R Under development (unstable) (2024-02-05 r85863 ucrt) -- "Unsuffered Consequences"
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> if(requireNamespace("dagitty")) {
+ library(pcalg)
+ (doExtras <- pcalg:::doExtras())
+ 
+ ## Minimalistic CRAN checks
+ 
+ ## Test 1 ############################
+ ## Test that "no adjustment set" and "empty adjustment set" are distinguished properly
+ x <- 1; y <- 2
+ cpdag <- matrix(c(0,1,1,0),2,2) ## 1 --- 2 => no adj set
+ dag <- matrix(c(0,1,0,0),2,2) ## 1 --> 2 => empty adj set
+ 
+ adjC <- adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "canonical")
+ adjD <- adjustment(amat = dag, amat.type = "dag", x = 1, y = 2, set.type = "canonical")
+ adjP <- adjustment(amat = dag, amat.type = "pdag", x = 1, y = 2, set.type = "canonical")
+ 
+ stopifnot(!identical(adjC, adjD), identical(adjD, adjP) )
+ 
+ ## Test 2 ###############################
+ gacVSadj <- function(amat, x, y ,z, V, type) {
+   ## gac(z) is TRUE IFF z is returned by adjustment()
+   ## x,y,z: col positions as used in GAC
+   ## Result: TRUE is result is equal
+   typeDG <- switch(type,
+                    dag = "dag",
+                    cpdag = "cpdag",
+                    mag = "mag",
+                    pag = "pag")
+   gacRes <- gac(amat,x,y, z, type)$gac 
+   adjRes <- adjustment(amat = amat, amat.type = typeDG, x = x, y = y, set.type = "all")
+   if (gacRes) { ## z is valid adj set
+     res <- any(sapply(adjRes, function(xx) setequal(z, xx)))
+   } else { ## z is not valid adj set
+     res <- all(!sapply(adjRes, function(xx) setequal(z, xx)))
+   }
+   res
+ }
+ 
+ xx <- TRUE
+ 
+ ## CPDAG 1: Paper Fig 1
+ mFig1 <- matrix(c(0,1,1,0,0,0, 1,0,1,1,1,0, 0,0,0,0,0,1,
+                   0,1,1,0,1,1, 0,1,0,1,0,1, 0,0,0,0,0,0), 6,6)
+ type <- "cpdag"
+ x <- 3; y <- 6
+ 
+ V <- as.character(1:ncol(mFig1))
+ rownames(mFig1) <- colnames(mFig1) <- V
+ 
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(2,4), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,5), V=V, type)
+ 
+ type <- "pag"
+ mFig3a <- matrix(c(0,1,0,0, 1,0,1,1, 0,1,0,1, 0,1,1,0), 4,4)
+ V <- as.character(1:ncol(mFig3a))
+ rownames(mFig3a) <- colnames(mFig3a) <- V
+ xx <- xx & gacVSadj(mFig3a, x=2,      y=4, z=NULL,   V=V, type)
+ 
+ ## DAG 1 from Marloes' Talk
+ mMMd1 <- matrix(c(0,1,0,1,0,0, 0,0,1,0,1,0, 0,0,0,0,0,1,
+                   0,0,0,0,0,0, 0,0,0,0,0,0, 0,0,0,0,0,0),6,6)
+ V <- as.character(1:ncol(mMMd1))
+ rownames(mMMd1) <- colnames(mMMd1) <- V
+ 
+ type <- "dag"
+ x <- 1; y <- 3
+ xx <- xx &  gacVSadj(mMMd1, x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(mMMd1, x,y, z= 2, V=V, type)
+ 
+ if (!xx) {
+   stop("Problem when testing function gacVSadj.")
+ } else {
+   message("OK, no issues were found.")
+ }
+ 
+ ############################################################
+ ## Extensive checks
+ ############################################################
+ if (doExtras) {
+ cat("doExtras is ON\n")
+ ## Test that "no adjustment set" and "empty adjustment set" are distinguished properly
+ x <- 1; y <- 2
+ cpdag <- matrix(c(0,1,1,0),2,2) ## 1 --- 2 => no adj set
+ dag <- matrix(c(0,1,0,0),2,2) ## 1 --> 2 => empty adj set
+ 
+ adjC <- adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "canonical")
+ adjD <- adjustment(amat = dag, amat.type = "dag", x = 1, y = 2, set.type = "canonical")
+ adjP <- adjustment(amat = dag, amat.type = "pdag", x = 1, y = 2, set.type = "canonical")
+ 
+ stopifnot(!identical(adjC, adjD), identical(adjD, adjP) )
+ 
+ adjCAll <- adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "all")
+ adjDAll <- adjustment(amat = dag, amat.type = "dag", x = 1, y = 2, set.type = "all")
+ adjPAll <- adjustment(amat = dag, amat.type = "pdag", x = 1, y = 2, set.type = "all")
+ 
+ stopifnot( !identical(adjCAll, adjDAll), identical(adjDAll, adjPAll) )
+ 
+ adjCMin <- adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "minimal")
+ adjDMin <- adjustment(amat = dag, amat.type = "dag", x = 1, y = 2, set.type = "minimal")
+ adjPMin <- adjustment(amat = dag, amat.type = "pdag", x = 1, y = 2, set.type = "minimal")
+ 
+ stopifnot( !identical(adjCMin, adjDMin), identical(adjDMin, adjPMin) )
+ 
+ 
+ #####################################################################################
+ ## Test 1: Compare CPDAG and PDAG implementation and validate all sets using gac()
+ #####################################################################################
+ nreps <- 100
+ simRes <- data.frame(setType = rep(NA, nreps), id = rep(NA,nreps), 
+                      rtCPDAG = rep(NA,nreps), rtPDAG = rep(NA, nreps),
+                      nSet = rep(NA, nreps), gacCheck = rep(NA, nreps))
+ proc.time()
+ for (i in 1:nreps) {
+   cat("i = ",i,"\n")
+   ## generate a graph
+   seed <- i
+   set.seed(seed)
+   p <- sample(x=5:10, size = 1)
+   prob <- sample(x=3:7/10, size = 1)
+   g <- pcalg:::randomDAG(p, prob)  ## true DAG
+   cpdag <- dag2cpdag(g)
+   cpdag.mat <- t(as(cpdag,"matrix")) ## has correct encoding
+ 
+   ## define input
+   amat <- cpdag.mat
+   x <- sample(x = 1:p, size = 1)
+   y <- sample(x = setdiff(1:p,x), size = 1)
+   set.type <- sample(x = c("all", "minimal"), size = 1)
+   simRes$setType[i] <- set.type
+   
+   ## run both methods
+   simRes$rtCPDAG[i] <- system.time(res1 <- adjustment(amat = amat, amat.type = "cpdag", x = x, y = y, set.type = set.type))[3]
+   simRes$rtPDAG[i] <- system.time(res2 <- adjustment(amat = amat, amat.type = "pdag", x = x, y = y, set.type = set.type))[3]
+   simRes$nSet[i] <- length(res1)
+   
+   if (length(res1) == 0) {
+     res1 <- vector("list", 0)
+   }
+   if (length(res2) == 0) {
+     res2 <- vector("list", 0)
+   }
+   ## compare results
+   simRes$id[i] <- identical(res1,res2)
+   
+   ## compare results with gac() based on "pdag"
+   if (length(res2) > 0) {
+     gc <- TRUE
+     for (j in 1:length(res2)) {
+       gc <- gc & gac(amat = amat, x = x, y = y, z = res2[[j]], type = "cpdag")$gac
+     }
+     simRes$gacCheck[i] <-  gc
+   }
+   
+ }
+ proc.time()
+ 
+ summary(simRes)
+ table(is.na(simRes$gacCheck), simRes$nSet == 0)
+ 
+ ################################################
+ ## Test 2: Check using predefined graphs
+ ################################################
+ gacVSadj <- function(amat, x, y ,z, V, type) {
+   ## gac(z) is TRUE IFF z is returned by adjustment()
+   ## x,y,z: col positions as used in GAC
+   ## Result: TRUE is result is equal
+   typeDG <- switch(type,
+                    dag = "dag",
+                    cpdag = "cpdag",
+                    mag = "mag",
+                    pag = "pag")
+   gacRes <- gac(amat,x,y, z, type)$gac 
+   adjRes <- adjustment(amat = amat, amat.type = typeDG, x = x, y = y, set.type = "all")
+   if (gacRes) { ## z is valid adj set
+     res <- any(sapply(adjRes, function(xx) setequal(z, xx)))
+   } else { ## z is not valid adj set
+     res <- all(!sapply(adjRes, function(xx) setequal(z, xx)))
+   }
+   res
+ }
+ 
+ xx <- TRUE
+ ##################################################
+ ## DAG / CPDAG
+ ##################################################
+ ## CPDAG 1: Paper Fig 1
+ mFig1 <- matrix(c(0,1,1,0,0,0, 1,0,1,1,1,0, 0,0,0,0,0,1,
+                   0,1,1,0,1,1, 0,1,0,1,0,1, 0,0,0,0,0,0), 6,6)
+ type <- "cpdag"
+ x <- 3; y <- 6
+ 
+ V <- as.character(1:ncol(mFig1))
+ rownames(mFig1) <- colnames(mFig1) <- V
+ 
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(2,4), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,5), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,2,1), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,5,1), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,2,5), V=V, type)
+ xx <- xx &  gacVSadj(mFig1,x,y, z=c(4,2,5,1), V=V, type)
+ xx <- xx & gacVSadj(mFig1,x,y, z= 2,    V=V, type)
+ xx <- xx & gacVSadj(mFig1,x,y, z= NULL, V=V, type)
+ 
+ ## CPDAG 2: Paper Fig 5a
+ mFig5a <- matrix(c(0,1,0,0,0, 1,0,1,0,0, 0,0,0,0,1, 0,0,1,0,0, 0,0,0,0,0), 5,5)
+ V <- as.character(1:ncol(mFig5a))
+ rownames(mFig5a) <- colnames(mFig5a) <- V
+ 
+ type <- "cpdag"
+ x <- c(1,5); y <- 4
+ xx <- xx &  gacVSadj(mFig5a, x,y, z=c(2,3), V=V, type)
+ xx <- xx & gacVSadj(mFig5a, x,y, z= 2,     V=V, type)
+ 
+ ## DAG 1 from Marloes' Talk
+ mMMd1 <- matrix(c(0,1,0,1,0,0, 0,0,1,0,1,0, 0,0,0,0,0,1,
+                   0,0,0,0,0,0, 0,0,0,0,0,0, 0,0,0,0,0,0),6,6)
+ V <- as.character(1:ncol(mMMd1))
+ rownames(mMMd1) <- colnames(mMMd1) <- V
+ 
+ type <- "dag"
+ x <- 1; y <- 3
+ xx <- xx &  gacVSadj(mMMd1, x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(mMMd1, x,y, z= 2, V=V, type)
+ xx <- xx &  gacVSadj(mMMd1, x,y, z= 4, V=V, type)
+ xx <- xx & gacVSadj(mMMd1, x,y, z= 5, V=V, type)
+ xx <- xx & gacVSadj(mMMd1, x,y, z= 6, V=V, type)
+ xx <- xx & gacVSadj(mMMd1, x,y, z=c(4,5), V=V, type)
+ 
+ ## DAG 2 from Marloes' Talk
+ mMMd2 <- matrix(c(0,1,0,1,0,0, 0,0,0,0,0,0, 0,1,0,0,1,0,
+                   0,0,0,0,1,0, 0,0,0,0,0,1, 0,0,0,0,0,0), 6,6)
+ V <- as.character(1:ncol(mMMd2))
+ rownames(mMMd2) <- colnames(mMMd2) <- V
+ 
+ type <- "dag"
+ x <- 4; y <- 6
+ xx <- xx &  gacVSadj(mMMd2, x,y, z= 1, V=V, type)
+ xx <- xx &  gacVSadj(mMMd2, x,y, z= 3, V=V, type)
+ xx <- xx & gacVSadj(mMMd2, x,y, z= 5, V=V, type)
+ xx <- xx & gacVSadj(mMMd2, x,y, z=c(1,5), V=V, type)
+ xx <- xx &  gacVSadj(mMMd2, x,y, z=c(1,2), V=V, type)
+ xx <- xx &  gacVSadj(mMMd2, x,y, z=c(1,3), V=V, type)
+ xx <- xx & gacVSadj(mMMd2, x,y, z= 2, V=V, type)
+ 
+ ##################################################
+ ## PAG
+ ##################################################
+ type <- "pag"
+ mFig3a <- matrix(c(0,1,0,0, 1,0,1,1, 0,1,0,1, 0,1,1,0), 4,4)
+ V <- as.character(1:ncol(mFig3a))
+ rownames(mFig3a) <- colnames(mFig3a) <- V
+ xx <- xx & gacVSadj(mFig3a, x=2,      y=4, z=NULL,   V=V, type)
+ 
+ mFig3b <- matrix(c(0,2,0,0, 3,0,3,3, 0,2,0,3, 0,2,2,0), 4,4)
+ V <- as.character(1:ncol(mFig3b))
+ rownames(mFig3b) <- colnames(mFig3b) <- V
+ xx <- xx & gacVSadj(mFig3b, x=2,      y=4, z=NULL,   V=V, type)
+ 
+ mFig3c <- matrix(c(0,3,0,0, 2,0,3,3, 0,2,0,3, 0,2,2,0), 4,4)
+ V <- as.character(1:ncol(mFig3c))
+ rownames(mFig3c) <- colnames(mFig3c) <- V
+ xx <- xx &  gacVSadj(mFig3c, x=2,      y=4, z=NULL,   V=V, type)
+ 
+ mFig4a <- matrix(c(0,0,1,0,0,0, 0,0,1,0,0,0, 2,2,0,3,3,2,
+                    0,0,2,0,2,2, 0,0,2,1,0,2, 0,0,1,3,3,0), 6,6)
+ V <- as.character(1:ncol(mFig4a))
+ rownames(mFig4a) <- colnames(mFig4a) <- V
+ xx <- xx & gacVSadj(mFig4a, x=3,      y=4, z=NULL,   V=V, type)
+ xx <- xx &  gacVSadj(mFig4a, x=3,      y=4, z= 6,     V=V, type)
+ xx <- xx &  gacVSadj(mFig4a, x=3,      y=4, z=c(1,6), V=V, type)
+ xx <- xx &  gacVSadj(mFig4a, x=3,      y=4, z=c(2,6), V=V, type)
+ xx <- xx &  gacVSadj(mFig4a, x=3,      y=4, z=c(1,2,6), V=V, type)
+ 
+ mFig4b <- matrix(c(0,0,1,0,0,0, 0,0,1,0,0,0, 2,2,0,0,3,2,
+                    0,0,0,0,2,2, 0,0,2,3,0,2, 0,0,2,3,2,0), 6,6)
+ V <- as.character(1:ncol(mFig4b))
+ rownames(mFig4b) <- colnames(mFig4b) <- V
+ xx <- xx & gacVSadj(mFig4b, x=3,      y=4, z=NULL,   V=V, type)
+ xx <- xx & gacVSadj(mFig4b, x=3,      y=4, z= 6,     V=V, type)
+ xx <- xx & gacVSadj(mFig4b, x=3,      y=4, z=c(5,6), V=V, type)
+ 
+ mFig5b <- matrix(c(0,1,0,0,0,0,0, 2,0,2,3,0,3,0, 0,1,0,0,0,0,0, 0,2,0,0,3,0,0,
+                    0,0,0,2,0,2,3, 0,2,0,0,2,0,0, 0,0,0,0,2,0,0), 7,7)
+ V <- as.character(1:ncol(mFig5b))
+ rownames(mFig5b) <- colnames(mFig5b) <- V
+ xx <- xx & gacVSadj(mFig5b, x=c(2,7), y=6, z=NULL,   V=V, type)
+ xx <- xx &  gacVSadj(mFig5b, x=c(2,7), y=6, z=c(4,5), V=V, type)
+ xx <- xx &  gacVSadj(mFig5b, x=c(2,7), y=6, z=c(4,5,1), V=V, type)
+ xx <- xx &  gacVSadj(mFig5b, x=c(2,7), y=6, z=c(4,5,3), V=V, type)
+ xx <- xx &  gacVSadj(mFig5b, x=c(2,7), y=6, z=c(1,3,4,5), V=V, type)
+ 
+ ## PAG in Marloes' talk
+ mMMp <- matrix(c(0,0,0,3,2,0,0, 0,0,0,0,1,0,0, 0,0,0,0,1,0,0, 2,0,0,0,0,3,2,
+                  3,2,2,0,0,0,3, 0,0,0,2,0,0,0, 0,0,0,2,2,0,0), 7,7)
+ V <- as.character(1:ncol(mMMp))
+ rownames(mMMp) <- colnames(mMMp) <- V
+ 
+ x <- c(5,6); y <- 7
+ xx <- xx & gacVSadj(mMMp, x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(mMMp, x,y, z= 1,   V=V, type)
+ xx <- xx & gacVSadj(mMMp, x,y, z= 4,   V=V, type)
+ xx <- xx & gacVSadj(mMMp, x,y, z= 2,   V=V, type)
+ xx <- xx & gacVSadj(mMMp, x,y, z= 3,   V=V, type)
+ xx <- xx & gacVSadj(mMMp, x,y, z=c(2,3), V=V, type)
+ xx <- xx &  gacVSadj(mMMp, x,y, z=c(1,4), V=V, type)
+ xx <- xx &  gacVSadj(mMMp, x,y, z=c(1,4,2), V=V, type)
+ xx <- xx &  gacVSadj(mMMp, x,y, z=c(1,4,3), V=V, type)
+ xx <- xx &  gacVSadj(mMMp, x,y, z=c(1,4,2,3), V=V, type)
+ 
+ ##################################################
+ ## V=V, type = "pag" -- Tests from Ema
+ ##################################################
+ type <- "pag"
+ pag.m <- readRDS(system.file(package="pcalg", "external", "gac-pags.rds"))
+ m1 <- pag.m[["m1"]]
+ V <- colnames(m1)
+ x <- 6; y <- 9
+ xx <- xx & gacVSadj(m1,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=1, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=3, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=4, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,7,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,5,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,5,7,8), V=V, type)
+ 
+ x <- c(6,8); y <- 9
+ xx <- xx & gacVSadj(m1,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=1, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=3, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=4, V=V, type)
+ xx <- xx &  gacVSadj(m1,x,y, z=c(2,3), V=V, type)
+ xx <- xx &  gacVSadj(m1,x,y, z=c(2,3,4), V=V, type)
+ xx <- xx &  gacVSadj(m1,x,y, z=c(2,3,7), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,5), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,3,5,7), V=V, type)
+ 
+ x <- 3; y <- 1
+ xx <- xx & gacVSadj(m1,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=4, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=5, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=6, V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,6), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,7,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,5,8), V=V, type)
+ xx <- xx & gacVSadj(m1,x,y, z=c(2,5,7,8), V=V, type)
+ 
+ m2 <- pag.m[["m2"]]
+ V <- colnames(m2)
+ x <- 3; y <-1
+ xx <- xx & gacVSadj(m2,x,y, z=NULL, V=V, type)
+ xx <- xx &  gacVSadj(m2,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=4, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=c(2,8), V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=8, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=9, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=c(2,8,9), V=V, type)
+ xx <- xx &  gacVSadj(m2,x,y, z=c(2,5), V=V, type)
+ 
+ x <- c(3,9); y <- 1
+ xx <- xx & gacVSadj(m2,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=4, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=c(2,8), V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=8, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=9, V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=c(2,8,9), V=V, type)
+ xx <- xx & gacVSadj(m2,x,y, z=c(2,5), V=V, type)
+ 
+ m3 <- pag.m[["m3"]]
+ V <- colnames(m3)
+ x <- 1; y <- 9
+ xx <- xx & gacVSadj(m3,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=3, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=5, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=7, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=8, V=V, type)
+ xx <- xx &  gacVSadj(m3,x,y, z=c(2,3), V=V, type)
+ xx <- xx &  gacVSadj(m3,x,y, z=c(5,7), V=V, type)
+ 
+ x <- 1; y <- 8
+ xx <- xx & gacVSadj(m3,x,y, z=NULL, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=2, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=3, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=5, V=V, type)
+ xx <- xx &  gacVSadj(m3,x,y, z=7, V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=9, V=V, type)
+ xx <- xx &  gacVSadj(m3,x,y, z=c(2,3), V=V, type)
+ xx <- xx & gacVSadj(m3,x,y, z=c(5,9), V=V, type)
+ 
+ if (!xx) {
+   stop("Problem when testing function gacVSadj.")
+ } else {
+   message("OK, no issues were found.")
+ }
+ 
+ ##################################################
+ ## given same graph, type=cpdag and type=pdag
+ ## should give same canonical set
+ ##################################################
+ m <- rbind(c(0,1,0,0,0,0),
+            c(1,0,1,0,0,0),
+            c(0,1,0,0,0,0),
+            c(0,0,0,0,0,0),
+            c(0,1,1,1,0,0),
+            c(1,0,1,1,1,0))
+ colnames(m) <- rownames(m) <- as.character(1:6)
+ 
+ ## You can see that the current adjustment function outputs different sets
+ ## if type = "cpdag" or type = "pdag" which shouldn't happen 
+ ## because it is the same graph:
+ res1 <- adjustment(m,amat.type="cpdag",2,4,set.type="canonical")
+ res2 <- adjustment(m,amat.type="pdag",2,4,set.type="canonical")
+ 
+ if (!all.equal(res1, res2)) {
+     stop("Canonical set is not the same for type=cpdag and type=pdag\n")
+ }
+ 
+ } ## doExtras
+ else {
+     cat("doExtras is OFF\n")
+ }
+ 
+ } # only if CRAN package  {dagitty} is available
Loading required namespace: dagitty
OK, no issues were found.
doExtras is OFF
> 
> proc.time()
   user  system elapsed 
   2.12    0.21    2.20