[Rsiena-commits] r190 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Dec 14 16:36:14 CET 2011 

Author: ripleyrm
Date: 2011-12-14 16:36:13 +0100 (Wed, 14 Dec 2011)
New Revision: 190

Modified:
   pkg/RSiena/DESCRIPTION
   pkg/RSiena/R/bayes.r
   pkg/RSiena/changeLog
   pkg/RSiena/inst/doc/RSiena_Manual.pdf
   pkg/RSiena/man/RSiena-package.Rd
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/bayes.r
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/doc/RSiena_Manual.tex
   pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
   pkg/RSienaTest/man/RSiena-package.Rd
Log:
Fix for bayes which got missed in the last commit.

Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSiena/DESCRIPTION	2011-12-14 15:36:13 UTC (rev 190)
@@ -1,7 +1,7 @@
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.189
+Version: 1.0.12.190
 Date: 2011-12-14
 Author: Various
 Depends: R (>= 2.10.0)

Modified: pkg/RSiena/R/bayes.r
===================================================================
--- pkg/RSiena/R/bayes.r	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSiena/R/bayes.r	2011-12-14 15:36:13 UTC (rev 190)
@@ -422,8 +422,8 @@
 		##seed <- NULL
 	}
    	z$FRAN <- getFromNamespace(model$FRANname, pkgname)
-    z <- z$FRAN(z, model, INIT=TRUE, data=data, effects=effects,
-                prevAns=prevAns)
+    z <- initializeFRAN(z, model, data=data, effects=effects,
+                prevAns=prevAns, initC=FALSE)
 	z$basicRate <- z$effects$basicRate
     z$nGroup <- z$f$nGroup
 	is.batch(TRUE)
@@ -465,7 +465,28 @@
     {
         z$priorSigma <- priorSigma
     }
-    z$ratePositions <- lapply(z$rateParameterPosition, unlist)
+  	groupPeriods <- attr(z$f, "groupPeriods")
+    netnames <- z$f$depNames
+	z$rateParameterPosition <-
+        lapply(1:z$nGroup, function(i, periods, data)
+           {
+               lapply(1:periods[i], function(j)
+                  {
+                      rateEffects <-
+                          z$effects[z$effects$basicRate &
+                                    z$effects$period == j &
+                                    z$effects$group == i,]
+                      rateEffects <-
+                          rateEffects[match(netnames,
+                                            rateEffects$name), ]
+                      tmp <- as.numeric(row.names(rateEffects))
+                      names(tmp) <- netnames
+                      tmp
+                  }
+                      )
+           }, periods=groupPeriods - 1, data=z$f[1:z$nGroup]
+               )
+	z$ratePositions <- lapply(z$rateParameterPosition, unlist)
     for (i in 1:z$nGroup)
     {
         use <- rep(FALSE, z$pp)

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSiena/changeLog	2011-12-14 15:36:13 UTC (rev 190)
@@ -1,11 +1,31 @@
-2011-12-10 R-forgre revision 188.
+2011-12-14 R-forge revision 190.
 
-	* added directory po with .pot files for translators.
-	* R/algorithms.r, R/phase2.r: rationalised algorithm code and
-	added function comment headers
+	* R/bayes.r: fix bugs from previous changes
+
+2011-12-14 R-forge revision 189.
+
+	* po/R-RSiena.pot, po/RSienaTest.pot added files for translators.
 	* doc/RSienaDeveloper.tex: updated to reflect changes in
 	algorithms and other minor details.
+	* data/allEffects.csv: fixed typo in shortName for symmetric
+	networks
+	* man/sienaModelCreate.Rd: updated details
+	* R/initializeFRAN.r, R/simstatsc.r, R/maxlikec.r, R/bayes.r,
+	R/phase1.r, R/phase2.r, R/robmon.r,
+	R/algorithms.r (RSienaTest only): rationalized and tidied code.
+	* man/maxlikec.Rd: removed file, details now in man/simstatsc.Rd.
+	* max/simstatsc.Rd: expanded to include maxlikec, initializeFRAN
+	and terminateFRAN.
+	* R/print01Report.r, R/printDataReport.r, R/sienaPrint.r, : minor
+	changes to reports.
+	* R/sienaeffects.r: fixed bug in error messages
+	* src/model/ml/MLSimulation.cpp, src/model/Model.cpp,
+	src/siena07Models.cpp: formatting source only.
 
+2011-12-07 R-forge revision 188.
+
+	* added directories po ready for translation files.
+
 2011-12-06 R-forge revision 187.
 
 	* src/siena07setup.cpp: correct change to name of included file in
@@ -22,7 +42,8 @@
 	src/model/Model.cpp, src/model/Model.h, src/model/State.cpp,
 	src/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h: added
 	facility to return log likelihood after simulation, stopped
-	returning of chains every iteration. Bug fixes for ML.
+	returning of chains every iteration. Bug fixes for ML. Added
+	R/algorithms.r to RSienaTest (previously in examples directory).
 
 2011-11-27 R-forge revision 185.
 

Modified: pkg/RSiena/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSiena/inst/doc/RSiena_Manual.pdf	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSiena/inst/doc/RSiena_Manual.pdf	2011-12-14 15:36:13 UTC (rev 190)
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Modified: pkg/RSiena/man/RSiena-package.Rd
===================================================================
--- pkg/RSiena/man/RSiena-package.Rd	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSiena/man/RSiena-package.Rd	2011-12-14 15:36:13 UTC (rev 190)
@@ -30,8 +30,8 @@
 \tabular{ll}{
 Package: \tab RSiena\cr
 Type: \tab Package\cr
-Version: \tab 1.0.12.187\cr
-Date: \tab 2011-12-06\cr
+Version: \tab 1.0.12.190\cr
+Date: \tab 2011-12-14\cr
 License: \tab GPL-2 \cr
 LazyLoad: \tab yes\cr
 }

Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSienaTest/DESCRIPTION	2011-12-14 15:36:13 UTC (rev 190)
@@ -1,7 +1,7 @@
 Package: RSienaTest
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.189
+Version: 1.0.12.190
 Date: 2011-12-14
 Author: Various
 Depends: R (>= 2.10.0)

Modified: pkg/RSienaTest/R/bayes.r
===================================================================
--- pkg/RSienaTest/R/bayes.r	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSienaTest/R/bayes.r	2011-12-14 15:36:13 UTC (rev 190)
@@ -423,7 +423,7 @@
 	}
    	z$FRAN <- getFromNamespace(model$FRANname, pkgname)
     z <- initializeFRAN(z, model, data=data, effects=effects,
-                prevAns=prevAns)
+                prevAns=prevAns, initC=FALSE)
 	z$basicRate <- z$effects$basicRate
     z$nGroup <- z$f$nGroup
 	is.batch(TRUE)
@@ -465,7 +465,28 @@
     {
         z$priorSigma <- priorSigma
     }
-    z$ratePositions <- lapply(z$rateParameterPosition, unlist)
+  	groupPeriods <- attr(z$f, "groupPeriods")
+    netnames <- z$f$depNames
+	z$rateParameterPosition <-
+        lapply(1:z$nGroup, function(i, periods, data)
+           {
+               lapply(1:periods[i], function(j)
+                  {
+                      rateEffects <-
+                          z$effects[z$effects$basicRate &
+                                    z$effects$period == j &
+                                    z$effects$group == i,]
+                      rateEffects <-
+                          rateEffects[match(netnames,
+                                            rateEffects$name), ]
+                      tmp <- as.numeric(row.names(rateEffects))
+                      names(tmp) <- netnames
+                      tmp
+                  }
+                      )
+           }, periods=groupPeriods - 1, data=z$f[1:z$nGroup]
+               )
+	z$ratePositions <- lapply(z$rateParameterPosition, unlist)
     for (i in 1:z$nGroup)
     {
         use <- rep(FALSE, z$pp)

Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSienaTest/changeLog	2011-12-14 15:36:13 UTC (rev 190)
@@ -1,3 +1,7 @@
+2011-12-14 R-forge revision 190.
+
+	* R/bayes.r: fix bugs from previous changes
+
 2011-12-14 R-forge revision 189.
 
 	* po/R-RSiena.pot, po/RSienaTest.pot added files for translators.
@@ -38,7 +42,8 @@
 	src/model/Model.cpp, src/model/Model.h, src/model/State.cpp,
 	src/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h: added
 	facility to return log likelihood after simulation, stopped
-	returning of chains every iteration. Bug fixes for ML.
+	returning of chains every iteration. Bug fixes for ML. Added
+	R/algorithms.r to RSienaTest (previously in examples directory).
 
 2011-11-27 R-forge revision 185.
 

Modified: pkg/RSienaTest/doc/RSiena_Manual.tex
===================================================================
--- pkg/RSienaTest/doc/RSiena_Manual.tex	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSienaTest/doc/RSiena_Manual.tex	2011-12-14 15:36:13 UTC (rev 190)
@@ -9423,8 +9423,10 @@
 repository.)
 \begin{small}
 \begin{itemize}
+\item 2011-12-14 R-forge revision 190
+Fixed bug in Bayes left over from R 189.
 \item 2011-12-14 R-forge revision 189
-\item Fixed minor bugs in reports and error messages.
+ Fixed minor bugs in reports and error messages.
 \item 2011-12-04 R-forge revision 186
 Fixed some bugs in ML estimation procedure which will alter the results
 slightly. Added algorithm functions to RSienaTest package.

Modified: pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSienaTest/inst/doc/RSiena_Manual.pdf	2011-12-14 13:27:34 UTC (rev 189)
+++ pkg/RSienaTest/inst/doc/RSiena_Manual.pdf	2011-12-14 15:36:13 UTC (rev 190)
@@ -5034,28 +5034,27 @@
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-/Length 1815      
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 190

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