...

manuscript/manuscript.Rmd

@@ -250,7 +250,7 @@ the ‘6 months’ category contains observations up to 9 months post-injury.
 Thus the figures include a small proportion of GOSE 1 representing patients 
 who died between 6 and 9 months.
 
-```{r gose-plots, echo=FALSE, fig.cap="GOSe sampling time distribution and distribution at per-protocol time points.", fig.height=5, fig.width=7}
+```{r gose-plots, echo=FALSE, fig.cap="GOSe sampling time distribution and distribution at per-protocol time points (actual date rounded to nearest).", fig.height=6, fig.width=6}
 p_gose_times <- df_gose %>% 
   ggplot(aes(Outcomes.DerivedCompositeGOSEDaysPostInjury / 30)) +
     geom_histogram(binwidth = 1) +
@@ -285,14 +285,14 @@ tmp <- df_gose %>%
 
 p1 <- tmp %>% 
   ggplot(aes(GOSe)) +
-    geom_bar(aes(fill = GOSe)) +
-    scale_fill_viridis_d(guide = guide_legend(nrow = 1)) +
+    geom_bar(aes(fill = GOSe), width = .66, color = "black") +
+    scale_fill_grey(start = .1, end = .9) + 
     facet_wrap(~t, nrow = 1) + 
     ylab("absolute count") +
     theme_bw() +
     theme(
       panel.grid.major.x = element_blank(),
-      legend.position = "bottom"
+      legend.position = "none"
     ) 
 
 p2 <- tmp %>% 
@@ -301,8 +301,8 @@ p2 <- tmp %>%
   group_by(t) %>% 
   mutate(freq = n / sum(n)) %>% 
   ggplot(aes(x = GOSe, y = freq)) +
-    geom_bar(aes(fill = GOSe), stat = "identity") +
-    scale_fill_viridis_d() + 
+    geom_bar(aes(fill = GOSe), width = .66, color = "black", stat = "identity") +
+    scale_fill_grey(start = .1, end = .9) + 
     facet_wrap(~t, nrow = 1) + 
     ylab("relative frequency") +
     theme_bw() +
@@ -311,23 +311,12 @@ p2 <- tmp %>%
       legend.position = "none"
     )
 
-g_legend <- function(a.gplot){
-  tmp <- ggplot_gtable(ggplot_build(a.gplot))
-  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
-  legend <- tmp$grobs[[leg]]
-  return(legend)
-}
-
 gridExtra::grid.arrange(
   p_gose_times,
-  gridExtra::arrangeGrob(
-    p1 + theme(legend.position = "none"),
-    p2 + theme(legend.position = "none"),
-    nrow = 1
-  ),
-  g_legend(p1), 
+  p1,
+  p2,
   nrow    = 3,
-  heights = c(10, 10, 1)
+  heights = c(1.5, 1, 1)
 )
 ```
 

models/msm/fit.R

@@ -73,7 +73,7 @@ fit <- msm(
   qmatrix   = Q,
   censor    = 99,
   pci       = c(90, 270),
-  censor.states = 1:7,
+  censor.states = 2:7, # cannot be dead at 6 months
   control   = list(
     fnscale = config$fnscale_msm,
     maxit   = config$maxiter_msm,

models/msm_age/fit.R

@@ -79,7 +79,7 @@ fit <- msm(
   qmatrix   = Q,
   censor    = 99,
   pci       = c(90, 270),
-  censor.states = 1:7,
+  censor.states = 2:7, # cannot be death at 6 month
   control   = list(
     fnscale = config$fnscale_msm,
     maxit   = config$maxiter_msm,