Fix some package issues

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

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) {

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,