R Under development (unstable) (2024-02-05 r85863 ucrt) -- "Unsuffered Consequences"
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> library(pcalg)
> 
> n.perm <- 5
> 
> set.seed(123)
> 
> # A: adjacency matrix of DAG;
> # B: adjacency matrix of CPDAG
> # Setting 3 by courtesy of Jonas Peters: in pcalg <= 2.0.8,
> # setting i = 3, k = 3 failed
> A <- list(
+   matrix(c(0,0,0,0,1, 0,0,1,0,1, 0,0,0,1,0, 0,0,0,0,0, 0,0,0,0,0), 5, 5, byrow = TRUE),
+   matrix(c(0,1,0,0,0, 0,0,0,1,0, 0,0,0,1,0, 0,0,0,0,1, 0,0,0,0,0), 5, 5, byrow = TRUE),
+   matrix(c(0,0,0,0, 1,0,0,0, 1,1,0,0, 1,1,1,0), 4, 4),
+   matrix(c(0,0,0,0, 1,0,0,0, 1,1,0,0, 1,1,1,0), 4, 4),
+   matrix(c(0,0,0,0, 1,0,0,0, 1,1,0,0, 1,1,1,0), 4, 4))
> B <- list(
+   matrix(c(0,0,0,0,1, 0,0,1,0,1, 0,1,0,1,0, 0,0,1,0,0, 0,0,0,0,0), 5, 5, byrow = TRUE),
+   matrix(c(0,1,0,0,0, 1,0,0,1,0, 0,0,0,1,0, 0,0,0,0,1, 0,0,0,0,0), 5, 5, byrow = TRUE),
+   matrix(c(0,1,1,1, 1,0,1,1, 1,1,0,1, 1,1,1,0), 4, 4),
+   matrix(c(0,1,1,0, 1,0,1,0, 1,1,0,0, 1,1,1,0), 4, 4),
+   matrix(c(0,0,0,0, 1,0,0,0, 1,1,0,1, 1,1,1,0), 4, 4))
> targets <- list(
+   list(integer(0)),
+   list(integer(0)),
+   list(integer(0)),
+   list(integer(0), 4),
+   list(integer(0), 2))
> 
> for (i in 1:length(A)) {
+   for (k in 1:n.perm) {
+     p <- nrow(A[[i]])
+     
+     ind <- if(k == 1) 1:p else sample.int(p)
+     permTargets <- lapply(targets[[i]], function(v) match(v, ind))
+     
+     # Test functionality with a matrix
+     B.hat <- dag2essgraph(A[[i]][ind, ind], targets = permTargets)
+     if (!all(B.hat == B[[i]][ind, ind])) {
+       stop(sprintf("True CPDAG not found! (setting: matrix, i = %d, k = %d)", i, k))
+     }
+     
+     # Test functionality with grephNEL objects
+     g <- as(A[[i]][ind, ind], "graphNEL")
+     pdag <- dag2essgraph(g, targets = permTargets)
+     B.hat <- as(pdag, "matrix")
+     if (!all(B.hat == B[[i]][ind, ind])) {
+       stop(sprintf("True CPDAG not found! (setting:  graphNEL, i = %d, k = %d)", i, k))
+     }
+     
+     # Test functionality with ParDAG/EssGraph objects
+     g <- as(A[[i]][ind, ind], "GaussParDAG")
+     pdag <- dag2essgraph(g, targets = permTargets)
+     B.hat <- as(pdag, "matrix")
+     if (!all(B.hat == B[[i]][ind, ind])) {
+       stop(sprintf("True CPDAG not found! (setting:  ParDAG, graphNEL, i = %d, k = %d)", i, k))
+     }
+     
+     # par(mfrow = c(1, 2))
+     # plot(g)
+     # plot(pdag)
+   }
+ }
> 
> proc.time()
   user  system elapsed 
   1.06    0.17    1.21