version 2.6-10

LiangyingYin · Mar 3, 2020 · ea4a57c · ea4a57c
1 parent d2e3cad
commit ea4a57c
Show file tree

Hide file tree

Showing 7 changed files with 65 additions and 65 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pcalg
-Version: 2.6-9
-Date: 2020-02-11
+Version: 2.6-10
+Date: 2020-03-3
 Title: Methods for Graphical Models and Causal Inference
 Description: Functions for causal structure
   learning and causal inference using graphical models. The main algorithms
@@ -51,6 +51,6 @@ Encoding: UTF-8
 License: GPL (>= 2)
 URL: http://pcalg.r-forge.r-project.org/
 RoxygenNote: 6.1.1
-Packaged: 2020-02-11 08:49:45 UTC; kalischm
+Packaged: 2020-03-03 12:31:36 UTC; kalischm
 Repository: CRAN
-Date/Publication: 2020-02-11 13:00:06 UTC
+Date/Publication: 2020-03-03 14:40:07 UTC
diff --git a/MD5 b/MD5
@@ -1,24 +1,24 @@
 1c213fc1c5a5ec68e7a5ba9293440dc3 *ChangeLog
-37d84a7531ceea244c781882060b0d93 *DESCRIPTION
+4b9b32644c238bb95ec960bbfc0bff0a *DESCRIPTION
 f813efd2d2208b900ae1d5ceb8dce2cf *NAMESPACE
 66963591a11cfdb002f5da9070f1500b *R/Aaux.R
 83c288d2212114e54bfe624e0edecaaa *R/AllClasses.R
 9f99e28f01bd00dedf565c6e01978676 *R/adjustment.R
 13a57456f8fd3ae055dd9a45ce6f933f *R/agesFuns.R
 709461024e0516af39a962661e2930d0 *R/deprecated.R
-4cccbecfa381ea1ad82c20e0151b239c *R/gacFuns.R
+2e96c58990915d4dd7e51976b224bbd2 *R/gacFuns.R
 8eff3a164a5b32a9c4818a1e840199c0 *R/genRandDAG.R
 5c33d7a0849fd620631eb901d6a6540d *R/gies.R
 aca17dcd6f37ce1136086a8bc285046e *R/isValidGraph.R
 b363657f7e2c52dc0f2aa083780fa0f7 *R/jointIda.R
 386ed9be1a524de90dfac185433b009a *R/lingamFuns.R
-cc462e22779cb4c455536d1f28811eb7 *R/optAdjSet.R
+ace998420ba6145fe7fe3c75c5892e66 *R/optAdjSet.R
 af4239ca324cb48eaac6b07fc0cf0061 *R/pcalg.R
 67ec62ad56d7cffaba4bee8f88797136 *R/pcalg2dagitty.R
 f84d95dd282c42c32595a27ca98f9a3d *R/possDeAn.R
 0db1ba6d57801a4d8fc6cdf996384a4d *R/zzz.R
 d599e23940bca0203504c0fa6b09e01c *TODO
-bd68b3d89307e8260f55874d7dbcf993 *build/vignette.rds
+94bed761e02266860aff243b04717fed *build/vignette.rds
 f832779eae511757a99906c7670fc0ad *cleanup
 7cbe431a233e6c454e24f7b92d63fe75 *data/datalist
 1d8d4c43b9cbb9dc9dd57acd59f565bf *data/gmB.rda
@@ -32,10 +32,10 @@ f832779eae511757a99906c7670fc0ad *cleanup
 4e33425acbef8bf36705d8a75622baa8 *inst/doc/mkVignettes.R
 cc46b1f49edd31faf5316d5cf4d6c1ce *inst/doc/pcalgDoc.R
 6581d4416f174d4d6f07a2a2d4b9d3cb *inst/doc/pcalgDoc.Rnw
-7c38555b6c1bbe4e36f53b8c8810e8f8 *inst/doc/pcalgDoc.pdf
+277b633e6b422057891d5e6722d84add *inst/doc/pcalgDoc.pdf
 01c5a9cb2024f1234d7c4aebb9762db5 *inst/doc/vignette2018.R
 65ba145dfc8ae12f50c95d77a8bf8600 *inst/doc/vignette2018.Rnw
-fe84a6e311f25d42e56c1f8042c8f07d *inst/doc/vignette2018.pdf
+23165d2276ae3dd8fee95d261b9b2da9 *inst/doc/vignette2018.pdf
 cee0b4475c720bf58c466e1495451b22 *inst/external/N_6_1000.rds
 0d84fdc119d76d992b72f9bdbd0e613d *inst/external/gac-pags.rds
 e7a2a9117d97986b2ab6afc6b4f77478 *inst/external/test_conservative_pc_data1.rda

diff --git a/R/gacFuns.R b/R/gacFuns.R
@@ -197,7 +197,7 @@ isAmenable <- function(m,x,y, type = "pag") {
                     ## check if there is a pdp from cand[j] to y without going through x[i]
                     ## cand could already be in y
                     ## pathOK <- ( length(intersect(y, possibleDeProper(m,cand[j],x[i]))) != 0 )
-                    pdpTemp <- possDe(m = m, x = cand[j], y = x[i],
+                    pdpTemp <- possDe(m = m, x = cand[j], y = x,
                                       possible = TRUE, ds = FALSE,
                                       type = type)
                     pathOK <- ( length(intersect(y, pdpTemp)) != 0 )

diff --git a/R/optAdjSet.R b/R/optAdjSet.R
@@ -51,57 +51,57 @@ optAdjSet <- function(graphEst, x.pos, y.pos){
 
 
 
-isAmenable <- function(m,x,y, type = "pag") {
-  ## INPUT: adj.matrix m; sets of node positions x and y; type in DAG, CPDAG,
-  ## MAG or PAG
-  ## OUTPUT: TRUE if m is amenabel wrt x,y; o/w FALSE
-  found <- FALSE ## if found == TRUE at any time, graph is not amenable wrt x,y
-  ## DAG is always amenable
-  if (type %in% c("pdag", "cpdag","dag","pag","mag")) { ##changed added dag just in case, makes no difference
-    if (type == "dag")  ## added the if case for dags
-      return(!found)
-    i <- 0
-    p <- length(x)
-
-    ## for all nodes in x, if amenability is still possible
-    while ( (i<p) & !found) {
-      i <- i+1
-      ## posDesc of x[i] without going through any other x node
-      ## posDesc <- possibleDeProper(m,x[i],x[-i])
-      posDesc <- possDe(m = m, x = x[i], y = x[-i], possible = TRUE,
-                        ds = FALSE, type = type)
-      ## potential problem for amenability only if there is a
-      ## pdp from x[i] to y
-      if ( length(intersect(y, posDesc)) != 0 ) {
-        nb <- as.vector(which(m[x[i],]!=0 | m[,x[i]]!=0)) ## nbrs of x[i]
-        ## potentially first node on pdp from x[i] to y; however, not yet sure
-        cand <- intersect(nb, posDesc)
-        j <- 0
-        ## for all candidate nodes, if amenability is still possible
-        ## (also covers case if cand is empty)
-        while ( (j<length(cand)) & !found ) {
-          j <- j+1
-          ## check if there is a pdp from cand[j] to y without going through x[i]
-          ## cand could already be in y
-          ## pathOK <- ( length(intersect(y, possibleDeProper(m,cand[j],x[i]))) != 0 )
-          pdpTemp <- possDe(m = m, x = cand[j], y = x[i],
-                            possible = TRUE, ds = FALSE,
-                            type = type)
-          pathOK <- ( length(intersect(y, pdpTemp)) != 0 )
-          if (pathOK) {
-            isPDAG <- (type == "pdag" | type == "cpdag") ##changed
-            PDAGproblem <- (isPDAG & (m[x[i],cand[j]] == 1)) ##changed
-            PAGproblem1 <- (!isPDAG & (m[x[i], cand[j]] != 2) & (m[cand[j], x[i]] != 3)) ##changed
-            isDirEdge <- ((m[x[i], cand[j]] == 2) & (m[cand[j], x[i]] == 3))
-            PAGproblem2 <- (!isPDAG & isDirEdge & !visibleEdge(m, x[i], cand[j])) ##changed
-            found <- (PDAGproblem | PAGproblem1 | PAGproblem2)
-          } ## if pathOK
-        } ## while cand
-      } ## if path from x[i] to y
-    } ## while x
-    return(!found)
-  } else { ## if graph type not known
-    cat("Not a valid graph type! Should be written in lowercase! \n")
-    return(NULL)
-  }
-}
+# isAmenable <- function(m,x,y, type = "pag") {
+#   ## INPUT: adj.matrix m; sets of node positions x and y; type in DAG, CPDAG,
+#   ## MAG or PAG
+#   ## OUTPUT: TRUE if m is amenabel wrt x,y; o/w FALSE
+#   found <- FALSE ## if found == TRUE at any time, graph is not amenable wrt x,y
+#   ## DAG is always amenable
+#   if (type %in% c("pdag", "cpdag","dag","pag","mag")) { ##changed added dag just in case, makes no difference
+#     if (type == "dag")  ## added the if case for dags
+#       return(!found)
+#     i <- 0
+#     p <- length(x)
+#     
+#     ## for all nodes in x, if amenability is still possible
+#     while ( (i<p) & !found) {
+#       i <- i+1
+#       ## posDesc of x[i] without going through any other x node
+#       ## posDesc <- possibleDeProper(m,x[i],x[-i])
+#       posDesc <- possDe(m = m, x = x[i], y = x[-i], possible = TRUE,
+#                         ds = FALSE, type = type)
+#       ## potential problem for amenability only if there is a
+#       ## pdp from x[i] to y
+#       if ( length(intersect(y, posDesc)) != 0 ) {
+#         nb <- as.vector(which(m[x[i],]!=0 | m[,x[i]]!=0)) ## nbrs of x[i]
+#         ## potentially first node on pdp from x[i] to y; however, not yet sure
+#         cand <- intersect(nb, posDesc)
+#         j <- 0
+#         ## for all candidate nodes, if amenability is still possible
+#         ## (also covers case if cand is empty)
+#         while ( (j<length(cand)) & !found ) {
+#           j <- j+1
+#           ## check if there is a pdp from cand[j] to y without going through x[i]
+#           ## cand could already be in y
+#           ## pathOK <- ( length(intersect(y, possibleDeProper(m,cand[j],x[i]))) != 0 )
+#           pdpTemp <- possDe(m = m, x = cand[j], y = x[i],
+#                             possible = TRUE, ds = FALSE,
+#                             type = type)
+#           pathOK <- ( length(intersect(y, pdpTemp)) != 0 )
+#           if (pathOK) {
+#             isPDAG <- (type == "pdag" | type == "cpdag") ##changed
+#             PDAGproblem <- (isPDAG & (m[x[i],cand[j]] == 1)) ##changed
+#             PAGproblem1 <- (!isPDAG & (m[x[i], cand[j]] != 2) & (m[cand[j], x[i]] != 3)) ##changed
+#             isDirEdge <- ((m[x[i], cand[j]] == 2) & (m[cand[j], x[i]] == 3))
+#             PAGproblem2 <- (!isPDAG & isDirEdge & !visibleEdge(m, x[i], cand[j])) ##changed
+#             found <- (PDAGproblem | PAGproblem1 | PAGproblem2)
+#           } ## if pathOK
+#         } ## while cand
+#       } ## if path from x[i] to y
+#     } ## while x
+#     return(!found)
+#   } else { ## if graph type not known
+#     cat("Not a valid graph type! Should be written in lowercase! \n")
+#     return(NULL)
+#   }
+# }
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/doc/pcalgDoc.pdf b/inst/doc/pcalgDoc.pdf
diff --git a/inst/doc/vignette2018.pdf b/inst/doc/vignette2018.pdf