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

R/utils.R

@@ -1,6 +1,7 @@
 #' Get tbl_kgx graph nodes table.
 #'
 #' @importFrom tidygraph as_tibble
+#' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
 #' print(nodes(g))
@@ -11,6 +12,7 @@ nodes.tbl_kgx <- function(x, ...) {
 #' Get tbl_kgx graph edges table.
 #'
 #' @importFrom tidygraph as_tibble
+#' @export
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
 #' print(edges(g))
@@ -46,7 +48,7 @@ edges <- function(x, ...) {
   UseMethod("edges")
 }
 
-
+#' @export
 explode <- function(x, ...) {
   UseMethod("explode")
 }