median survival time added to output summary statistics in stan model

R/stan_code_blocks.R

@@ -283,6 +283,7 @@ create_code_skeleton <- function(n_grp) {
       cglue_data(ids,
                  "vector[t_max] S_{id};
       vector[nTx] rmst_{id};
+      vector[nTx] median_{id};
       matrix[t_max, nTx] S_{id}_pred;
       real mean_{id};
       int idx_{id};
@@ -417,6 +418,7 @@ make_summary_estimates <- function(model, id) {
     "// restricted mean survival time
     for (i in 1:nTx) {{
       rmst_{id}[i] = cf_{id}[i]*t_max + (1 - cf_{id}[i])*rmst_{model}(", params, ", t_max);
+      median_{id}[i] = median_surv_{model}(", params, ");
     }\n\n")
 }
 

inst/stan/include/distributions.stan

@@ -71,6 +71,13 @@ real rmst_exp (real rate, real tmax) {
   return rmst;
 }
 
+// median survival time
+real median_surv_exp (real rate) {
+  real tmed;
+  tmed = log(2)/rate;
+  return tmed;
+}
+
 
 /**
 * weibull
@@ -123,6 +130,13 @@ real rmst_weibull (real shape, real scale, real tmax) {
   return rmst;
 }
 
+// median survival time
+real median_surv_weibull (real shape, real scale) {
+  real tmed;
+  tmed = scale * pow(log(2), 1/shape);
+  return tmed;
+}
+
 /**
 * gompertz
 *
@@ -199,6 +213,13 @@ real rmst_gompertz (real shape, real scale, real tmax) {
   return rmst;
 }
 
+// median survival time
+real median_surv_gompertz (real scale, real shape) {
+  real tmed;
+  tmed = 1/shape * log(log(2)*shape/scale + 1);
+  return tmed;
+}
+
 
 /**
 * log-logistic
@@ -270,6 +291,15 @@ real rmst_loglogistic (real scale, real shape, real tmax) {
   return rmst;
 }
 
+//TODO
+// // median survival time
+// real median_surv_loglogistic (real scale, real shape) {
+//   real tmed;
+//   tmed = ;
+//   return tmed;
+// }
+
+
 /**
 * generalised gamma
 *
@@ -400,6 +430,12 @@ real rmst_lognormal (real mu, real sigma, real tmax) {
   return rmst;
 }
 
+// median survival time
+real median_surv_lognormal (real mu) {
+  real tmed;
+  tmed = exp(mu);
+  return tmed;
+}
 
 /**
 * combined (non-cured) mortality