From 33cc33f81ae0325f804d6c5c4125f3ee73e9370a Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 24 Feb 2022 14:51:15 +0100
Subject: [PATCH] ranking: Remove caching for optimization

---
 R/ranking.R | 59 ++++++++++++++++++++++++-----------------------------
 1 file changed, 27 insertions(+), 32 deletions(-)

diff --git a/R/ranking.R b/R/ranking.R
index 233698b..47ec098 100644
--- a/R/ranking.R
+++ b/R/ranking.R
@@ -65,41 +65,36 @@ optimal_weights <- function(analysis, methods, reference_gene_ids,
         stop("Invalid analyis. Use geposan::analyze().")
     }
 
-    cached(
-        "optimization",
-        c(analysis$preset, methods, reference_gene_ids, target),
-        { # nolint
-            # Compute the target rank of the reference genes when applying the
-            # weights.
-            target_rank <- function(factors) {
-                data <- ranking(analysis, as.list(factors))
 
-                result <- data[
-                    gene %chin% reference_gene_ids,
-                    if (target == "min") {
-                        min(rank)
-                    } else if (target == "max") {
-                        max(rank)
-                    } else if (target == "mean") {
-                        mean(rank)
-                    } else {
-                        stats::median(rank)
-                    }
-                ]
+    # Compute the target rank of the reference genes when applying the
+    # weights.
+    target_rank <- function(factors) {
+        data <- ranking(analysis, as.list(factors))
 
-                if (result > 0) {
-                    result
-                } else {
-                    Inf
-                }
+        result <- data[
+            gene %chin% reference_gene_ids,
+            if (target == "min") {
+                min(rank)
+            } else if (target == "max") {
+                max(rank)
+            } else if (target == "mean") {
+                mean(rank)
+            } else {
+                stats::median(rank)
             }
+        ]
 
-            initial_factors <- rep(1.0, length(methods))
-            names(initial_factors) <- methods
-
-            optimal_factors <- stats::optim(initial_factors, target_rank)$par
-
-            as.list(optimal_factors / max(abs(optimal_factors)))
+        if (result > 0) {
+            result
+        } else {
+            Inf
         }
-    )
+    }
+
+    initial_factors <- rep(1.0, length(methods))
+    names(initial_factors) <- methods
+
+    optimal_factors <- stats::optim(initial_factors, target_rank)$par
+
+    as.list(optimal_factors / max(abs(optimal_factors)))
 }