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##' Publish cause-specific Cox models
##'
##' The cause-specific hazard ratio's are combined into one table.
##' @title Tabulizing cause-specific hazard ratio from all causes with confidence limits and Wald test p-values.
##' @param object Cause-specific hazard model obtained with
##' \code{CSC}.
##' @param cause Show a table for this cause. If omitted, list all
##' causes.
##' @param confint.method See \code{regressionTable}
##' @param pvalue.method See \code{regressionTable}
##' @param factor.reference See \code{regressionTable}
##' @param units See \code{regressionTable}
##' @param print If \code{TRUE} print the table(s).
##' @param ... passed on to control formatting of parameters,
##' confidence intervals and p-values. See
##' \code{summary.regressionTable}.
##' @return Table with cause-specific hazard ratios, confidence limits and p-values.
##' @author Thomas Alexander Gerds <tab@@biostat.ku.dk>
##' @examples
##' if (requireNamespace("riskRegression",quietly=TRUE)){
##' library(riskRegression)
##' library(prodlim)
##' library(survival)
##' data(Melanoma,package="riskRegression")
##' fit1 <- CSC(list(Hist(time,status)~sex,Hist(time,status)~invasion+epicel+age),
##' data=Melanoma)
##' publish(fit1)
##' publish(fit1,pvalue.stars=TRUE)
##' publish(fit1,factor.reference="inline",units=list("age"="years"))
##'
##' # wide format (same variables in both Cox regression formula)
##' fit2 <- CSC(Hist(time,status)~invasion+epicel+age, data=Melanoma)
##' publish(fit2)
##'
##' # with p-values
##' x <- publish(fit2,print=FALSE)
##' table <- cbind(x[[1]]$regressionTable,
##' x[[2]]$regressionTable[,-c(1,2)])
##' }
##'
##' @export
publish.CauseSpecificCox <- function(object,
cause,
confint.method,
pvalue.method,
factor.reference="extraline",
units=NULL,
print=TRUE,
...){
if (missing(confint.method)) confint.method="default"
if (missing(pvalue.method))
pvalue.method=switch(confint.method,
"robust"={"robust"},
"simultaneous"={"simultaneous"},
"default")
if (missing(cause)) {
clist <- lapply(object$models,function(m){
## m$call$data <- object$call$data
pm <- regressionTable(m,
pvalue.method=pvalue.method,
confint.method=confint.method,
print=FALSE,
factor.reference=factor.reference,
units=units,...)
summary.regressionTable(pm,print=FALSE,...)
})
cause1 <- clist[[1]]$regressionTable
## colnames(cause1) <- paste(names(object$models)[[1]],names(cause1),sep=".")
cause2 <- clist[[2]]$regressionTable
if (NROW(cause1)==NROW(cause2)){
table=cbind(cause1[,1:2],"A"=paste(cause1[,3],cause1[,4]),"B"=paste(cause2[,3],cause2[,4]))
colnames(table)[3:4] <- object$causes
}else{table <- NULL}
## colnames(cause2) <- paste(names(object$models)[[2]],names(cause2),sep=".")
out <- clist
} else{
m <- object$models[[cause]]
## m$call$data <- object$call$data
pm <- regressionTable(m,
pvalue.method=pvalue.method,
confint.method=confint.method,
print=FALSE,
factor.reference=factor.reference,
units=units,...)
## now pm is a regression table
out <- summary.regressionTable(pm,print=FALSE,...)$regressionTable
}
if (print==TRUE) {
if (is.null(table))
lapply(1:length(out),function(i){
publish(names(out)[[i]])
publish(out[[i]]$regressionTable)
})
else{
publish(table,...)
}
}
invisible(out)
}
#----------------------------------------------------------------------
### publish.CauseSpecificCox.R ends here
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