#' xtable method for summary.coxph
#'
#' xtable method for summary.coxph
#' @param x a \code{summary.coxph} object
#' @param digits digits
#' @param print.coef print beta?
#' @param print.se.coef print se(beta)?
#' @param print.z print z?
#' @param print.exp.coef print HR
#' @param print.exp.coef.lci print HR lower confint
#' @param print.exp.coef.uci print HR upper confint
#' @param print.p print p?
#' @param ... other things passed to \code{xtable::xtable}
#'
#' @export
xtable.summary.coxph <- function(x,
digits = 3,
print.coef = FALSE,
print.se.coef = FALSE,
print.z = FALSE,
print.exp.coef = TRUE,
print.exp.coef.lci = TRUE,
print.exp.coef.uci = TRUE,
print.p = TRUE,
...)
{
savedig <- options(digits = digits)
on.exit(options(savedig))
coeffs <- x$coefficients
ci <- x$conf.int
results <- as.data.frame(cbind(coeffs, ci))
column_select <- c('coef',
'se(coef)',
'z',
'exp(coef)',
'lower .95',
'upper .95',
'Pr(>|z|)')[
c(print.coef,
print.se.coef,
print.z,
print.exp.coef,
print.exp.coef.lci,
print.exp.coef.uci,
print.p)
]
final_result <- results[ , column_select]
names(final_result)[names(final_result) %in% 'exp(coef)'] <- 'HR'
final_result$`Pr(>|z|)` <- lbmisc::pretty_pval(
final_result$`Pr(>|z|)`,
equal = FALSE
)
xt <- xtable::xtable(final_result,
digits = digits,
...)
xtable::align(xt) <- rep('r', ncol(final_result) + 1)
xt
}
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