[Rsiena-commits] r113 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSiena/src RSiena/src/model RSiena/src/model/ml RSiena/src/model/variables RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/man RSienaTest/src RSienaTest/src/model RSienaTest/src/model/ml RSienaTest/src/model/variables

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Jul 10 17:11:47 CEST 2010 

Author: ripleyrm
Date: 2010-07-10 17:11:46 +0200 (Sat, 10 Jul 2010)
New Revision: 113

Modified:
   pkg/RSiena/DESCRIPTION
   pkg/RSiena/R/sienaDataCreate.r
   pkg/RSiena/R/sienaModelCreate.r
   pkg/RSiena/R/simstatsc.r
   pkg/RSiena/changeLog
   pkg/RSiena/inst/doc/s_man400.pdf
   pkg/RSiena/man/RSiena-package.Rd
   pkg/RSiena/man/sienaModelCreate.Rd
   pkg/RSiena/src/model/Model.cpp
   pkg/RSiena/src/model/Model.h
   pkg/RSiena/src/model/ml/Chain.cpp
   pkg/RSiena/src/model/ml/MLSimulation.cpp
   pkg/RSiena/src/model/ml/MLSimulation.h
   pkg/RSiena/src/model/ml/NetworkChange.cpp
   pkg/RSiena/src/model/variables/NetworkVariable.cpp
   pkg/RSiena/src/siena07.cpp
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/sienaDataCreate.r
   pkg/RSienaTest/R/sienaModelCreate.r
   pkg/RSienaTest/R/simstatsc.r
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/doc/s_man400.tex
   pkg/RSienaTest/inst/doc/s_man400.pdf
   pkg/RSienaTest/man/RSiena-package.Rd
   pkg/RSienaTest/man/sienaModelCreate.Rd
   pkg/RSienaTest/src/model/Model.cpp
   pkg/RSienaTest/src/model/Model.h
   pkg/RSienaTest/src/model/ml/Chain.cpp
   pkg/RSienaTest/src/model/ml/MLSimulation.cpp
   pkg/RSienaTest/src/model/ml/MLSimulation.h
   pkg/RSienaTest/src/model/ml/NetworkChange.cpp
   pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
   pkg/RSienaTest/src/siena07.cpp
Log:
Fix for bipartite networks returning simulations, endowment effects scores, more ML code

Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/DESCRIPTION	2010-07-10 15:11:46 UTC (rev 113)
@@ -1,8 +1,8 @@
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.11.111
-Date: 2010-07-03
+Version: 1.0.11.113
+Date: 2010-07-10
 Author: Various
 Depends: R (>= 2.9.0), xtable
 Imports: Matrix

Modified: pkg/RSiena/R/sienaDataCreate.r
===================================================================
--- pkg/RSiena/R/sienaDataCreate.r	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/R/sienaDataCreate.r	2010-07-10 15:11:46 UTC (rev 113)
@@ -561,6 +561,8 @@
         attr(depvars[[i]], 'vals') <- vector("list", observations)
         attr(depvars[[i]], 'nval') <- rep(NA, observations)
         attr(depvars[[i]], 'noMissing') <- rep(0, observations)
+        attr(depvars[[i]], 'noMissingEither') <- rep(0, observations -1)
+        attr(depvars[[i]], 'nonMissingEither') <- rep(0, observations -1)
         if (type == 'behavior')
         {
             attr(depvars[[i]], 'noMissing') <- FALSE
@@ -580,6 +582,10 @@
                 attr(depvars[[i]], "nval")[j + 1] <-  sum(!is.na(myvector2))
                 attr(depvars[[i]], 'noMissing')[j] <- sum(is.na(myvector1))
                 attr(depvars[[i]], 'noMissing')[j+1] <- sum(is.na(myvector2))
+                attr(depvars[[i]], 'noMissingEither')[j] <-
+                    sum(is.na(myvector2) | is.na(myvector1))
+                attr(depvars[[i]], 'nonMissingEither')[j] <-
+                    sum(!(is.na(myvector2) | is.na(myvector1)))
             if (all(mydiff >= 0, na.rm=TRUE))
                 attr(depvars[[i]], 'downonly')[j] <- TRUE
             if (all(mydiff <= 0, na.rm=TRUE))
@@ -618,6 +624,16 @@
                 {
                     mymat1 <- myarray[[j]]
                     mymat2 <- myarray[[j + 1]]
+                    ## remove diagonals if not bipartite
+                    if (attr(depvars[[i]], "type") != "bipartite")
+                    {
+                        diag(mymat1) <- NA
+                        diag(mymat2) <- NA
+                    }
+                    attr(depvars[[i]], 'noMissingEither')[j] <-
+                        sum(is.na(mymat1) | is.na(mymat2))
+                    attr(depvars[[i]], 'nonMissingEither')[j] <-
+                        sum(!(is.na(mymat1) | is.na(mymat2)))
                     ##remove structural values
                     x1 <- mymat1 at x
                     x2 <- mymat2 at x
@@ -625,12 +641,6 @@
                     x2[x2 %in% c(10, 11)] <- NA
                     mymat1 at x <- x1
                     mymat2 at x <- x2
-                    ## remove diagonals if not bipartite
-                    if (attr(depvars[[i]], "type") != "bipartite")
-                    {
-                        diag(mymat1) <- NA
-                        diag(mymat2) <- NA
-                    }
                     mydiff <- mymat2 - mymat1
                     attr(depvars[[i]], 'distance')[j] <- sum(mydiff != 0,
                                                              na.rm = TRUE)
@@ -643,15 +653,19 @@
                 {
                     mymat1 <- myarray[, , j]
                     mymat2 <- myarray[, , j + 1]
-                    ##remove structural values
-                    mymat1[mymat1 %in% c(10,11)] <- NA
-                    mymat2[mymat2 %in% c(10,11)] <- NA
                     ## remove diagonals if not bipartite
                     if (attr(depvars[[i]], "type") != "bipartite")
                     {
                         diag(mymat1) <- NA
                         diag(mymat2) <- NA
                     }
+                    attr(depvars[[i]], 'noMissingEither')[j] <-
+                        sum(is.na(mymat1) | is.na(mymat2))
+                    attr(depvars[[i]], 'nonMissingEither')[j] <-
+                        sum(!(is.na(mymat1) | is.na(mymat2)))
+                    ##remove structural values
+                    mymat1[mymat1 %in% c(10,11)] <- NA
+                    mymat2[mymat2 %in% c(10,11)] <- NA
                     mydiff <- mymat2 - mymat1
                     attr(depvars[[i]], 'distance')[j] <- sum(mydiff != 0,
                                                              na.rm = TRUE)
@@ -1358,14 +1372,26 @@
     cvnodeSets <- namedVector(NA, vCovars)
     dycnodeSets <- namedVector(NA, dycCovars, listType=TRUE)
     dyvnodeSets <- namedVector(NA, dyvCovars, listType=TRUE)
-    totalMissings <- namedVector(0, netnames)
+  #  totalMissings <- namedVector(0, netnames, listType=TRUE)
+  #  nonMissingCount <- namedVector(0, netnames, listType=TRUE)
     observations <- 0
     periodNos <- rep(NA, 2)
+    numberMissingNetwork <- rep(0, 2)
+    numberMissingBehavior <- rep(0, 2)
+    numberNonMissingNetwork <- rep(0, 2)
+    numberNonMissingBehavior <- rep(0, 2)
     groupPeriods <- namedVector(NA, names(objlist))
     for (i in 1:length(objlist))
     {
+        newobs <- objlist[[i]]$observations
+        periodNos[observations + (1 : (newobs - 1))] <-
+            observations + i - 1 + (1 : (newobs - 1))
         for (j in 1:length(objlist[[i]]$depvars))
         {
+            numberMissingBehavior[observations + (1 : (newobs - 1))] <- 0
+            numberNonMissingBehavior[observations + (1 : (newobs - 1))] <- 0
+            numberMissingNetwork[observations + (1 : (newobs - 1))] <- 0
+            numberNonMissingNetwork[observations + (1 : (newobs - 1))] <- 0
             varname <- names(objlist[[i]]$depvars)[j]
             netnamesub <- match(varname, netnames)
             if (is.na(netnamesub))
@@ -1418,8 +1444,25 @@
             {
                 structural[netnamesub] <- TRUE
             }
-            totalMissings[netnamesub] <- totalMissings[netnamesub] +
-                sum(attribs[["noMissing"]])
+            if (attribs[["type"]] == "behavior")
+            {
+                numberMissingBehavior[observations + (1 : (newobs - 1))] <-
+                    numberMissingBehavior[observations + (1 : (newobs - 1))] +
+                        attribs[["noMissingEither"]]
+                numberNonMissingBehavior[observations + (1 : (newobs - 1))] <-
+                    numberNonMissingBehavior[observations +
+                                             (1 : (newobs - 1))] +
+                                                 attribs[["nonMissingEither"]]
+            }
+            else
+            {
+                numberMissingNetwork[observations + (1 : (newobs - 1))] <-
+                    numberMissingNetwork[observations + (1 : (newobs - 1))] +
+                        attribs[["noMissingEither"]]
+                numberNonMissingNetwork[observations + (1 : (newobs - 1))] <-
+                    numberNonMissingNetwork[observations + (1 : (newobs - 1))] +
+                        attribs[["nonMissingEither"]]
+            }
         }
         thisHigher <- attr(objlist[[i]], "higher")
         thisDisjoint <- attr(objlist[[i]], "disjoint")
@@ -1504,9 +1547,6 @@
                 stop('Inconsistent node Sets')
             }
         }
-        newobs <- objlist[[i]]$observations
-        periodNos[observations + (1 : (newobs - 1))] <-
-                  observations + i - 1 + (1 : (newobs - 1))
         observations <- observations + objlist[[i]]$observations - 1
         groupPeriods[i] <- newobs
     }
@@ -1578,7 +1618,11 @@
     attr(group, 'netnames') <- netnames
     attr(group, 'symmetric') <- symmetric
     attr(group, 'structural') <- structural
-    attr(group, "totalMissings") <- totalMissings
+ #   attr(group, "totalMissings") <- totalMissings
+    attr(group, "numberNonMissingNetwork") <- numberNonMissingNetwork
+    attr(group, "numberMissingNetwork") <- numberMissingNetwork
+    attr(group, "numberNonMissingBehavior") <- numberNonMissingBehavior
+    attr(group, "numberMissingBehavior") <- numberMissingBehavior
     attr(group, 'allUpOnly') <- allUpOnly
     attr(group, 'allDownOnly') <- allDownOnly
     attr(group, 'anyUpOnly') <- anyUpOnly

Modified: pkg/RSiena/R/sienaModelCreate.r
===================================================================
--- pkg/RSiena/R/sienaModelCreate.r	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/R/sienaModelCreate.r	2010-07-10 15:11:46 UTC (rev 113)
@@ -17,7 +17,8 @@
              condvarno=0, condname='',
              firstg=0.2, cond=NA, findiff=FALSE,  seed=NULL,
              pridg=0.1, prcdg=0.1, prper=0.3, pripr=0.25, prdpr=0.25,
-             prirms=0.0, prdrms=0.0)
+             prirms=0.0, prdrms=0.0, maximumPermutationLength=40,
+             minimumPermutationLength=2, initialPermutationLength=20)
 {
     model <- NULL
     model$projname <- projname
@@ -81,6 +82,9 @@
     model$prdpr <- prdpr
     model$prirms <- prirms
     model$prdrms <- prdrms
+    model$maximumPermutationLength <- maximumPermutationLength
+    model$minimumPermutationLength <- minimumPermutationLength
+    model$initialPermutationLength <- initialPermutationLength
     class(model) <- "sienaModel"
     model
 }

Modified: pkg/RSiena/R/simstatsc.r
===================================================================
--- pkg/RSiena/R/simstatsc.r	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/R/simstatsc.r	2010-07-10 15:11:46 UTC (rev 113)
@@ -1620,7 +1620,7 @@
         attr(f, "compositionChange") <- attr(data, "compositionChange")
         attr(f, "exooptions") <- attr(data, "exooptions")
         attr(f, "groupPeriods") <- attr(data, "groupPeriods")
-        attr(f, "totalMissings") <- attr(data, "totalMissings")
+      #  attr(f, "totalMissings") <- attr(data, "totalMissings")
 
         if (x$maxlike && x$FinDiff.method)
         {
@@ -1846,35 +1846,21 @@
         ## set up chains and do initial steps
         simpleRates <- TRUE
 
-        ## sum the missings to calculate the relevant probabilities
-        totalMissings <- attr(f, "totalMissings")
         types <- attr(f, "types")
-        use <- types != "behavior"
-        ## use arbitrary n for now
-        n <- length(f[[1]]$nodeSets[[1]])
-        if (sum(use) > 0)
-        {
-            netMissings <- sum(totalMissings[use])
-            prmin <- netMissings / (netMissings + sum(use) * n * (n - 1))
-        }
-        else
-        {
-            prmin <- 0.0
-        }
-        use <- types == "behavior"
-        if (sum(use) > 0)
-        {
-            behMissings <- sum(totalMissings[types == "behavior"])
-            prmib <- behMissings / (behMissings + sum(use) * n)
-        }
-        else
-        {
-            prmib <- 0.0
-        }
+        nbrNonMissNet <- attr(f, "numberMissingNetwork")
+        nbrMissNet <- attr(f, "numberMissingNetwork")
+        nbrNonMissBeh <- attr(f, "numberMissingBehavior")
+        nbrMissBeh <- attr(f, "numberMissingBehavior")
+
+        prmin <-   nbrMissNet/ (nbrMissNet + nbrNonMissNet)
+        prmib <-   nbrMissBeh/ (nbrMissBeh + nbrNonMissBeh)
+        cat (prmin, prmib, '\n')
         z$probs <- c(x$pridg, x$prcdg, x$prper, x$pripr, x$prdpr, x$prirms,
                      x$prdrms, prmin, prmib)
         ans <- .Call("mlMakeChains", PACKAGE=pkgname, pData, pModel,
-                     simpleRates, z$probs)
+                     simpleRates, z$probs, x$minimumPermutationLength,
+                     x$maximumPermutationLength,
+                     x$initialPermutationLength)
         f$chain <- ans[[2]]
         ##store address of simulation object
         f$pMLSimulation <- ans[[1]][[1]]

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/changeLog	2010-07-10 15:11:46 UTC (rev 113)
@@ -1,3 +1,17 @@
+2010-07-10 R-forge revision 113
+
+	* src/model/variables/NetworkVariable.cpp: bug fix for endowment
+	effects, since a recent change
+	* src/model/ml/NetworkChange: bug fix, could not return bipartite
+	simulations. 
+	* src/siena07.cpp, src/model/Model.h, src/model/Model.cpp,
+	src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h,
+	R/simstatsc.r, R/sienaDataCreate.r, R/sienaModelCreate.r: adaptive
+	permutation length and probabilities for missings for ML 
+	(in progress still!)
+	* src/model/ml/Chain.cpp: removed structural links from initial
+	chain (ML)
+
 2010-07-04 R-forge revision 112
 
 	* R/sienautils.r: fix bug with groups and constant dyadic

Modified: pkg/RSiena/inst/doc/s_man400.pdf
===================================================================
--- pkg/RSiena/inst/doc/s_man400.pdf	2010-07-04 12:33:21 UTC (rev 112)
+++ pkg/RSiena/inst/doc/s_man400.pdf	2010-07-10 15:11:46 UTC (rev 113)
@@ -499,21 +499,20 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 113

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