Merge pull request #10 from LucasKook/dev

Add survival forests

.gitignore

@@ -44,4 +44,4 @@ inst/results*
 *.pdf
 *.sh
 *.sav
-
+model-classes/

NAMESPACE

@@ -24,5 +24,6 @@ export(lmICP)
 export(polrICP)
 export(pvalues)
 export(rangerICP)
+export(survforestICP)
 export(survregICP)
 import(tram)

R/alias.R

@@ -386,3 +386,31 @@ rangerICP <- function(formula, data, env, verbose = TRUE, type = "residual",
   ret$call <- call
   ret
 }
+
+#' nonparametric ICP for right-censored observations with ranger GCM
+#' @rdname tramicp-alias
+#'
+#' @inheritParams dicp
+#'
+#' @export
+#'
+#' @examples
+#' \donttest{
+#' set.seed(12)
+#' d <- dgp_dicp(mod = "coxph", n = 3e2)
+#' d$Y <- survival::Surv(d$Y, sample(0:1, 3e2, TRUE, prob = c(0.1, 0.9)))
+#' survforestICP(Y ~ X1 + X2 + X3, data = d, env = ~ E)
+#' }
+#'
+survforestICP <- function(formula, data, env, verbose = TRUE, type = "residual",
+                          test = "gcm.test", controls = NULL, alpha = 0.05,
+                          baseline_fixed = TRUE, greedy = FALSE, max_size = NULL,
+                          mandatory = NULL, ...) {
+  call <- match.call()
+  ret <- dicp(formula = formula, data = data, env = env, modFUN = survforest,
+              verbose = verbose, type = type, test = test, controls = controls,
+              alpha = alpha, baseline_fixed = baseline_fixed, greedy = greedy,
+              max_size = max_size, mandatory = mandatory, ... = ...)
+  ret$call <- call
+  ret
+}

R/controls.R

@@ -79,7 +79,7 @@ dicp_controls <- function(
 
 .test_fun <- function(type, test, ctest) {
   if (is.function(test))
-    return(list(test = "custom", test_fun = test_fun, test_name = ctest))
+    return(list(test = "custom", test_fun = test, test_name = ctest))
 
   if (type %in% c("wald", "partial")) {
     ctest <- "wald"

R/helpers.R

@@ -309,3 +309,27 @@ residuals.ranger <- function(object, newdata = NULL, newy = NULL, ...) {
     return(character(0))
   ret
 }
+
+survforest <- function(formula, data, ...) {
+  tms <- .get_terms(formula)
+  if (identical(tms$me, character(0))) {
+    return(survival::coxph(formula, data))
+  }
+  rf <- ranger::ranger(formula, data, ...)
+  class(rf) <- c("survforest", class(rf))
+  rf$y <- stats::model.response(stats::model.frame(formula, data))
+  rf$data <- data
+  rf
+}
+
+residuals.survforest <- function(object, ...) {
+  times <- object$y[, 1]
+  status <- object$y[, 2]
+  pred <- stats::predict(object, data = object$data)
+  idx <- match(times, pred$unique.death.times)
+  preds <- pred$survival
+  ipreds <- sapply(seq_len(nrow(preds)), \(smpl) {
+    -log(preds[smpl, idx[smpl]])
+  })
+  status - ipreds
+}

R/invariance-types.R

@@ -27,8 +27,8 @@
 
   ### Return
   if (set == 1) tset <- "Empty"
-  structure(list(set = tset, test = tst, coef = stats::coef(m), tram = m$tram),
-            class = "dICPtest")
+  structure(list(set = tset, test = tst, coef = stats::coef(m), tram = m$tram,
+                 rYX = r, rEX = e), class = "dICPtest")
 
 }
 

R/tramicp.R

@@ -211,8 +211,8 @@ invariant_sets <- function(object, with_pvalues = FALSE) {
         modFUN = modFUN, data = data, controls = controls,
         mandatory = mandatory, ... = ...
       )
-
-      if (.get_pvalue(ret$test) > controls$alpha) {
+      tpv <- .get_pvalue(ret$test)
+      if (!is.nan(tpv) && tpv > controls$alpha) {
         MI <- c(MI, lps[[set]])
       }
 

README.md

@@ -96,7 +96,9 @@ the `dicp()` function, for instance, after loading `tramME`, `dicp(..., modFUN =
 "BoxCoxME")` can be used.
 
 Nonparametric ICP via the GCM test [4] and random forests for the two
-regressions is implemented in the alias `rangerICP()`.
+regressions is implemented in the alias `rangerICP()`. Survival forests
+are supported for right-censored observations and implemented in 
+`survforestICP()`.
 
 # Replication materials