mg_to_igraph is now igraph() 🎨

DESCRIPTION

@@ -23,23 +23,24 @@ URL: https://mangal.io
 BugReports: https://github.com/mangal-wg/rmangal/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 Imports:
     httr (>= 1.3.1),
     igraph,
     jsonlite (>= 1.5),
     memoise,
     purrr,
     sf
-RoxygenNote: 6.1.1
 Suggests:
+    ggraph,
     knitr,
     magrittr,
     mapview,
     rmarkdown,
     taxize,
+    tidygraph,
     testthat,
     tibble,
     USAboundaries
+RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as.igraph,mgNetwork)
+S3method(as.igraph,mgNetworksCollection)
 S3method(get_citation,mgNetwork)
 S3method(get_citation,mgNetworksCollection)
 S3method(get_collection,default)
@@ -9,21 +11,20 @@ S3method(get_collection,mgSearchNetworks)
 S3method(get_collection,mgSearchNodes)
 S3method(get_collection,mgSearchReference)
 S3method(get_collection,mgSearchTaxonomy)
-S3method(mg_to_igraph,mgNetwork)
-S3method(mg_to_igraph,mgNetworksCollection)
 S3method(print,mgNetwork)
 S3method(print,mgNetworksCollection)
+export(as.igraph)
 export(avail_type)
 export(clear_cache_rmangal)
 export(combine_mgNetworks)
 export(get_citation)
 export(get_collection)
 export(get_network_by_id)
 export(get_network_by_id_indiv)
-export(mg_to_igraph)
 export(search_datasets)
 export(search_interactions)
 export(search_networks)
 export(search_nodes)
 export(search_reference)
 export(search_taxonomy)
+importFrom(igraph,as.igraph)

R/mg_to_igraph.R → R/as.igraph.R

@@ -7,26 +7,10 @@
 #' An object of class `igraph` for a `mgNetwork` object and a list of
 #' `igraph` objects for `mgNetworksCollection`.
 #'
-#'
-#' @examples
-#' insects_networks <- get_collection(search_networks(query='insect%'))
-#' # Apply mg_to_igraph on one specific network
-#' insects_network <- insects_networks[[1]]
-#' ig_network <- mg_to_igraph(insects_network)
-#' # Apply mg_to_igraph on networks collection
-#' ig_coll_networks <- mg_to_igraph(insects_networks)
-#' # Plot igraph object with vertex label
-#' plot(ig_network, vertex.label = insects_network$nodes$taxonomy.name)
-#' @export
-
-mg_to_igraph <- function(x, ...) {
-    UseMethod("mg_to_igraph", x)
-}
-
-
-#' @describeIn mg_to_igraph Convert`mgNetwork` objects to `igraph` objects.
-#' @export
-mg_to_igraph.mgNetwork <- function(x, ...) {
+#' @importFrom igraph as.igraph
+#' @describeIn as.igraph Convert `mgNetwork` objects to `igraph` objects.
+#' @export 
+as.igraph.mgNetwork <- function(x, ...) {
     # Simple test to know if the graph is directed or undirected
     directed <- ifelse(all(x$edges$direction == "directed"), TRUE, FALSE)
     # Move id edge to the last column
@@ -40,8 +24,11 @@ mg_to_igraph.mgNetwork <- function(x, ...) {
 }
 
 
-#' @describeIn  mg_to_igraph Convert `mgNetworksCollection` objects to `igraph` objects.
+#' @describeIn as.igraph Convert `mgNetworksCollection` objects to a list of `igraph` objects.
 #' @export
-mg_to_igraph.mgNetworksCollection <- function(x, ...) {
-    lapply(x, mg_to_igraph.mgNetwork)
+as.igraph.mgNetworksCollection <- function(x, ...) {
+    lapply(x, as.igraph.mgNetwork)
 }
+
+#' @export
+igraph::as.igraph

R/combine_mgNetworks.R

@@ -1,4 +1,4 @@
-#' Combine Mangal networks.
+#' Combine Mangal networks
 #'
 #' Combine `mgNetworksCollection` and `mgNetwork` objects into a
 #' `mgNetworksCollection` object.

tests/testthat/helper-rmangal.R

@@ -1,2 +1,2 @@
-cl_df <- c("tbl_df", "tbl",  "data.frame")
+cl_df <- c("tbl_df", "tbl", "data.frame")
 nm_co <-  c("network", "nodes", "edges", "dataset", "reference")

tests/testthat/test-as.igraph.R

@@ -1,8 +1,8 @@
 context("mg_to_igraph")
 
 # Prep test on mgNetwork
-net_100 <- mg_to_igraph(get_network_by_id(100))
-net_collection <- mg_to_igraph(get_collection(search_datasets("closs")))
+net_100 <- as.igraph(get_network_by_id(100))
+net_collection <- as.igraph(get_collection(search_datasets("closs")))
 
 test_that("expected behavior", {
   expect_equal(length(net_collection), 12)

vignettes/rmangal.R

@@ -0,0 +1,16 @@
+## ----setup, include = FALSE----------------------------------------------
+knitr::opts_chunk$set(
+  message = FALSE,
+  collapse = TRUE,
+  comment = "#>"
+)
+# library(sf)
+
+## ----echo = FALSE--------------------------------------------------------
+knitr::include_graphics("figs/data_structure.svg")
+
+## ----load_packages-------------------------------------------------------
+library(rmangal)
+library(magrittr) # for the pip %>%
+library(tibble) # to use tibbles, enhanced data frames
+

vignettes/rmangal.Rmd

@@ -364,7 +364,7 @@ website](https://igraph.org/r/)) object and then to carry out network analysis:
 
 ```{R}
 library(igraph)
-ig_lagoons <- search_datasets(query = 'lagoon') %>% get_collection %>% mg_to_igraph
+ig_lagoons <- search_datasets(query = 'lagoon') %>% get_collection %>% as.igraph
 ## Modularity analysis for the first network
 modularity(ig_lagoons[[1]], membership(cluster_walktrap(ig_lagoons[[1]])))
 ## Degree values for all networks