update

report.Rmd

@@ -546,23 +546,20 @@ recode.age <- function(dat, ages) {
 dat.age.rec <- dat[!is.na(dat$age.rec), ]
 class.age <- function(age) {
   if (age < 2) { 
-    return("0,1")
+    return("0-1")
   } else if (age < 6) {
-    return("2,3,4,5")
+    return("2-5")
   } else if (age < 11) {
-    return("6,7,8,9,10")
+    return("6-10")
   } else if (age < 19) {
     return("11-18")
   }
 }
-```
-
-```{r}
 dat.age.rec$age.group <- sapply(dat.age.rec$age.rec, class.age) |>
   factor(levels = c(
-    "0,1",
+    "0-1",
-    "2,3,4,5",
+    "2-5",
-    "6,7,8,9,10",
+    "6-10",
     "11-18"
   ))
 
@@ -574,9 +571,6 @@ cox.age.rec <- coxph(Surv(follow.up, death) ~ age.group, data = dat.age.rec)
 emmeans(cox.age.rec, pairwise ~ age.group, type = "response")
 ```
 
-```{r}
-cox.age.rec |> ggsurvfit()
-```
 
 
 # Exercise 7
@@ -705,6 +699,7 @@ H1: PH-assumption doesn't hold
 # different cox model!!
 cox.final <- coxph(Surv(follow.up, death) ~ tx.type + age.rec + hla.match + age.donor, data = dat)
 cox.zph(cox.final)
+cox.final
 ```
 
 
@@ -715,6 +710,11 @@ A non-random pattern or slope in a plot of scaled residuals against time indicat
 plot(cox.zph(cox.final))
 ```
 
+```{r, fig.width=10, fig.height=10}
+plot(cox.zph(cox.final))
+```
+
+
 
 
 NOTES: