version 2.4-2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pcalg
-Version: 2.2-4
-Date: 2015-07-22
+Version: 2.4-2
+Date: 2016-09-21
 Title: Methods for Graphical Models and Causal Inference
 Description: Functions for causal structure
   learning and causal inference using graphical models. The main algorithms
@@ -18,10 +18,14 @@ Authors@R: c(person("Markus","Kalisch",
   person("Alain", "Hauser", role="aut"),  person("Martin","Maechler", role="aut"),
   person("Diego", "Colombo", role="ctb"), person("Doris", "Entner", role="ctb"),
   person("Patrik","Hoyer", role="ctb"),   person("Antti", "Hyttinen", role="ctb"),
-  person("Jonas", "Peters", role="ctb"))
+  person("Jonas", "Peters", role="ctb"), person("Nicoletta", "Andri",
+  role="ctb"), person("Emilija", "Perkovic", role="ctb"), person("Preetam",
+  "Nandy", role="ctb"), person("Philipp", "Ruetimann", role="ctb"),
+  person("Daniel", "Stekhoven", role="ctb"), person("Manuel", "Schuerch", role="ctb"))
 Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
-  Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
-  Antti Hyttinen [ctb], Jonas Peters [ctb]
+  Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb],
+  Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb],
+  Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
 Depends: R (>= 3.0.2)
 LinkingTo: Rcpp (>= 0.11.0), RcppArmadillo, BH
 Imports: stats, graphics, utils, methods, abind, graph, RBGL, igraph,
@@ -33,6 +37,6 @@ NeedsCompilation: yes
 Encoding: UTF-8
 License: GPL (>= 2)
 URL: http://pcalg.r-forge.r-project.org/
-Packaged: 2015-07-22 14:53:53 UTC; maechler
+Packaged: 2016-09-23 09:30:59 UTC; maechler
 Repository: CRAN
-Date/Publication: 2015-07-23 09:21:52
+Date/Publication: 2016-09-26 16:47:02

MD5

@@ -1,152 +1,162 @@
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@@ -159,4 +169,4 @@ cd40b46d3274a112953423a19f78d4c4 *tests/test_wgtMatrix.R
 35fe720fff87739bb6b7bfe79d204d33 *vignettes/Figure2FAT.pdf
 f930246d4cfb62c9d2fb0d954be5042d *vignettes/Mybib.bib
 b9564ddd59a06782310989e8f33db55e *vignettes/jsslogo.jpg
-5d1cffaf8fa0e09882b92d5f6c5f95ee *vignettes/pcalgDoc.Rnw
+43598f8f02fb3b909c846a048c7360c8 *vignettes/pcalgDoc.Rnw

NAMESPACE

@@ -11,7 +11,7 @@ importFrom("utils", combn, str)
 
 importFrom("graphics", par, plot.default, plot, title)
 
-## try to import all we need, but not more
+importMethodsFrom("methods", coerce, show)
 importFrom("methods",
            setClass, setClassUnion, setMethod, setOldClass, setValidity,
            getClass, getClassDef, callGeneric, as, is, extends,
@@ -132,15 +132,18 @@ export(trueCov,
        gds,
        simy,
        mat2targets,
-       # targets2mat,
+       targets2mat,
        dag2essgraph,
        ## --- end{Alain}
        fciPlus,
-       LINGAM,
+       lingam, LINGAM,
        randDAG,
        unifDAG,
        unifDAG.approx,
-       gac)
+       gac,
+       ## no longer: use as(*,"amat")
+       ##  displayAmat,
+       pdag2allDags)
 
 ## These are "internal" i.e., in man/pcalg-internal.Rd
 ## _FIXME ?_                     ---------------------
@@ -173,7 +176,12 @@ exportClasses("pcAlgo",
               "GaussL0penObsScore",
               "EssGraph")
 
-exportMethods("summary", "show", "plot")
+exportMethods(# needed? "coerce",# <- defined via setAs(., ..) used via  as(A, "class_B")
+              "summary", "show", "plot")
 
 S3method(print, fciAlgo)
+S3method(print, pcAlgo)
+S3method(print, amat)
+## FIXME: TODO
+# S3method(print, LINGAM)
 

R/Aaux.R

@@ -16,6 +16,47 @@
 log.q1pm <- function(r) log1p(2*r/(1-r))
 
 
+## MM: "Lifted" from Matrix package ~/R/Pkgs/Matrix/R/Auxiliaries.R
+## "Theory" behind this: /u/maechler/R/MM/MISC/lower-tri-w.o-matrix.R
+indTri <- function(n, upper = TRUE, diag = FALSE) {
+    ## Indices of (strict) upper/lower triangular part
+    ## == which(upper.tri(diag(n), diag=diag) or
+    ##	  which(lower.tri(diag(n), diag=diag) -- but
+    ## more efficiently for largish 'n'
+    stopifnot(length(n) == 1, n == (n. <- as.integer(n)), (n <- n.) >= 0)
+    if(n <= 2) {
+        if(n == 0) return(integer(0))
+        if(n == 1) return(if(diag) 1L else integer(0))
+        ## else n == 2
+        v <- if(upper) 3L else 2L
+	return(if(diag) c(1L, v, 4L) else v)
+    }
+
+    ## n >= 3 [also for n == 2 && diag (==TRUE)] :
+
+    ## First, compute the 'diff(.)' of the result [fast, using integers]
+    n. <- if(diag) n else n - 1L
+    n1 <- n. - 1L
+    ## all '1' but a few
+    r <- rep.int(1L, choose(n.+1, 2) - 1)
+    tt <- if(diag) 2L else 3L
+    r[cumsum(if(upper) 1:n1 else n.:2)] <- if(upper) n:tt else tt:n
+    ## now have differences; revert to "original":
+    cumsum(c(if(diag) 1L else if(upper) n+1L else 2L, r))
+}
+
+##' Count Edges, for directed graphs, *not* as numEdges(g)
+##' but such that  "<-->" or "<--o" ... counts as 1
+##' (for undirected graphs, this is the same as numEdges(.))
+numGedges <- function(amat) {
+    dimnames(amat) <- NULL # speed
+    A <- (amat + t(amat)) != 0
+    n <- nrow(A)
+    if(n <= 40) ## faster
+	sum(A[lower.tri(A)])
+    else
+	sum(A[indTri(n)])
+}
 
 check.Rgraphviz <- function() {
   if(!requireNamespace("Rgraphviz"))