Survival Analysis Report

Simulating Data

set.seed(123)
n <- 500
data <- data.frame(
  time = rexp(n, rate = 0.1),
  status = sample(0:1, n, replace = TRUE),
  arm = sample(c("A", "B"), n, replace = TRUE),
  ctDNA_9p24.1 = sample(c(0, 1), n, replace = TRUE),
  MTB_baseline = runif(n, 0, 100),
  MTB_C3D1 = rnorm(n, mean = 0, sd = 1),
  MTB_EOT = sample(c(0, 1), n, replace = TRUE),
  EBV_ctDNA = sample(c(0, 1), n, replace = TRUE),
  EBER_ISH = sample(c(0, 1), n, replace = TRUE)
)

Survival Analysis Function

do_survival_analysis <- function(data, variable, threshold, cohort_label) {
  data <- data %>%
    mutate(Group = factor(ifelse(get(variable) > threshold, "High", "Low")))
  
  fit <- survfit(Surv(time, status) ~ Group, data = data)
  ggsurvplot(fit, data = data, pval = TRUE)
  
  cox_fit <- tryCatch({
    coxph(Surv(time, status) ~ Group, data = data)
  }, error = function(e) return(NULL))
  
  if (!is.null(cox_fit)) {
    cox_results <- summary(cox_fit)$coefficients %>%
      as.data.frame() %>%
      tibble::rownames_to_column(var = "Variable") %>%
      mutate(across(where(is.numeric), ~ signif(.x, 3))) # Round numbers to 3 significant figures
    print(knitr::kable(cox_results))
  } else {
    message("Survival analysis for ", variable, " in ", cohort_label, " skipped due to insufficient data.")
  }
}

Perform Survival Analyses

do_survival_analysis(data, "ctDNA_9p24.1", 0, "Entire Cohort")

## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | 0.0103|      1.01|    0.128| 0.0806|              0.936|

for (arm in unique(data$arm)) {
  do_survival_analysis(filter(data, arm == arm), "ctDNA_9p24.1", 0, paste("Arm", arm))
}

## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | 0.0103|      1.01|    0.128| 0.0806|              0.936|
## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | 0.0103|      1.01|    0.128| 0.0806|              0.936|

do_survival_analysis(data, "MTB_baseline", median(data$MTB_baseline, na.rm = TRUE), "Entire Cohort")

## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.031|     0.969|    0.127| -0.245|              0.807|

for (arm in unique(data$arm)) {
  do_survival_analysis(filter(data, arm == arm), "MTB_baseline", median(data$MTB_baseline, na.rm = TRUE), paste("Arm", arm))
}

## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.031|     0.969|    0.127| -0.245|              0.807|
## 
## 
## |Variable |   coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.031|     0.969|    0.127| -0.245|              0.807|

do_survival_analysis(data, "EBV_ctDNA", 0, "Entire Cohort")

## 
## 
## |Variable |    coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|-------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.0716|     0.931|    0.127| -0.564|              0.573|

for (arm in unique(data$arm)) {
  do_survival_analysis(filter(data, arm == arm), "EBV_ctDNA", 0, paste("Arm", arm))
}

## 
## 
## |Variable |    coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|-------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.0716|     0.931|    0.127| -0.564|              0.573|
## 
## 
## |Variable |    coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|-------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.0716|     0.931|    0.127| -0.564|              0.573|

do_survival_analysis(data, "EBER_ISH", 0, "Validation Cohort")

## 
## 
## |Variable |    coef| exp(coef)| se(coef)|      z| Pr(>|z|)|
## |:--------|-------:|---------:|--------:|------:|------------------:|
## |GroupLow | -0.0645|     0.938|    0.128| -0.502|              0.615|