changed definition of locf

models/locf/fit.R

@@ -18,11 +18,11 @@ df <- readRDS(inputfile) %>%
     )
   )
 
-impute_locf <- function(t, GOSE, tolerance, t_pred) {
+impute_locf <- function(t, GOSE, t_pred) {
   res  <- numeric(length(t_pred))
   res[] <- NA_integer_
   for (i in 1:length(t_pred)) {
-    res[i] <- GOSE[t < t_pred[i] + tolerance] %>%
+    res[i] <- GOSE[t < t_pred[i] & t > 76] %>%
       tail(1) %>% # use last if multiple available
       ifelse(length(.) == 0, NA, .)
   }
@@ -34,7 +34,11 @@ df_posteriors <- df %>%
   arrange(gupi, Outcomes.DerivedCompositeGOSE) %>%
   do(
     t = config$t_out,
-    GOSE_predicted = impute_locf(.$Outcomes.DerivedCompositeGOSEDaysPostInjury, .$Outcomes.DerivedCompositeGOSE %>% as.character %>% as.integer, config$t_buffer, config$t_out)
+    GOSE_predicted = impute_locf(
+      .$Outcomes.DerivedCompositeGOSEDaysPostInjury,
+      .$Outcomes.DerivedCompositeGOSE %>% as.character %>% as.integer,
+      config$t_out
+    )
   ) %>%
   unnest %>%
   mutate(

reports/imputations.Rmd

@@ -41,8 +41,8 @@ imputations.
 
 ```{r, fig.height=7, fig.width=7}
 caret::confusionMatrix(
-    df_imputations$Subject.DerivedImputed180DaysGOSE %>% factor,
-    df_imputations$Subject.GOSE6monthEndpointDerived %>% factor
+    df_imputations$Subject.DerivedImputed180DaysGOSE %>% factor(levels = 1:8),
+    df_imputations$Subject.GOSE6monthEndpointDerived %>% factor(levels = 1:8)
   ) %>% 
   as.matrix %>% as_tibble %>%
   mutate(