Merge pull request #74 from schochastics/edgelist

expose convert_edgelist (#56)

NAMESPACE

@@ -2,9 +2,13 @@
 
 S3method(as_pkgrefs,default)
 S3method(as_pkgrefs,sessionInfo)
+S3method(convert_edgelist,default)
+S3method(convert_edgelist,rang)
+S3method(convert_edgelist,ranglet)
 S3method(print,rang)
 S3method(print,ranglet)
 export(as_pkgrefs)
+export(convert_edgelist)
 export(dockerise)
 export(dockerise_rang)
 export(dockerize)

R/edgelist.R

@@ -0,0 +1,51 @@
+#' Convert Data Structures to rang edgelist
+#'
+#' This generic function converts several data structures provided by rang into an edgelist of package dependencies.
+#' @param x, supported data structures are `rang` and `ranglet` S3 objects
+#' @param ..., not used
+#' @return a data frame of directed edges of dependencies
+#' @details the resulting data frame can be converted to an igraph object for plotting and analysis via the function [igraph::graph_from_data_frame()]
+#' @export
+#' @examples
+#' \donttest{
+#' if (interactive()) {
+#'     graph <- resolve(pkgs = c("openNLP", "LDAvis", "topicmodels", "quanteda"),
+#'                 snapshot_date = "2020-01-16")
+#'                 
+#'     # dependency edgelist of a single package
+#'     convert_edgelist(graph$ranglets[[1]])
+#'     
+#'     # full dependency edgelist
+#'     convert_edgelist(graph)
+#' }
+#' }
+convert_edgelist <- function(x, ...) {
+    UseMethod("convert_edgelist", x)
+}
+
+#' @rdname convert_edgelist
+#' @export
+convert_edgelist.default <- function(x, ...){
+    stop(paste("don't know how to convert an object of type",class(x),"to a rang edgelist"), call. = FALSE)
+}
+
+#' @rdname convert_edgelist
+#' @export
+convert_edgelist.ranglet <- function(x, ...){
+    output <- data.frame(from = x$pkgref, to = .extract_queryable_dependencies(x$original, x$no_enhances, x$no_suggests))
+    for (dep in x$deps) {
+        if (!.is_terminal_node(dep, x$no_enhances)) {
+          el <- data.frame(from = unique(dep$x_pkgref), to = .extract_queryable_dependencies(dep, x$no_enhances, x$no_suggests))
+          output <- rbind(output, el)
+       }
+    }
+    output
+}
+
+#' @rdname convert_edgelist
+#' @export
+convert_edgelist.rang <- function(x, ...){
+    el <- do.call("rbind",lapply(x$ranglets,convert_edgelist))
+    rownames(el) <- NULL
+    el
+}

R/resolve.R

@@ -366,17 +366,6 @@ print.rang <- function(x, all_pkgs = FALSE, ...) {
     }
 }
 
-convert_edgelist <- function(x) {
-    output <- data.frame(x = x$pkg, y = .extract_queryable_dependencies(x$original, x$no_enhances, x$no_suggests))
-    for (dep in x$deps) {
-        if (!.is_terminal_node(dep, x$no_enhances)) {
-            el <- data.frame(x = unique(dep$x), y = .extract_queryable_dependencies(dep, x$no_enhances, x$no_suggests))
-            output <- rbind(output, el)
-        }
-    }
-    output
-}
-
 ## extract all the pkgrefs of deps and pkgs: for .sysreqs
 .extract_pkgrefs <- function(rang) {
     original_pkgrefs <- names(rang$ranglets)

tests/testthat/test-edgelist.R

@@ -0,0 +1,19 @@
+test_that("convert ranglet to edgelist", {
+  graph <- readRDS("../testdata/graph.RDS")
+  el <- convert_edgelist(graph$ranglets[[1]])
+  expect_s3_class(el,"data.frame")
+  expect_equal(nrow(el),4L)
+})
+
+test_that("convert rang to edgelist", {
+  graph <- readRDS("../testdata/graph.RDS")
+  el <- convert_edgelist(graph)
+  expect_s3_class(el,"data.frame")
+  expect_equal(nrow(el),121L)
+})
+
+test_that("convert edgelist error", {
+  expect_error(convert_edgelist("abc"))
+  expect_error(convert_edgelist(42))
+  expect_error(convert_edgelist(cbind(1:5,6:10)))
+})