cleanup for successful build

.Rbuildignore

@@ -12,3 +12,5 @@
 node_modules$
 package-lock\.json$
 package\.json$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@
 .Rdata
 .httr-oauth
 .DS_Store
+/doc/
+/Meta/

NAMESPACE

@@ -1,25 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(edges,tbl_kgx)
 S3method(explode,tbl_kgx)
-S3method(select_nodes,monarch_kg)
+S3method(nodes,tbl_kgx)
 export(cypher_query)
 export(cypher_query_df)
 export(edges)
+export(explode)
 export(fetch_edges)
 export(monarch_search)
 export(nodes)
 export(query_ids)
-export(select_nodes)
 export(summarize_neighborhood)
 export(summarize_neighborhood_edges)
 export(summarize_neighborhood_nodes)
 export(tbl_kgx)
 import(dplyr)
 import(tidygraph)
 importFrom(assertthat,assert_that)
-importFrom(dplyr,mutate)
 importFrom(neo2R,cypher)
 importFrom(tibble,tibble)
-importFrom(tidygraph,activate)
 importFrom(tidygraph,as_tibble)
 importFrom(tidygraph,tbl_graph)

R/cypher_query.R

@@ -6,10 +6,6 @@
 #' @param cats_list A list of vectors of categories.
 #' @param cats_prefs An ordered preference list over categories.
 #' @return A vector of normalized categories.
-#' @examples
-#' categories_list <- list(c("A", "B", "C"), c("D", "E", "F"))
-#' categories_prefs <- c("B", "E", "A", "D", "C", "F")
-#' normalize_categories(categories_list, categories_prefs)
 normalize_categories <- function(cats_list, cats_prefs) {
 	normed <- unlist(lapply(cats_list, function(categories) {
 		positions <- match(categories, cats_prefs)

R/fetch.R

@@ -11,11 +11,11 @@
 #' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
-#' phenos <- g %>%
+#' phenos <- g |>
 #'   fetch_edges(predicates = "biolink:has_phenotype", result_categories = "biolink:PhenotypicFeature")
 #'
-#' ancestors <- g %>%
-#'  fetch_edges(predicates = "biolink:subclass_of", transitive = TRUE)
+#' ancestors <- g |>
+#'  fetch_edges(predicates = "biolink:subclass_of", transitive = TRUE, direction = "out")
 #'
 #' @import tidygraph
 #' @import dplyr
@@ -110,6 +110,7 @@ fetch_edges <- function(g,
                                                     predicates = predicates,
                                                     result_categories = result_categories))
 
+
     result <- result %>%
         tidygraph::activate(nodes) %>%
         mutate(pcategory = normalize_categories(category, options("kg_prefs")$kg_prefs$monarch_kg$category_priority))

R/utils.R

@@ -1,6 +1,9 @@
 #' Get tbl_kgx graph nodes table.
 #'
 #' @importFrom tidygraph as_tibble
+#' @param x Input graph
+#' @param ... Other options (unused)
+#' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
 #' print(nodes(g))
@@ -11,6 +14,9 @@ nodes.tbl_kgx <- function(x, ...) {
 #' Get tbl_kgx graph edges table.
 #'
 #' @importFrom tidygraph as_tibble
+#' @param x Input graph
+#' @param ... Other options (unused)
+#' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
 #' print(edges(g))
@@ -21,7 +27,8 @@ edges.tbl_kgx <- function(x, ...) {
 
 #' Get graph nodes table.
 #'
-#' @param x A graph object
+#' @param x Input graph
+#' @param ... Other options (unused)
 #' @return A tibble with the nodes of the graph
 #' @importFrom tidygraph as_tibble
 #' @export
@@ -37,6 +44,8 @@ nodes <- function(x, ...) {
 #'
 #' @return A tibble with the edges of the graph
 #' @importFrom tidygraph as_tibble
+#' @param x Input graph
+#' @param ... Other options (unused)
 #' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
@@ -46,14 +55,23 @@ edges <- function(x, ...) {
   UseMethod("edges")
 }
 
-
+#' Explode a graph into a list of single-node graphs.
+#'
+#' @param x Input graph
+#' @param ... Other options (unused)
+#' @return A list of single-node graphs
+#' @export
+#' @examples
+#' g <- monarch_search("fanconi anemia", limit = 5)
+#' print(explode(g))
 explode <- function(x, ...) {
   UseMethod("explode")
 }
 
 #' Explode a graph into a list of single-node graphs.
 #'
-#' @param x A graph object
+#' @param x Input graph
+#' @param ... Other options (unused)
 #' @return A list of single-node graphs
 #' @importFrom tidygraph as_tibble
 #' @export