adjacency: Revert to density estimate

This reverts commit 23bb499d3a.

R/adjacency.R

@@ -1,7 +1,31 @@
+#' Find the densest value in the data.
+#'
+#' This function assumes that data represents a continuous variable and finds
+#' a single value with the highest estimated density. This can be used to
+#' estimate the mode of the data. If there is only one value that value is
+#' returned. If multiple density maxima with the same density exist, their mean
+#' is returned.
+#'
+#' @param data The input data.
+#'
+#' @return The densest value of data.
+#'
+#' @export
+densest <- function(data) {
+    as.numeric(if (length(data) <= 0) {
+        NULL
+    } else if (length(data) == 1) {
+        data
+    } else {
+        density <- stats::density(data)
+        mean(density$x[density$y == max(density$y)])
+    })
+}
+
 #' Score genes based on their proximity to the reference genes.
 #'
 #' @param estimate A function that will be used to summarize the distance
-#'   values for each gene. By default, [median()] is used.
+#'   values for each gene. See [densest()] for the default implementation.
 #' @param combination A function that will be used to combine the different
 #'   distances to the reference genes. By default [min()] is used. That means
 #'   the distance to the nearest reference gene will be scored.
@@ -9,7 +33,7 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-adjacency <- function(estimate = stats::median, combination = min) {
+adjacency <- function(estimate = densest, combination = min) {
     method(
         id = "adjacency",
         name = "Adjacency",