Rename method proximity to distance

R/method_proximity.R

@@ -1,54 +0,0 @@
-#' Score the distance of genes to the telomeres across species.
-#'
-#' A score will be given to each gene such that 0.0 corresponds to the maximal
-#' distance across all genes and 1.0 corresponds to a distance of 0.
-#'
-#' @param id Unique ID for the method and its results.
-#' @param name Human readable name for the method.
-#' @param description Method description.
-#' @param summarize A function for combining the different proximities into one
-#'   metric. By default, [stats::median()] is used. Other suggested options
-#'   include [min()] and [mean()].
-#'
-#' @return An object of class `geposan_method`.
-#'
-#' @export
-proximity <- function(id = "proximity",
-                      name = "Proximity",
-                      description = "Proximity to telomeres",
-                      summarize = stats::median) {
-  method(
-    id = id,
-    name = name,
-    description = description,
-    function(preset, progress) {
-      species_ids <- preset$species_ids
-      gene_ids <- preset$gene_ids
-
-      cached("proximity", c(species_ids, gene_ids), {
-        # Prefilter distances by species and gene.
-        data <- geposan::distances[
-          species %chin% preset$species_ids &
-            gene %chin% preset$gene_ids
-        ]
-
-        # Compute the score as described above.
-        data <- data[,
-          .(combined_distance = as.double(summarize(distance))),
-          by = "gene"
-        ]
-
-        # Normalize scores.
-        data[, score := 1 - combined_distance / max(combined_distance)]
-
-        progress(1.0)
-
-        result(
-          method = "proximity",
-          scores = data[, .(gene, score)],
-          details = list(data = data)
-        )
-      })
-    }
-  )
-}