Rename method proximity to distance

NAMESPACE

@@ -14,6 +14,7 @@ export(clustering)
 export(compare)
 export(correlation)
 export(densest)
+export(distance)
 export(method)
 export(neural)
 export(optimal_weights)
@@ -24,7 +25,6 @@ export(plot_rankings)
 export(plot_scores)
 export(plot_scores_by_position)
 export(preset)
-export(proximity)
 export(ranking)
 export(result)
 export(validate)

R/method.R

@@ -33,11 +33,11 @@ method <- function(id, name, description, func) {
 #' @export
 all_methods <- function() {
   list(
+    distance(),
+    adjacency(),
     clustering(),
     correlation(),
-    neural(),
-    adjacency(),
-    proximity()
+    neural()
   )
 }
 

R/method_distance.R

@@ -13,9 +13,9 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-proximity <- function(id = "proximity",
-                      name = "Proximity",
-                      description = "Proximity to telomeres",
+distance <- function(id = "distance",
+                      name = "Distance",
+                      description = "Distance to telomeres",
                       summarize = stats::median) {
   method(
     id = id,
@@ -25,7 +25,7 @@ proximity <- function(id = "proximity",
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids
 
-      cached("proximity", c(species_ids, gene_ids), {
+      cached("distance", c(species_ids, gene_ids), {
         # Prefilter distances by species and gene.
         data <- geposan::distances[
           species %chin% preset$species_ids &
@@ -39,12 +39,12 @@ proximity <- function(id = "proximity",
         ]
 
         # Normalize scores.
-        data[, score := 1 - combined_distance / max(combined_distance)]
+        data[, score := combined_distance / max(combined_distance)]
 
         progress(1.0)
 
         result(
-          method = "proximity",
+          method = "distance",
           scores = data[, .(gene, score)],
           details = list(data = data)
         )

man/distance.Rd

@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/method_proximity.R
-\name{proximity}
-\alias{proximity}
+% Please edit documentation in R/method_distance.R
+\name{distance}
+\alias{distance}
 \title{Score the distance of genes to the telomeres across species.}
 \usage{
-proximity(
-  id = "proximity",
-  name = "Proximity",
-  description = "Proximity to telomeres",
+distance(
+  id = "distance",
+  name = "Distance",
+  description = "Distance to telomeres",
   summarize = stats::median
 )
 }