save second censoring models

analysis/ccw.R

@@ -369,7 +369,8 @@ if (model == "cox"){
   if (period == "ba1" & contrast == "all"){ # no start of alternative treatments by design
     data_trt_long <-
       data_trt_long %>%
-      mutate(p_uncens2_plr = 1)}
+      mutate(p_uncens2_plr = 1)
+    model_cens2_trt <- "no alternative censoring"}
   else{
     data_trt_long_grace <- 
       data_trt_long %>%

analysis/data_ccw/dens_weights.R

@@ -34,7 +34,7 @@ if(length(args)==0){
   period <- "ba1"
   contrast <- "all"
   outcome <- "primary"
-  model <- "cox"
+  model <- "plr"
   subgrp <- "full"
   supp <- "main"
 } else {
@@ -106,11 +106,11 @@ hist <- map(.x = arms,
 q_s <-
   data_long %>%
   group_by(arm, fup) %>%
-  summarise(tibble::enframe(quantile(cmlp_uncens, probs = c(0, 0.025, 0.05, 0.95, 0.975, 1)), 
-                            name = "quantile", "cmlp_uncens"),
+  summarise(tibble::enframe(quantile(cmlp_uncens * cmlp_uncens2, probs = c(0, 0.025, 0.05, 0.95, 0.975, 1)), 
+                            name = "quantile", "cmlp_uncens_prod"),
             .groups = "keep") %>%
   mutate(quantile = str_remove(quantile, pattern = "%")) %>%
-  pivot_wider(values_from = cmlp_uncens,
+  pivot_wider(values_from = cmlp_uncens_prod,
               names_from = quantile,
               names_prefix = "q_")
 q_w_s <-

project.yaml

@@ -1064,7 +1064,7 @@ actions:
       highly_sensitive:
         data: output/plr/data/data_long_all_plr.feather
         model01: output/plr/models/plr_cens_control_all_plr.rds
-        model02: output/plr/models/plr_cens_trt_all_plr.rds
+        model02: output/plr/models/plr_cens*_trt_all_plr.rds
         model1: output/plr/models/km_trt_all_plr.rds
         model2: output/plr/models/km_control_all_plr.rds
         model3: output/plr/models/cox_w_all_plr.rds