Merge pull request #33 from frederikfabriciusbjerre/copilot/fix-scrambled-vertex-indices

Fix vertex index scrambling when converting from igraph to caugi

Author: frederikfabriciusbjerre

R/caugi_graph.R

@@ -224,7 +224,21 @@ caugi_graph <- S7::new_class(
     }
 
     # All unique nodes
-    nodes <- tibble::tibble(name = unique(c(edges$from, edges$to, declared)))
+    # When declared nodes are provided and contain ALL edge nodes,
+    # preserve their order (important for igraph conversion)
+    edge_node_names <- unique(c(edges$from, edges$to))
+    if (length(declared) > 0L && all(edge_node_names %in% declared)) {
+      # Declared contains all edge nodes: preserve declared order
+      all_node_names <- unique(declared)
+    } else if (length(declared) > 0L) {
+      # Declared exists but doesn't contain all edge nodes:
+      # use edge order first, then add declared isolates (old behavior)
+      all_node_names <- unique(c(edge_node_names, declared))
+    } else {
+      # No declared nodes: use edge order (old behavior)
+      all_node_names <- edge_node_names
+    }
+    nodes <- tibble::tibble(name = all_node_names)
     n <- nrow(nodes)
     id <- seq_len(n) - 1L
     names(id) <- nodes$name

tests/testthat/test-as_caugi.R

@@ -219,6 +219,23 @@ test_that("igraph with no edges, but with nodes, works", {
   expect_setequal(nodes(cg0)[["name"]], c("A", "B", "C"))
 })
 
+test_that("igraph vertex order is preserved when converting to caugi", {
+  skip_if_not_installed("igraph")
+  
+  # Create igraph with specific vertex names (V1...V10)
+  # Add edges that would naturally scramble the order if we use unique(c(from, to))
+  set.seed(1022)
+  g <- igraph::sample_gnm(10, 5) |> igraph::as_directed(mode = "acyclic")
+  igraph::V(g)$name <- paste0("V", 1:length(igraph::V(g)))
+  
+  # Convert to caugi
+  cg <- as_caugi(g, class = "DAG")
+  
+  # Vertex order should be preserved
+  expect_equal(V(cg)$name, igraph::V(g)$name)
+  expect_equal(V(cg)$name, paste0("V", 1:10))
+})
+
 # ──────────────────────────────────────────────────────────────────────────────
 # ─────────────────────────── graphNEL conversion ──────────────────────────────
 # ──────────────────────────────────────────────────────────────────────────────

tests/testthat/test-caugi_graph.R

@@ -373,8 +373,26 @@ test_that("caugi_graph(vector mode) works with isolated nodes", {
   expect_equal(cg_vec_1, cg_vec_2)
 })
 
+test_that("caugi_graph preserves node order from nodes parameter", {
+  # When nodes parameter is provided, its order should be preserved
+  # even when edges reference nodes in different order
+  cg <- caugi_graph(
+    from = c("V3", "V7", "V2"),
+    edge = c("-->", "-->", "-->"),
+    to = c("V1", "V9", "V5"),
+    nodes = paste0("V", 1:10),
+    class = "DAG"
+  )
+  
+  # Node order should match the provided nodes parameter
+  expect_equal(V(cg)$name, paste0("V", 1:10))
+  
+  # Edges should still be present and correct
+  expect_equal(nrow(edges(cg)), 3)
+})
+
 # ──────────────────────────────────────────────────────────────────────────────
-# ────────────────────────────────── Errors ────────────────────────────────────
+# ────────────────────────────────────── Errors ────────────────────────────────
 # ──────────────────────────────────────────────────────────────────────────────
 
 test_that("caugi_graph errors with trailing commas", {