#' Print Cox Mixed effects regression output with CI and P values
#'
#' This is a wrapper around broom:::tidy that adds formatted confidence intervals and p values
#' @param crr_mod Output from coxme
#' @param d Decimal places used for HR and confidence interval
#' @param d_pVal Decimal places used for p value.
#' @param sub_out String to from variable names to replace with sub_in
#' @param sub_in String to from variable names to replace instead of sub_out
#' @export
#' @examples
#' \dontrun{
#' format_tidy_coxme()
#' }
format_tidy_coxme <- function(mod,d=2,d_pVal=3,sub_out = NULL,sub_in = NULL){
digi <- paste0("%.",d,"f")
if(!is.null(sub_out)) {Variable = gsub(sub_out,sub_in,names(mod$coef))
}else{Variable = names(mod$coef)}
n_here = mod$n[2]
sd = sqrt(diag(vcov(mod)))
logHR = mod$coef
lowCI = logHR - 1.96*sd/sqrt(n_here)
highCI = logHR + 1.96*sd/sqrt(n_here)
tab = cbind(
Variable = Variable,
HazardRatio = paste0(sprintf(digi,exp(logHR))," (",sprintf(digi,exp(lowCI)),",",sprintf(digi,exp(highCI)),")"),
Pvalue = format_pval((1-pnorm(abs(mod$coef/sd)))*2,equal="",d=d_pVal)
)
rownames(tab) = NULL
return(tab)
}
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