5)])
plot(x$time,x$survival.ratio[,2],type="s",xlab="time",ylab="risk",col=cols[1],lty=ltys[1],ylim=ylim,...)
plotConfRegion(x$time,x$survival.ratio[,c(4,5)],col=cols[1])
}
if (is.null(legend)) legend("topleft",levels(x$strata),col=cols,lty=ltys)
}
# }}}
###{{{ summary
##' @export
summary.survivalG <- function(object,...) {
res <- list(risk=object$risk,difference=object$difference,ratio=object$ratio,survival.ratio=object$survival.ratio)
class(res) <- "summary.survivalG"
res
}
##' @export
print.summary.survivalG <- function(x,...) {
cat("risk:\n")
print(x$risk,...)
cat("\n")
cat("Average Treatment effects (G-estimator) :\n")
print(x$difference,...)
cat("\n")
cat("Average Treatment effect risk-ratio (G-estimator) :\n")
print(x$ratio$coefmat,...)
cat("\n")
cat("Average Treatment effect (1-risk=survival)-ratio (G-estimator) :\n")
print(x$survival.ratio$coefmat,...)
cat("\n")
}
###}}} summary
##' Fast additive hazards model with robust standard errors
##'
##' Fast Lin-Ying additive hazards model with a possibly stratified baseline.
##' Robust variance is default variance with the summary.
##'
##' influence functions (iid) will follow numerical order of given cluster variable
##' so ordering after $id will give iid in order of data-set.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param no.baseline to fit model without baseline hazard
##' @param ... Additional arguments to phreg
##' @author Thomas Scheike
##' @examples
##'
##' data(bmt); bmt$time <- bmt$time+runif(408)*0.001
##' out <- aalenMets(Surv(time,cause==1)~tcell+platelet+age,data=bmt)
##' summary(out)
##'
##' ## out2 <- timereg::aalen(Surv(time,cause==1)~const(tcell)+const(platelet)+const(age),data=bmt)
##' ## summary(out2)
##'
##' @export
aalenMets <- function(formula,data=data,no.baseline=FALSE,...)
{# {{{
formula.call <- formula
x <- phreg(formula,data=data,no.opt=TRUE,...)
xx <- x$cox.prep
### computation of intZHZ matrix, and gamma and baseline ##################
# {{{
eXb <- c(xx$sign) * c(xx$weights)
S0 = c(revcumsumstrata(eXb,xx$strata,xx$nstrata))
S0[S0==0] <- 1
E=apply(eXb*xx$X,2,revcumsumstrata,xx$strata,xx$nstrata)/S0;
if (no.baseline) E <- 0*E
###if (!no.int) E <- cbind(1,E)
###if (no.int) X <- xx$X else X <- cbind(1,xx$X)
###if (no.int) XX <- xx$XX else { XX <- .Call("vecCPMat",X)$XX }
X <- xx$X; XX <- xx$XX
###
S2=apply(eXb*XX,2,revcumsumstrata,xx$strata,xx$nstrata)
E2 <- .Call("vecCPMat",E)$XX
###
dts <- c(diffstrata(xx$time,xx$strata,xx$nstrata))
dt <- diff(c(0,xx$time))
###
intZbar <- apply(E*dts,2,cumsumstrata,xx$strata,xx$nstrata)
intZHZt <- apply((S2-S0*E2)*dts,2,cumsum)
p <- ncol(E)
intZHZ <- matrix(.Call("XXMatFULL",tail(intZHZt,1),p,PACKAGE="mets")$XXf,p,p)
IintZHZ <- solve(intZHZ)
intZHdN <- matrix(x$gradient,ncol(E),1)
XJ <- X[xx$jumps+1,]
if (no.baseline) intZHdN <- matrix(apply(XJ,2,sum),ncol(E),1)
gamma <- IintZHZ %*% intZHdN
###if (!no.int) nn <- c("int",colnames(x$X)) else
nn <- colnames(x$X)
rownames(gamma) <- nn
x$cumhaz[,2] <- x$cumhaz[,2]- intZbar[xx$jumps+1,] %*% gamma
# }}}
### iid gamma #########################################
# {{{
id <- xx$id
if (no.baseline==FALSE) {
mm <- X * c(X %*% gamma) * c(xx$time)+ apply( E* c(E %*% gamma)*dts,2,cumsumstrata,xx$strata,xx$nstrata) - X* c(intZbar %*% gamma) - c(X %*% gamma)* intZbar
mm <- c(xx$weights*xx$sign) * mm
mm <- apply(mm,2,sumstrata,id,max(id)+1)
###
MGt <- t(x$hessian %*% t(lava::iid(x))) + mm
XJ2l <- .Call("vecCPMat",x$U)$XX
XJ2l <- matrix(apply(XJ2l,2,sum),nrow=1)
varmg <- matrix(.Call("XXMatFULL",XJ2l,p,PACKAGE="mets")$XXf,p,p)
varmg <- IintZHZ %*% varmg %*% IintZHZ
} else {
mm <- X * c(X %*% gamma) * c(xx$time)
mm <- c(xx$weights*xx$sign) * mm
mm <- apply(mm,2,sumstrata,id,max(id)+1)
XJ2l <- .Call("vecCPMat",XJ)$XX
XJ2l <- matrix(apply(XJ2l,2,sum),nrow=1)
varmg <- matrix(.Call("XXMatFULL",XJ2l,p,PACKAGE="mets")$XXf,p,p)
varmg <- IintZHZ %*% varmg %*% IintZHZ
XdN <- apply(XJ,2,sumstrata,id[xx$jumps+1],max(id)+1)
MGt <- XdN-mm
}
iid <- MGt %*% IintZHZ
# }}}
### output #########################################
# {{{
coef <- c(gamma)
names(coef) <- nn
x$coef <- coef
x$var <- crossprod(iid)
x$varmg <- varmg
x$iid <- iid
x$intZHdN <- intZHdN
x$intZHZ <- intZHZ
x$formula <- formula.call
x$ihessian <- IintZHZ
## score of gamma
x$gradient <- c(intZHdN-intZHZ %*% gamma)
x$no.opt <- FALSE
class(x) <- c(class(x),"aalenMets")
# }}}
return(x)
}# }}}
aalenMetsOld <- function(formula,data=data,...)
{# {{{
formula.call <- formula
x <- phreg(formula,data=data,no.opt=TRUE,...)
xx <- x$cox.prep
###ii <- solve(x$hessian)
###S0i <- rep(0,length(xx$strata))
###S0i[xx$jumps+1] <- 1/x$S0
###Z <- xx$X
###U <- E <- matrix(0,nrow(xx$X),x$p)
###E[xx$jumps+1,] <- x$E
###U[xx$jumps+1,] <- x$U
###cumhaz <- cbind(xx$time,cumsumstrata(S0i,xx$strata,xx$nstrata))
###EdLam0 <- apply(E*S0i,2,cumsumstrata,xx$strata,xx$nstrata)
### computation of intZHZ matrix, and gamma and baseline ##################
# {{{
eXb <- c(xx$sign) * c(xx$weights)
S0 = c(revcumsumstrata(eXb,xx$strata,xx$nstrata))
E=apply(eXb*xx$X,2,revcumsumstrata,xx$strata,xx$nstrata)/S0;
S2=apply(eXb*xx$XX,2,revcumsumstrata,xx$strata,xx$nstrata)
###
###E2=.Call("vecMatMat",E,E)$vXZ;
E2 <- .Call("vecCPMat",E)$XX
###
dts <- c(diffstrata(xx$time,xx$strata,xx$nstrata))
dt <- diff(c(0,xx$time))
###
intZbar <- apply(E*dts,2,cumsumstrata,xx$strata,xx$nstrata)
intZHZt <- apply((S2-S0*E2)*dts,2,cumsum)
intZHZ <- matrix(0,ncol(E),ncol(E));
intZHZ[lower.tri(intZHZ,diag=TRUE)] <- tail(intZHZt,1)
intZHZ<- intZHZ+t(intZHZ)
diag(intZHZ) <- diag(intZHZ)/2
###intZHZ <- matrix(tail(intZHZt,1),ncol(E), ncol(E))
IintZHZ <- solve(intZHZ)
intZHdN <- matrix(x$gradient,ncol(E),1)
gamma <- IintZHZ %*% intZHdN
rownames(gamma) <- colnames(x$X)
x$cumhaz[,2] <- x$cumhaz[,2]- intZbar[xx$jumps+1,] %*% gamma
# }}}
### iid gamma #########################################
# {{{
mm <- xx$X * c(xx$X %*% gamma) * c(xx$time)+ apply( E* c(E %*% gamma)*dts,2,cumsumstrata,xx$strata,xx$nstrata) - xx$X* c(intZbar %*% gamma) - c(xx$X %*% gamma)* intZbar
mm <- c(xx$weights) * mm
id <- xx$id
mm <- apply(mm,2,sumstrata,id,max(id)+1)
MGt <- t(x$hessian %*% t(iid(x))) + mm
iid <- MGt %*% IintZHZ
# }}}
coef <- c(gamma)
names(coef) <- rownames(gamma)
x$coef <- coef
x$var <- crossprod(iid)
x$iid <- iid
x$intZHdN <- intZHdN
x$intZHZ <- intZHZ
x$formula <- formula.call
x$ihessian <- IintZHZ
## score of gamma
x$gradient <- c(intZHdN-intZHZ %*% gamma)
x$no.opt <- FALSE
class(x) <- c(class(x),"aalenMets")
return(x)
}# }}}
##' Kaplan-Meier with robust standard errors
##'
##' Kaplan-Meier with robust standard errors
##' Robust variance is default variance and obtained from the predict call
##' @param formula formula with 'Surv' 'Event' outcome
##' @param data data frame
##' @param ... Additional arguments to phreg
##' @author Thomas Scheike
##' @examples
##' library(mets)
##' data(sTRACE)
##' sTRACE$cluster <- sample(1:100,500,replace=TRUE)
##' out1 <- km(Surv(time,status==9)~strata(vf,chf),data=sTRACE)
##' out2 <- km(Surv(time,status==9)~strata(vf,chf)+cluster(cluster),data=sTRACE)
##'
##' summary(out1,times=1:3)
##' summary(out2,times=1:3)
##'
##' par(mfrow=c(1,2))
##' plot(out1,se=TRUE)
##' plot(out2,se=TRUE)
##' @export
km <- function(formula,data=data,...)
{# {{{
### coxo <- phreg(formula,data=data,...)
### coxo <- robust.phreg(coxo)
### chaz <- coxo$cumhaz[,2]
### time <- coxo$cumhaz[,1]
### if (robust) std.err <- coxo$robse.cumhaz[,2] else std.err <- coxo$se.cumhaz[,2]
### strat <- coxo$strata[coxo$jumps]
### S0i <- rep(0,length(coxo$S0))
### S0i[coxo$S0>0] <- 1/coxo$S0[coxo$S0>0]
### kmt <- exp(cumsumstrata(log(1-S0i),strat,coxo$nstrata))
### ### to use basehazplot.phreg
### res <- list(cumhaz=cbind(time,kmt),se.cumhaz=cbind(time,kmt*std.err),time=time,surv=kmt,
### strata=strat,nstrata=coxo$nstrata,jumps=1:length(kmt),strata.name=coxo$strata.name,strata.level=coxo$strata.level,
### model.frame=coxo$model.frame,formula=coxo$formula)
res <- phreg(formula,data=data,...)
rhs <- update(formula,-1~.)
varss <- all.vars(rhs)
## find all strata
first <- c(headstrata(res$strata.call,res$nstrata))
ddf <- data[first,varss]
pres <- predict(res,ddf,robust=TRUE,...)
pres$formula <- formula
pres$call <- match.call()
attr(pres,"data") <- ddf
class(pres) <- c("km","predictphreg")
return(pres)
}# }}}
##' @export
summary.km <- function(object,times=NULL,type=c("cif","cumhaz","surv")[3],...) { ## {{{
out <- summary.predictrecreg(object,times=times,type=type[1],...)
return(out)
} ## }}}
##' @export
plot.km <- function(x,...) { ## {{{
plot.predictphreg(x,...)
}# }}}
###predict.km <- function(object,newdata,...) { ## {{{
## take strata after readPhreg
### take relevant parts of prediction that is only for each strata
## out <- predict.phreg(object,newdata,se=se,conf.type=conf.type[1],...)
###}# }}}
##' Cumulative incidence with robust standard errors
##'
##' Cumulative incidence with robust standard errors
##' @param formula formula with 'Event' outcome and strata (only!)
##' @param data data frame
##' @param cause NULL looks at all, otherwise specify which cause to consider
##' @param cens.code censoring code "0" is default, and death is cens.code!=0
##' @param death.code alternative to cens.code give codes of death
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @examples
##' data(bmt)
##' bmt$cluster <- sample(1:100,408,replace=TRUE)
##' out1 <- cif(Event(time,cause)~+1,data=bmt,cause=1)
##' out2 <- cif(Event(time,cause)~+1+cluster(cluster),data=bmt,cause=1)
##'
##' par(mfrow=c(1,2))
##' plot(out1,se=TRUE)
##' plot(out2,se=TRUE)
##' @export
cif <- function(formula,data=data,cause=1,cens.code=0,death.code=NULL,...)
{# {{{
cl <- match.call()
m <- match.call(expand.dots = TRUE)[1:3]
special <- c("strata", "cluster","offset")
Terms <- terms(formula, special, data = data)
m$formula <- Terms
m[[1]] <- as.name("model.frame")
m <- eval(m, parent.frame())
Y <- model.extract(m, "response")
if (!inherits(Y,"Event")) stop("Expected a 'Event'-object")
if (ncol(Y)==2) {
exit <- Y[,1]
entry <- NULL ## rep(0,nrow(Y))
status <- Y[,2]
} else {
entry <- Y[,1]
exit <- Y[,2]
status <- Y[,3]
}
id <- strata <- NULL
if (!is.null(attributes(Terms)$specials$cluster)) {
ts <- survival::untangle.specials(Terms, "cluster")
Terms <- Terms[-ts$terms]
id <- m[[ts$vars]]
}
if (!is.null(stratapos <- attributes(Terms)$specials$strata)) {
ts <- survival::untangle.specials(Terms, "strata")
Terms <- Terms[-ts$terms]
strata <- m[[ts$vars]]
strata.name <- ts$vars
} else strata.name <- NULL
if (!is.null(offsetpos <- attributes(Terms)$specials$offset)) {
ts <- survival::untangle.specials(Terms, "offset")
Terms <- Terms[-ts$terms]
offset <- m[[ts$vars]]
}
X <- model.matrix(Terms, m)
if (!is.null(intpos <- attributes(Terms)$intercept))
X <- X[,-intpos,drop=FALSE]
if (ncol(X)==0) X <- matrix(nrow=0,ncol=0)
id.orig <- id;
if (!is.null(id)) {
ids <- sort(unique(id))
nid <- length(ids)
if (is.numeric(id)) id <- fast.approx(ids,id)-1 else {
id <- as.integer(factor(id,labels=seq(nid)))-1
}
} else id <- as.integer(seq_along(exit))-1;
statusE <- 1*(status %in% cause)
if (is.null(death.code)) statusD <- 1*(!(status %in% cens.code)) else statusD <- 1*(status %in% death.code)
data$statusE__ <- statusE
data$statusD__ <- statusD
data$strata__ <- strata
### setting up formulae for the two phreg (cause of interest and death)
if (is.null(id.orig)) {
formid <- update.formula(formula,~.+cluster(id))
data$id <- id
} else formid <- formula
tt <- terms(formid)
tt <- delete.response(tt)
formid <- formula(tt)
if (ncol(Y)==3) {
formE <- as.formula(paste("Surv(entry,exit,statusE__)~+1"))
formD <- as.formula(paste("Surv(entry,exit,statusD__)~+1"))
} else {
formE <- as.formula(paste("Surv(exit,statusE__)~+1"))
formD <- as.formula(paste("Surv(exit,statusD__)~+1"))
}
formE <- update.formula(formE,formid)
formD <- update.formula(formD,formid)
if (sum(statusE)==0) warning("No events of type 1\n");
coxE <- phreg(formE,data=data,...)
coxS <- phreg(formD,data=data,...)
### cif
if (sum(statusE)>0) cifo <- recurrentMarginalPhreg(coxE,coxS) else cifo <- coxE
## to work with predict function
## cifo$no.opt <- TRUE
### to use basehazplot.phreg
class(cifo) <- c("cif","phreg")
attr(cifo,"cause") <- cause
attr(cifo,"cens.code") <- cens.code
attr(cifo,"death.code") <- death.code
return(cifo)
}# }}}
##' @export
plot.cif <- function(x,se=FALSE,ylab=NULL,ylim=c(0,1),conf.type=c("log","plain"),...) { ## {{{
if (inherits(x,"cif") & is.null(ylab)) ylab <- "Probability"
baseplot(x,se=se,ylab=ylab,ylim=ylim,restrict="prob",conf.type=conf.type[1],...)
} ## }}}
##' @export
summary.cif <- function(object,se=FALSE,ylab=NULL,times=NULL,conf.type=c("log","plain"),...) { ## {{{
if (inherits(object,"cif") & is.null(ylab)) ylab <- "Probability"
out <- summaryRecurrentobject(object,name="probability",times=times,conf.type=conf.type[1],restrict="prob",...)
return(out)
} ## }}}
##' Proportional odds survival model
##'
##' Semiparametric Proportional odds model, that has the advantage that
##' \deqn{
##' logit(S(t|x)) = \log(\Lambda(t)) + x \beta
##' }
##' so covariate effects give OR of survival.
##'
##' This is equivalent to using a hazards model
##' \deqn{
##' Z \lambda(t) \exp(x \beta)
##' }
##' where Z is gamma distributed with mean and variance 1.
##'
##' @param formula formula with 'Surv' outcome (see \code{coxph})
##' @param data data frame
##' @param offset offsets for exp(x beta) terms
##' @param weights weights for score equations
##' @param ... Additional arguments to lower level funtions
##' @author Thomas Scheike
##' @references
##'
##' The proportional odds cumulative incidence model for competing risks,
##' Eriksson, Frank and Li, Jianing and Scheike, Thomas and Zhang, Mei-Jie,
##' Biometrics, 2015, 3, 687--695, 71,
##'
##' @examples
##' data(TRACE)
##' dcut(TRACE) <- ~.
##' out1 <- logitSurv(Surv(time,status==9)~vf+chf+strata(wmicat.4),data=TRACE)
##' summary(out1)
##' gof(out1)
##' plot(out1)
##' @export
logitSurv <- function(formula,data,offset=NULL,weights=NULL,...)
{# {{{
out <- phreg(formula,data,offset=offset,weights=weights,propodds=1,...)
out$se.cumhaz <- NULL
return(out)
}# }}}
## {{{ Utility functions, cumsumstrata ....
##' @export
tailstrata <- function(strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("tailstrataR",length(strata),strata,nstrata,PACKAGE="mets")
if (any(res$found<0.5)) { warning("Not all strata found"); cat((1:nstrata)[res$found>0.5]); }
return(res$where)
}# }}}
##' @export
headstrata <- function(strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("headstrataR",length(strata),strata,nstrata,PACKAGE="mets")
if (any(res$found<0.5)) { warning("Not all strata found"); cat((1:nstrata)[res$found>0.5]); }
return(res$where)
}# }}}
##' @export
sumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("sumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
cumsumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("cumsumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
diffstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("diffstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsumstrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("revcumsumstrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsum2strata <- function(x,strata,nstrata,strata2,nstrata2,lag=FALSE)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
res <- .Call("revcumsum2strataR",as.double(x),strata,nstrata,strata2,nstrata2,PACKAGE="mets")
return(res)
}# }}}
##' @export
revcumsum2stratafdN <- function(x,y,strata,nstrata,strata2,nstrata2,startx)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
if (length(x)!=length(y)) stop("length of x and y must be same\n");
res <- .Call("revcumsum2stratafdNR",as.double(x),as.double(y),strata,nstrata,strata2,nstrata2,as.double(startx),PACKAGE="mets")
return(res)
}# }}}
##' @export
cumsum2strata <- function(x,y,strata,nstrata,strata2,nstrata2,startx)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (any(strata2<0) | any(strata2>nstrata2-1)) stop("strata2 index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (length(x)!=length(strata2)) stop("length of x and strata2 must be same\n");
res <- .Call("cumsum2strataR",as.double(x),as.double(y),strata,nstrata,strata2,nstrata2,as.double(startx),PACKAGE="mets")
return(res)
}# }}}
##' @export
vecAllStrata <- function(x,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
res <- .Call("vecAllStrataR",x,strata,nstrata,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsum <- function(x)
{# {{{
res <- .Call("revcumsumR",x,PACKAGE="mets")$res
return(res)
}# }}}
##' @export
revcumsumstratasum <- function(x,strata,nstrata,type="all")
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (type=="sum") res <- .Call("revcumsumstratasumR",x,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumstratasumR",x,strata,nstrata)$lagsum
if (type=="all") res <- .Call("revcumsumstratasumR",x,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumstratasum <- function(x,strata,nstrata,type="all")
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (length(x)!=length(strata)) stop("length of x and strata must be same\n");
if (type=="sum") res <- .Call("cumsumstratasumR",x,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("cumsumstratasumR",x,strata,nstrata)$lagsum
if (type=="all") res <- .Call("cumsumstratasumR",x,strata,nstrata)
return(res)
}# }}}
##' @export
matdoubleindex <- function(x,rows,cols,xvec=NULL)
{# {{{
if (!is.matrix(x)) stop("x must be matrix")
ncols <- ncol(x); nrows <- nrow(x)
## to avoid warnings when going to C, get rid of Inf
cols[cols==Inf] <- ncol(x)+1;
rows[rows==Inf] <- nrow(x)+1;
if (length(rows)==1) rows <- rep(rows,length(cols))
if (length(cols)==1) cols <- rep(cols,length(rows))
if (length(cols)!=length(rows)) stop("rows and cols different lengths\n");
if (is.null(xvec)) { assign <- 0; xvec <- 1} else {
assign <- 1;
if (length(cols)!=length(xvec)) stop("rows and cols and xvec differ \n");
}
res <- .Call("Matdoubleindex",x,rows-1,cols-1,length(cols),assign,xvec)$mat
return(res)
}# }}}
##' @export
mdi <- function(x,...) matdoubleindex(x,...)
##' @export
covfr <- function(x,y,strata,nstrata)
{# {{{
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfR",x,y,strata,nstrata)
return(res)
}# }}}
##' @export
revcumsumidstratasum <- function(x,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$lagsum
if (type=="lagsumsquare") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)$lagsumsquare
if (type=="all") res <- .Call("revcumsumidstratasumR",x,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
revcumsumidstratasumCov <- function(x,y,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$sum
if (type=="lagsum") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$lagsum
if (type=="lagsumsquare") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$lagsumsquare
if (type=="all") res <- .Call("revcumsumidstratasumCovR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumidstratasumCov <- function(x,y,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("cumsumidstratasumCovR",x,y,id,nid,strata,nstrata)$sum
else res <- .Call("cumsumidstratasumCovR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
cumsumidstratasum <- function(x,id,nid,strata,nstrata,type="all")
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
if (type=="sum") res <- .Call("cumsumidstratasumR",x,id,nid,strata,nstrata)$sum
else res <- .Call("cumsumidstratasumR",x,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
covfridstrata <- function(x,y,id,nid,strata,nstrata)
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfstrataR",x,y,id,nid,strata,nstrata)
return(res)
}# }}}
##' @export
covfridstrataCov <- function(x,y,x1,y1,id,nid,strata,nstrata)
{# {{{
if (any(id<0) | any(id>nid-1)) stop("id index not ok\n");
if (any(strata<0) | any(strata>nstrata-1)) stop("strata index not ok\n");
res <- .Call("covrfstrataCovR",x,y,x1,y1,id,nid,strata,nstrata)
return(res)
}# }}}
## }}}
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