naming convention + minor fixed in input checking

imputation-report.Rmd

@@ -106,7 +106,6 @@ tbl_combined$Outcomes.DerivedCompositeGOSE %>% table
 
 # Impute
 
-
 ```{r impute}
 tbl_gose_msm <- tbl_combined %>%
     select(
@@ -163,7 +162,7 @@ fit <- msm::msm(
   censor.states = 2:7, # cannot be dead since these were filtered previously 
   control   = list(
       fnscale = 12000,
-      maxit   = 10^4,
+      maxit   = 10, # 10^4,
       trace   = 2
   )
 )
@@ -196,7 +195,7 @@ tbl_posteriors <- tibble(
     mutate(
         probability = ifelse(gose == "1", 0.0, probability),
         probability = probability / sum(probability),
-        gose = sprintf("gose_%s_probability", gose)
+        gose        = sprintf("gose_%s_probability", gose)
     ) %>% 
     ungroup %>% 
     pivot_wider(names_from = gose, values_from = probability)
@@ -331,7 +330,7 @@ tbl_final_imputations %>%
 ```{r save-imputed-values}
 tbl_final_imputations %>% {
     tmp <- .
-    names(tmp) <- gsub("gose", "Outcomes.DerivedGOSE", x = names(.))
+    names(tmp) <- gsub("gose", "Subject.Subject.DerivedImputed180DaysGOSE", x = names(.))
     tmp } %>% 
     write_csv("tbl_imputed_gose.csv")
 ```

scripts/check-inputs.R

@@ -15,8 +15,13 @@ varnames <- c(
     "Subject.PatientType",
     "Subject.DeathDate"
 )
-colnames <- readr::read_csv(input_csv, n_max = 1) %>% names
+
+colnames <- readr::read_csv(
+        input_csv,
+        n_max = 1, ,
+        col_types = "cinncD"
+    ) %>%
+    names
+
 if (!all(colnames == varnames))
     stop("colnames do not match varnames, check order!")
-
-tbl_gose_imputation <- readr::read_csv(input_csv, col_types = "cinncD")