update

slides.Rmd

@@ -590,7 +590,7 @@ test.new.var(old.vars, "year", 5)
 
 `year` has the smallest $p$-value
 
-## `tx.type` + `age.rec` + `hla.match` + `age.donor` + `year`
+## `tx.type` + `age.rec` + `hla.match` + `age.donor` + `year` + ?
 
 ```{r, echo=TRUE}
 old.vars <- c("tx.type", "age.rec", "hla.match", "age.donor", "year")
@@ -613,7 +613,7 @@ cox.full <- coxph(surv.full, data = dat, method = "breslow")
 cox.full
 ```
 
-```{r, fig.width=7, fig.height=5}
+```{r, fig.width=6, fig.height=6}
 tidy(cox.full, exponentiate = TRUE, conf.int = TRUE) |>
   mutate(
     term = recode(
@@ -635,7 +635,7 @@ tidy(cox.full, exponentiate = TRUE, conf.int = TRUE) |>
   geom_point(size = 2) +
   labs(
     title = "Hazard Ratios from Full Cox Model",
-    x = "Hazard Ratio",
+    x = "Log Hazard Ratio",
     y = NULL
   ) +
   my.theme
@@ -696,6 +696,59 @@ tidy(cox.full.1, exponentiate = TRUE, conf.int = TRUE) |>
 ```
 
 
+```{r, fig.width=6, fig.height=6}
+hr.full <- tidy(cox.full, exponentiate = TRUE, conf.int = TRUE)
+hr.full.1 <- tidy(cox.full.1, exponentiate = TRUE, conf.int = TRUE)
+hr.compare <- bind_rows(
+  hr.full |>
+    mutate(model = "Full model with year"),
+  hr.full.1 |>
+    mutate(model = "Model without year")
+) |>
+  mutate(
+    term = recode(
+      term,
+      "tx.typeLiving" = "Living donor",
+      "age.rec" = "Recipient age",
+      "hla.match" = "HLA match",
+      "age.donor" = "Donor age",
+      "year" = "Transplant year"
+    ),
+    term = factor(
+      term,
+      levels = c(
+        "Transplant year",
+        "Living donor",
+        "Recipient age",
+        "Donor age",
+        "HLA match"
+      )
+    )
+  )
+ggplot(hr.compare, aes(x = estimate, y = term, color = model)) +
+  geom_vline(xintercept = 1, linetype = "dashed") +
+  geom_errorbarh(
+    aes(xmin = conf.low, xmax = conf.high),
+    height = 0.2,
+    position = position_dodge(width = 0.6)
+  ) +
+  geom_point(
+    size = 2.5,
+    position = position_dodge(width = 0.6)
+  ) +
+  scale_x_log10() +
+  labs(
+    title = "Hazard Ratios from Cox Models",
+    x = "Log Hazard Ratio",
+    y = NULL,
+    color = NULL
+  ) +
+  my.theme
+```
+
+
+
+