From f2bc4318a2f4f1cab20a8d8d96644565ddf06cbe Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Tue, 23 Nov 2021 09:42:21 +0100
Subject: [PATCH] Fix some package issues

---
 R/neural.R    | 5 ++++-
 R/ranking.R   | 2 +-
 man/preset.Rd | 3 +--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/neural.R b/R/neural.R
index c36bc98..7e78a2b 100644
--- a/R/neural.R
+++ b/R/neural.R
@@ -133,7 +133,10 @@ neural <- function(preset, progress = NULL, seed = 49641) {
             colnames(data_matrix) <- NULL
             data_matrix <- keras::normalize(data_matrix)
 
-            data[gene %chin% gene_ids, score := predict(model, data_matrix)]
+            data[
+                gene %chin% gene_ids,
+                score := stats::predict(model, data_matrix)
+            ]
 
             if (!is.null(progress)) {
                 progress_buffer <<- progress_buffer + progress_step
diff --git a/R/ranking.R b/R/ranking.R
index 0dcbfa7..6782a98 100644
--- a/R/ranking.R
+++ b/R/ranking.R
@@ -75,7 +75,7 @@ optimal_weights <- function(analysis, methods, reference_gene_ids,
         } else if (target == "mean") {
             mean(rank)
         } else {
-            median(rank)
+            stats::median(rank)
         }]
 
         if (result > 0) {
diff --git a/man/preset.Rd b/man/preset.Rd
index ceb42ff..1b5d969 100644
--- a/man/preset.Rd
+++ b/man/preset.Rd
@@ -5,8 +5,7 @@
 \title{Create a new preset.}
 \usage{
 preset(
-  methods = c("clusteriness", "clusteriness_positions", "correlation",
-    "correlation_positions", "neural", "proximity"),
+  methods = c("clusteriness", "correlation", "neural", "proximity"),
   species_ids = NULL,
   gene_ids = NULL,
   reference_gene_ids = NULL,