fixed msm-age

models/msm_age/fit.R

@@ -31,11 +31,14 @@ df_gose <- readRDS(inputfile) %>%
 
 # translate to msm formatting
 tmp <- df_gose %>%
-  group_by(gupi) %>%
-  summarize_all(first) %>%
-  mutate(
-    Outcomes.DerivedCompositeGOSEDaysPostInjury = config$t_out_msm + .5, # needed to offset
-    Outcomes.DerivedCompositeGOSE = 99
+  rbind(
+    df_gose %>%
+      group_by(gupi) %>%
+      summarize_all(first) %>%
+      mutate(
+        Outcomes.DerivedCompositeGOSEDaysPostInjury = config$t_out_msm + .5, # needed to offset
+        Outcomes.DerivedCompositeGOSE = 99
+      )
   ) %>%
   arrange(gupi, Outcomes.DerivedCompositeGOSEDaysPostInjury) %>%
   mutate(
@@ -71,7 +74,7 @@ fit <- msm(
   subject   = tmp$gupi,
   data      = tmp,
   obstype   = tmp$obstype,
-  covariates = ~ age,
+  covariates = ~ Subject.Age,
   gen.inits = TRUE,
   qmatrix   = Q,
   censor    = 99,