Allow customizing method metadata

R/method_adjacency.R

@@ -28,6 +28,9 @@ densest <- function(data) {
 #' combined. The resulting value is compared to the reference genes and
 #' determines the gene's score in relation to other genes.
 #'
+#' @param id Unique ID for the method and its results.
+#' @param name Human readable name for the method.
+#' @param description Method description.
 #' @param distance_estimate A function that will be used to summarize the
 #'   distance values for each gene. See [densest()] for the default
 #'   implementation.
@@ -39,11 +42,15 @@ densest <- function(data) {
 #' @seealso [species_adjacency()]
 #'
 #' @export
-adjacency <- function(distance_estimate = densest, summarize = stats::median) {
+adjacency <- function(id = "adjacency",
+                      name = "Adjacency",
+                      description = "Adjacency to reference genes",
+                      distance_estimate = densest,
+                      summarize = stats::median) {
   method(
-    id = "adjacency",
-    name = "Adjacency",
-    description = "Adjacency to reference genes",
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_clustering.R

@@ -70,16 +70,22 @@ clusteriness <- function(data,
 #' The result will be cached and can be reused for different presets, because
 #' it is independent of the reference genes in use.
 #'
+#' @param id Unique ID for the method and its results.
+#' @param name Human readable name for the method.
+#' @param description Method description.
+#'
 #' @return An object of class `geposan_method`.
 #'
 #' @seealso [clusteriness()]
 #'
 #' @export
-clustering <- function() {
-  method(
-    id = "clustering",
+clustering <- function(id = "clustering",
     name = "Clustering",
-    description = "Clustering of genes",
+                       description = "Clustering of genes") {
+  method(
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_correlation.R

@@ -1,5 +1,8 @@
 #' Score genes based on their correlation with the reference genes.
 #'
+#' @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 correlation
 #'   coefficients into one metric. By default, [stats::median()] is used. Other
 #'   suggested options include [max()] and [mean()].
@@ -7,11 +10,14 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-correlation <- function(summarize = stats::median) {
+correlation <- function(id = "correlation",
+                        name = "Correlation",
+                        description = "Correlation with reference genes",
+                        summarize = stats::median) {
   method(
-    id = "correlation",
-    name = "Correlation",
-    description = "Correlation with reference genes",
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_neural.R

@@ -1,5 +1,8 @@
 #' Find genes by training and applying a neural network.
 #'
+#' @param id Unique ID for the method and its results.
+#' @param name Human readable name for the method.
+#' @param description Method description.
 #' @param seed The seed will be used to make the results reproducible.
 #' @param n_models This number specifies how many sets of training data should
 #'   be created. For each set, there will be a model trained on the remaining
@@ -14,11 +17,16 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-neural <- function(seed = 180199, n_models = 5, control_ratio = 0.5) {
+neural <- function(id = "neural",
+                   name = "Neural",
+                   description = "Assessment by neural network",
+                   seed = 180199,
+                   n_models = 5,
+                   control_ratio = 0.5) {
   method(
-    id = "neural",
-    name = "Neural",
-    description = "Assessment by neural network",
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_proximity.R

@@ -3,6 +3,9 @@
 #' 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()].
@@ -10,11 +13,14 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-proximity <- function(summarize = stats::median) {
+proximity <- function(id = "proximity",
+                      name = "Proximity",
+                      description = "Proximity to telomeres",
+                      summarize = stats::median) {
   method(
-    id = "proximity",
-    name = "Proximity",
-    description = "Proximity to telomeres",
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_species_adjacency.R

@@ -4,6 +4,9 @@
 #' to the reference genes within that species. Afterwards, the results are
 #' summarized across species and determine the gene's score.
 #'
+#' @param id Unique ID for the method and its results.
+#' @param name Human readable name for the method.
+#' @param description Method description.
 #' @param distance_estimate Function for combining the distance differences
 #'   within one species.
 #' @param summarize Function for summarizing the distance values across species.
@@ -13,12 +16,15 @@
 #' @seealso [adjacency()]
 #'
 #' @export
-species_adjacency <- function(distance_estimate = stats::median,
+species_adjacency <- function(id = "species_adjacency",
+                              name = "Species adj.",
+                              description = "Species adjacency",
+                              distance_estimate = stats::median,
                               summarize = stats::median) {
   method(
-    id = "species_adjacency",
-    name = "Species adj.",
-    description = "Species adjacency",
+    id = id,
+    name = name,
+    description = description,
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids