Improved error handling functions in CoxPH

IKNL · May 3, 2024 · 16cd060 · 16cd060
1 parent 7c11f09
commit 16cd060
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Showing 3 changed files with 28 additions and 23 deletions.
diff --git a/vtg.coxph/src/R/RPC_compute_summed_z.R b/vtg.coxph/src/R/RPC_compute_summed_z.R
@@ -13,18 +13,19 @@
 #'   numeric vector with sums and named index with covariates.
 RPC_compute_summed_z <- function(df, subset_rules, expl_vars, time_col,
                                  censor_col, types = NULL, extend_data = TRUE) {
-
-  # Data pre-processing specific to EURACAN
-  if (extend_data){
-    df <- vtg.preprocessing::extend_data(df)
-  }
+  # Data pre-processing and filtering specific to EURACAN
   df <- tryCatch(
-    vtg.preprocessing::subset_data(df, subset_rules),
+    {
+      if (extend_data) {
+        df <- vtg.preprocessing::extend_data(df)
+      }
+      df <- vtg.preprocessing::subset_data(df, subset_rules)
+      df
+    },
     error = function(e) {
-      return(vtg::error_format(conditionMessage(e)))
+      vtg::error_format(conditionMessage(e))
     }
   )
-
   if (!is.null(df$error)) {
     vtg::log$error(df$error)
     return(df)

diff --git a/vtg.coxph/src/R/RPC_get_unique_event_times_and_counts.R b/vtg.coxph/src/R/RPC_get_unique_event_times_and_counts.R
@@ -9,17 +9,19 @@
 RPC_get_unique_event_times_and_counts <- function(df, expl_vars, subset_rules, time_col,
                                                   censor_col, types = NULL,
                                                   extend_data = TRUE) {
-  # Data pre-processing specific to EURACAN
-  if (extend_data){
-    df <- vtg.preprocessing::extend_data(df)
-  }
+  # Data pre-processing and filtering specific to EURACAN
   df <- tryCatch(
-    vtg.preprocessing::subset_data(df, subset_rules),
+    {
+      if (extend_data) {
+        df <- vtg.preprocessing::extend_data(df)
+      }
+      df <- vtg.preprocessing::subset_data(df, subset_rules)
+      df
+    },
     error = function(e) {
-      return(vtg::error_format(conditionMessage(e)))
+      vtg::error_format(conditionMessage(e))
     }
   )
-
   if (!is.null(df$error)) {
     vtg::log$error(df$error)
     return(df)
@@ -36,7 +38,7 @@ RPC_get_unique_event_times_and_counts <- function(df, expl_vars, subset_rules, t
   time <- df[df[, censor_col] == 1, time_col]
   print(time)
   print(length(time) == 0)
-  if (length(time) < 2){
+  if (length(time) < 2) {
     vtg::log$warn("< 2 events found in the data!")
     return(data.frame(time = numeric(), Freq = numeric()))
   }

diff --git a/vtg.coxph/src/R/RPC_perform_iteration.R b/vtg.coxph/src/R/RPC_perform_iteration.R
@@ -14,17 +14,19 @@
 RPC_perform_iteration <- function(df, subset_rules, expl_vars, time_col,
                                   censor_col, beta, unique_event_times,
                                   types = NULL, extend_data = TRUE) {
-  # Data pre-processing specific to EURACAN
-  if (extend_data){
-    df <- vtg.preprocessing::extend_data(df)
-  }
+  # Data pre-processing and filtering specific to EURACAN
   df <- tryCatch(
-    vtg.preprocessing::subset_data(df, subset_rules),
+    {
+      if (extend_data) {
+        df <- vtg.preprocessing::extend_data(df)
+      }
+      df <- vtg.preprocessing::subset_data(df, subset_rules)
+      df
+    },
     error = function(e) {
-      return(vtg::error_format(conditionMessage(e)))
+      vtg::error_format(conditionMessage(e))
     }
   )
-
   if (!is.null(df$error)) {
     vtg::log$error(df$error)
     return(df)