update

.lintr

@@ -1,5 +1,6 @@
 linters: lintr::linters_with_defaults(
     object_name_linter = lintr::object_name_linter(
         styles = c("snake_case", "dotted.case")
-    )
+    ),
+    trailing_whitespace_linter = NULL
   )

report.Rmd

@@ -1,5 +1,5 @@
 ---
-title: foo
+title: "foo"
 execute:
   cache: true
   freeze: auto

slides.Rmd

@@ -21,6 +21,7 @@ library(gt)
 library(ggsurvfit)
 library(gridExtra)
 library(survminer)
+library(broom)
 ```
 
 
@@ -32,9 +33,9 @@ dat <- dat |>
   mutate(
     sex = factor(sex, levels = c(0,1), labels = c("Female","Male")),
     tx.type = factor(tx.type, levels = c(0,1), labels = c("Cadaveric","Living")),
-    hla.match = factor(hla.match),
-    year = factor(year)
-  )
+    # hla.match = factor(hla.match),
+    # year = factor(year)
+)
 ```
 
 ```{r}
@@ -244,11 +245,11 @@ plot.tx.donor
 # Overall Kaplan-Meier Curve
 
 ```{r}
-km_all <- survfit(Surv(follow.up, death) ~ 1, data = dat)
+km.all <- survfit(Surv(follow.up, death) ~ 1, data = dat)
 ```
 
 ```{r, fig.width=7, fig.height=5}
-km_all |>
+km.all |>
   ggsurvfit(type = "survival") +
   add_confidence_interval() +
   scale_y_continuous(limits = c(0, 1)) +
@@ -261,7 +262,74 @@ km_all |>
 ```
 
 ```{r}
-summary(km_all, times = c(0, 4, 8, 12))
+header_bg   <- "#A83262"  # burgundy/magenta from right panel
+header_text <- "white"
+body_bg     <- "#FFF4CC"  # light cream
+stripe_bg   <- "#F6E8C3"  # slightly darker cream
+text_color  <- "#333333"
+border_col  <- "#D8C8A5"
+```
+
+```{r}
+times <- seq(0, 12, 2)
+summary(km.all, times = times)[c("time", "n.risk", "surv")] |>
+  as.data.frame() |>
+  gt() |>
+  tab_header(
+    title = "Overall Kaplan-Meier Survival Summary"
+  ) |>
+  cols_label(
+    time = "Follow-up Time",
+    n.risk = "Number at Risk",
+    surv = "Survival Probability"
+  ) |>
+  fmt_number(
+    columns = surv,
+    decimals = 3
+  ) |>
+  tab_options(
+    table.font.size = px(15),
+    heading.title.font.size = px(20),
+    column_labels.font.weight = "bold"
+  )
+
+```
+
+```{r}
+summary(km.all, times = times)[c("time", "n.risk", "surv")] |>
+  as.data.frame() |>
+  gt() |>
+  tab_header(
+    title = "Overall Kaplan-Meier Survival Summary"
+  ) |>
+  cols_label(
+    time = "Follow-up Time",
+    n.risk = "Number at Risk",
+    surv = "Survival Probability"
+  ) |>
+  fmt_number(columns = surv, decimals = 3) |>
+  fmt_number(columns = time, decimals = 0) |>
+  tab_style(
+    style = list(
+      cell_fill(color = "#A83262"),
+      cell_text(color = "white", weight = "bold")
+    ),
+    locations = cells_column_labels()
+  ) |>
+  tab_style(
+    style = cell_fill(color = "#FFF4CC"),
+    locations = cells_body()
+  ) |>
+  opt_row_striping(row_striping = TRUE) |>
+  tab_options(
+    row.striping.background_color = "#F6E8C3",
+    table.border.top.color = "#A83262",
+    table.border.bottom.color = "#A83262",
+    column_labels.border.bottom.color = "#A83262",
+    table.font.size = px(16),
+    heading.title.font.size = px(18),
+    table.background.color = "#FFF4CC"
+  )
 ```
 
 # Cox Model (with intervals?)
@@ -434,29 +502,229 @@ eme.age.rec.group$contrast |>
 
 # Identifying Predictors
 
-TODO: write a more generic function
+```{r}
+# From exercise 9
+Waldtest <- function(coxph.object, idx) {
+  b <- coxph.object$coef[idx]
+  Sig <- coxph.object$var[idx, idx]
+  Wald <- b %*% solve(Sig) %*% b
+  p <- 1 - pchisq(as.numeric(Wald), df = length(idx))
+  return(data.frame(Wald = Wald, df = length(idx), p = p))
+}
+
+test.new.var <- function(old.vars, new.var, i=1) {
+  new.surv <- reformulate(
+    termlabels = c(old.vars, new.var),
+    response = "Surv(follow.up, death)"
+  )
+  cox.fit <- coxph(new.surv, data = dat, method = "breslow")
+  print(cox.fit)
+  Waldtest(cox.fit, i)
+}
+```
+
+## Start with nothing
+
+```{r, echo=TRUE}
+old.vars <- c()
+test.new.var(old.vars, "tx.type", 1)
+test.new.var(old.vars, "hla.match", 1)
+test.new.var(old.vars, "age.donor", 1)
+test.new.var(old.vars, "age.rec", 1)
+test.new.var(old.vars, "cold.isc", 1)
+test.new.var(old.vars, "sex", 1)
+test.new.var(old.vars, "year", 1)
+```
+## `tx.type` + ?
+
+```{r, echo=TRUE}
+old.vars <- c("tx.type")
+
+# test.new.var(old.vars, "hla.match", 2:7)
+test.new.var(old.vars, "hla.match", 2)
+test.new.var(old.vars, "age.donor", 2)
+test.new.var(old.vars, "age.rec", 2)
+test.new.var(old.vars, "cold.isc", 2)
+test.new.var(old.vars, "sex", 2)
+test.new.var(old.vars, "year", 2)
+```
+
+`age.rec` has the smallest $p$-value
+
+## `tx.type` + `age.rec` + ?
+
+```{r, echo=TRUE}
+old.vars <- c("tx.type", "age.rec")
+
+test.new.var(old.vars, "hla.match", 3)
+test.new.var(old.vars, "age.donor", 3)
+test.new.var(old.vars, "cold.isc", 3)
+test.new.var(old.vars, "sex", 3)
+test.new.var(old.vars, "year", 3)
+```
+
+`hla.match` has the smallest $p$-value
+
+## `tx.type` + `age.rec` + `hla.match` + ?
+
+```{r, echo=TRUE}
+old.vars <- c("tx.type", "age.rec", "hla.match")
+
+test.new.var(old.vars, "age.donor", 4)
+test.new.var(old.vars, "cold.isc", 4)
+test.new.var(old.vars, "sex", 4)
+test.new.var(old.vars, "year", 4)
+```
+
+`age.donor` has the smallest $p$-value
+
+## `tx.type` + `age.rec` + `hla.match` + `age.donor` + ? 
+
+```{r, echo=TRUE}
+old.vars <- c("tx.type", "age.rec", "hla.match", "age.donor")
+
+test.new.var(old.vars, "cold.isc", 5)
+test.new.var(old.vars, "sex", 5)
+test.new.var(old.vars, "year", 5)
+```
+
+`year` has the smallest $p$-value
+
+## `tx.type` + `age.rec` + `hla.match` + `age.donor` + `year`
+
+```{r, echo=TRUE}
+old.vars <- c("tx.type", "age.rec", "hla.match", "age.donor", "year")
+
+test.new.var(old.vars, "cold.isc", 6)
+test.new.var(old.vars, "sex", 6)
+```
+
+Neither has $p$-value less than 0.05. Stop.
+
+# Full Model
 
 ```{r}
+surv.full <- Surv(follow.up + death) ~ tx.type + age.rec + hla.match +
+                 age.donor + year
+cox.full <- coxph(surv.full, data = dat, method = "breslow")
+```
+
+```{r, echo=TRUE}
+cox.full
+```
+
+```{r, fig.width=7, fig.height=5}
+tidy(cox.full, exponentiate = TRUE, conf.int = TRUE) |>
+  mutate(
+    term = recode(
+      term,
+      "tx.typeLiving" = "Living donor",
+      "age.rec" = "Recipient age",
+      "hla.match" = "HLA match",
+      "age.donor" = "Donor age",
+      "year" = "Transplant year"
+    )
+  ) |>
+  ggplot(aes(x = estimate, y = reorder(term, estimate))) +
+  geom_vline(xintercept = 1, linetype = "dashed") +
+  geom_errorbarh(
+    aes(xmin = conf.low, xmax = conf.high),
+    height = 0.2
+  ) +
+  scale_x_log10() +
+  geom_point(size = 2) +
+  labs(
+    title = "Hazard Ratios from Full Cox Model",
+    x = "Hazard Ratio",
+    y = NULL
+  ) +
+  my.theme
+```
+
+## What happened to `year`?
+
+```{r}
+ggplot(data = dat) +
+  geom_boxplot(aes(x = factor(year), y = follow.up))
+```
+
+```{r}
+ggplot(data = dat) +
+  geom_boxplot(aes(x = factor(year), y = follow.up)) +
+  facet_grid(death ~ .)
+```
+
+Probabily want to omit it
+
+## Without `year`
+
+```{r}
+surv.full.1 <- Surv(follow.up + death) ~ tx.type + age.rec + hla.match +
+                 age.donor
+cox.full.1 <- coxph(surv.full.1, data = dat, method = "breslow")
+```
+
+```{r, echo=TRUE}
+cox.full.1
+```
+
+```{r, fig.width=7, fig.height=5}
+tidy(cox.full.1, exponentiate = TRUE, conf.int = TRUE) |>
+  mutate(
+    term = recode(
+      term,
+      "tx.typeLiving" = "Living donor",
+      "age.rec" = "Recipient age",
+      "hla.match" = "HLA match",
+      "age.donor" = "Donor age",
+    )
+  ) |>
+  ggplot(aes(x = estimate, y = reorder(term, estimate))) +
+  geom_vline(xintercept = 1, linetype = "dashed") +
+  geom_errorbarh(
+    aes(xmin = conf.low, xmax = conf.high),
+    height = 0.2
+  ) +
+  scale_x_log10() +
+  geom_point(size = 2) +
+  labs(
+    title = "Hazard Ratios from Full Cox Model (Without Year)",
+    x = "Hazard Ratio",
+    y = NULL
+  ) +
+  my.theme
+```
+
+
+
+
+
+
+
+
+---
+
+TODO: write a more generic function (UPDATE: FAILED)
+
+<details>
+
+```{r, eval=FALSE}
+# WARNING: BAD, DO NOT USE.
+vars <- c("hla.match", "age.donor", "age.rec", "cold.isc", "year", "sex", 
+          "tx.type")
+included <- vars == "tx.type"
+
 Waldtest <- function(cox.fit, i.betas){
   q <- length(i.betas)
   coefs <- cox.fit$coefficients
   var <- cox.fit$var[i.betas, i.betas]
   Wald <- coefs[i.betas]%*%solve(var)%*%coefs[i.betas]
   p.value <- 1-pchisq(as.numeric(Wald), df = q)
-  print(p.value)
   return(p.value)
 }
-```
 
-```{r}
-vars <- c("hla.match", "age.donor", "age.rec", "cold.isc", "year", "sex", 
-          "tx.type")
-included <- vars == "tx.type"
-included <- c(FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE)
-included <- c(FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE)
 
-find.best.surv <- function(included) {
-  print('---')
+find.model.vars <- function(included) {
   test.vars <- vars[!included]
   p.values <- sapply(test.vars, function(test.var) {
     new.surv <- reformulate(
@@ -464,31 +732,24 @@ find.best.surv <- function(included) {
       response = "Surv(follow.up, death)"
     )
     fit.tx <- coxph(new.surv, data = dat)
-    Waldtest(fit.tx, sum(included))
+    Waldtest(fit.tx, 1)
   })
-  if (sum(p.values > 0.05) == sum(included)) {
-    print(3)
+  if (all(p.values > 0.05)) {
     return(included)
   }
-  if (sum(included == TRUE) == length(included)) {
-    print(2)
-    return(included)
-  }
-  print(1)
-  print(which.min(p.values))
-  print(included)
-  print(p.values)
-  print(which.min(p.values))
-  included[which.min(p.values)] <- TRUE
-  print(included)
-  # find.best.surv(included)
+  new.var <- names(p.values)[which.min(p.values)]
+  included[which(vars == new.var)] <- TRUE
+  return(find.model.vars(included))
 }
 
-
-find.best.surv(included)
+included <- find.model.vars(included)
+vars[included]
 
 ```
 
+</details>
+
+
 ```{r}
 # surv <- Surv(follow.up, death) ~ tx.type + age.rec + hla.match
 # fit.cox.model(surv, 3)