05. Survival Analysis

{
    if (is.null(cox_basic) || is.null(cox_basic$hazard_ratios)) 
        return(NULL)
    hr <- cox_basic$hazard_ratios
    for (col in names(hr)) {
        if (is.numeric(hr[[col]])) {
            hr[[col]] <- if (col == "p.value") 
                signif(hr[[col]], 4)
            else round(hr[[col]], 3)
        }
    }
    caption <- paste0("Cox PH model: age + gender. ", "term = covariate name. ", 
        "HR (hazard ratio) > 1 = increased hazard (worse survival). ", 
        "CI = 95% confidence interval for HR. ", "p.value = Wald test significance. ", 
        "n = ", cox_basic$n, " patients, ", cox_basic$n_events, 
        " events. C-index = ", round(cox_basic$concordance, 3), 
        ". ", "* p < 0.05, ** p < 0.01, *** p < 0.001.")
    DT::datatable(hr, rownames = FALSE, filter = "top", options = list(pageLength = 15, 
        scrollX = TRUE), caption = htmltools::tags$caption(style = "caption-side: top; text-align: left;", 
        caption))
}

{
    if (is.null(cox_full) || is.null(cox_full$hazard_ratios)) 
        return(NULL)
    hr <- cox_full$hazard_ratios
    for (col in names(hr)) {
        if (is.numeric(hr[[col]])) {
            hr[[col]] <- if (col == "p.value") 
                signif(hr[[col]], 4)
            else round(hr[[col]], 3)
        }
    }
    caption <- paste0("Multivariate Cox PH model with clinical and cytogenetic covariates. ", 
        "term = covariate name. ", "HR > 1 = increased hazard (worse survival). ", 
        "CI = 95% confidence interval. ", "n = ", cox_full$n, 
        " patients, ", cox_full$n_events, " events. ", "C-index = ", 
        round(cox_full$concordance, 3), ". ", "Covariates: ", 
        paste(cox_full$covariates_used, collapse = ", "), ".")
    DT::datatable(hr, rownames = FALSE, filter = "top", options = list(pageLength = 15, 
        scrollX = TRUE), caption = htmltools::tags$caption(style = "caption-side: top; text-align: left;", 
        caption))
}

{
    cox_for_ph <- if (!is.null(cox_full)) 
        cox_full
    else cox_basic
    if (is.null(cox_for_ph) || is.null(cox_for_ph$ph_test)) 
        return(NULL)
    ph <- cox_for_ph$ph_test
    ph_table <- as.data.frame(ph$table)
    ph_table$variable <- rownames(ph_table)
    ph_table <- ph_table[, c("variable", "chisq", "p")]
    names(ph_table) <- c("Variable", "Chi-squared", "p-value")
    ph_table$`Chi-squared` <- round(ph_table$`Chi-squared`, 2)
    ph_table$`p-value` <- signif(ph_table$`p-value`, 4)
    caption <- paste0("Proportional hazards assumption test (cox.zph). ", 
        "Variable = covariate tested. ", "Chi-squared = Schoenfeld residual test statistic. ", 
        "p-value < 0.05 indicates the PH assumption may be violated ", 
        "(hazard ratio changes over time). ", "If violated, time-varying coefficients or stratification ", 
        "should be considered.")
    DT::datatable(ph_table, rownames = FALSE, filter = "top", 
        options = list(pageLength = 15, scrollX = TRUE), caption = htmltools::tags$caption(style = "caption-side: top; text-align: left;", 
            caption))
}

{
    if (is.null(cox_basic) || is.null(cox_full)) 
        return(NULL)
    if (is.null(cox_basic$concordance) || is.null(cox_full$concordance)) 
        return(NULL)
    comp <- data.frame(Model = c("Basic (age + gender)", paste0("Full (", 
        paste(cox_full$covariates_used, collapse = " + "), ")")), 
        N = c(cox_basic$n, cox_full$n), Events = c(cox_basic$n_events, 
            cox_full$n_events), C_index = c(round(cox_basic$concordance, 
            3), round(cox_full$concordance, 3)), stringsAsFactors = FALSE)
    caption <- paste0("Cox model comparison. ", "Model = covariates included. ", 
        "N = patients with complete data for all covariates. ", 
        "Events = observed deaths. ", "C-index = concordance statistic ", 
        "(0.5 = random, 1.0 = perfect discrimination). ", "Higher C-index indicates better prognostic discrimination.")
    DT::datatable(comp, rownames = FALSE, filter = "top", options = list(pageLength = 10, 
        scrollX = TRUE), colnames = c("Model", "N", "Events", 
        "C-index"), caption = htmltools::tags$caption(style = "caption-side: top; text-align: left;", 
        caption))
}