R/stat.R

In vinash85/avinash: What the package does (short line)

extract_coxme_table <- function (mod){
    beta <- mod$coefficients #$fixed is not needed
    nvar <- length(beta)
    nfrail <- nrow(mod$var) - nvar
    se <- sqrt(diag(mod$var)[nfrail + 1:nvar])
    z<- round(beta/se, 2)
    p<- signif(1 - pchisq((beta/se)^2, 1), 2)
    table=data.frame(cbind(beta,se,z,p))
    return(table)
}

eval.coxme = function(dat, dtx){
require(coxme)
    tryCatch(
        {
            dtx$col = dat
            dtx = dtx[!is.na(col)]
            dtx = dtx[dataset %in% names(which(table(dtx$dataset) > 10))] 
            aa =  coxme(Surv(Survival, Event) ~ col + (1|dataset), dtx)
            extract_coxme_table(aa)
        },error=  function(e) rep(NA,4))
}