[Rsiena-commits] r208 - in pkg: RSiena RSiena/R RSiena/data RSiena/inst/doc RSiena/inst/examples RSiena/man RSiena/src/data RSiena/src/model RSiena/src/model/effects/generic RSiena/src/model/ml RSiena/src/model/variables RSiena/tests RSienaTest RSienaTest/R RSienaTest/data RSienaTest/doc RSienaTest/inst/doc RSienaTest/inst/examples RSienaTest/man RSienaTest/src/data RSienaTest/src/model RSienaTest/src/model/effects RSienaTest/src/model/effects/generic RSienaTest/src/model/ml RSienaTest/src/model/variables RSienaTest/tests RSienaTest/tests/testrefs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Mar 25 17:42:54 CEST 2012 

Author: ripleyrm
Date: 2012-03-25 17:42:52 +0200 (Sun, 25 Mar 2012)
New Revision: 208

Added:
   pkg/RSiena/inst/examples/Sampson_t2.txt
   pkg/RSiena/inst/examples/Sampson_t3.txt
   pkg/RSiena/inst/examples/Sampson_t4.txt
   pkg/RSiena/inst/examples/vtextexoreal.dat
   pkg/RSienaTest/doc/MCMCandRM.pdf
   pkg/RSienaTest/inst/examples/Sampson_t2.txt
   pkg/RSienaTest/inst/examples/Sampson_t3.txt
   pkg/RSienaTest/inst/examples/Sampson_t4.txt
   pkg/RSienaTest/inst/examples/vtextexoreal.dat
   pkg/RSienaTest/tests/effectsTest.R
   pkg/RSienaTest/tests/sampson.r
   pkg/RSienaTest/tests/testrefs/
   pkg/RSienaTest/tests/testrefs/M07compare.out
   pkg/RSienaTest/tests/testrefs/M08compare.out
   pkg/RSienaTest/tests/testrefs/M09compare.out
   pkg/RSienaTest/tests/testrefs/M10compare.out
   pkg/RSienaTest/tests/testrefs/M11compare.out
   pkg/RSienaTest/tests/testrefs/M12compare.out
   pkg/RSienaTest/tests/testrefs/M13compare.out
   pkg/RSienaTest/tests/testrefs/M14compare.out
   pkg/RSienaTest/tests/testrefs/M25compare.out
   pkg/RSienaTest/tests/testrefs/M26compare.out
   pkg/RSienaTest/tests/testrefs/M27compare.out
   pkg/RSienaTest/tests/testrefs/M28compare.out
   pkg/RSienaTest/tests/testrefs/M29compare.out
   pkg/RSienaTest/tests/testrefs/M30compare.out
   pkg/RSienaTest/tests/testrefs/M31compare.out
   pkg/RSienaTest/tests/testrefs/M32compare.out
   pkg/RSienaTest/tests/testrefs/M33compare.out
   pkg/RSienaTest/tests/testrefs/M34compare.out
   pkg/RSienaTest/tests/testrefs/M35compare.out
   pkg/RSienaTest/tests/testrefs/M36compare.out
   pkg/RSienaTest/tests/testrefs/M37compare.out
   pkg/RSienaTest/tests/testrefs/M38compare.out
   pkg/RSienaTest/tests/testrefs/M39compare.out
   pkg/RSienaTest/tests/testrefs/M40compare.out
   pkg/RSienaTest/tests/testrefs/M41compare.out
   pkg/RSienaTest/tests/testrefs/M42compare.out
   pkg/RSienaTest/tests/testrefs/M43compare.out
   pkg/RSienaTest/tests/testrefs/M44compare.out
   pkg/RSienaTest/tests/testrefs/M45compare.out
   pkg/RSienaTest/tests/testrefs/M46compare.out
   pkg/RSienaTest/tests/testrefs/M47compare.out
   pkg/RSienaTest/tests/testrefs/M48compare.out
   pkg/RSienaTest/tests/testrefs/M49compare.out
   pkg/RSienaTest/tests/testrefs/M50compare.out
   pkg/RSienaTest/tests/testrefs/M51compare.out
   pkg/RSienaTest/tests/testrefs/M52compare.out
   pkg/RSienaTest/tests/testrefs/M53compare.out
   pkg/RSienaTest/tests/testrefs/M54compare.out
   pkg/RSienaTest/tests/testrefs/M55compare.out
   pkg/RSienaTest/tests/testrefs/M56compare.out
   pkg/RSienaTest/tests/testrefs/M57compare.out
   pkg/RSienaTest/tests/testrefs/M58compare.out
   pkg/RSienaTest/tests/testrefs/M59compare.out
   pkg/RSienaTest/tests/testrefs/M60compare.out
   pkg/RSienaTest/tests/testrefs/M61compare.out
   pkg/RSienaTest/tests/testrefs/M62compare.out
   pkg/RSienaTest/tests/testrefs/M63compare.out
   pkg/RSienaTest/tests/testrefs/M64compare.out
   pkg/RSienaTest/tests/testrefs/M65compare.out
   pkg/RSienaTest/tests/testrefs/MI01compare.out
   pkg/RSienaTest/tests/testrefs/MI02compare.out
   pkg/RSienaTest/tests/testrefs/MI03compare.out
   pkg/RSienaTest/tests/testrefs/MI04compare.out
   pkg/RSienaTest/tests/testrefs/MI05compare.out
   pkg/RSienaTest/tests/testrefs/MI06compare.out
   pkg/RSienaTest/tests/testrefs/MI07compare.out
   pkg/RSienaTest/tests/testrefs/sienaMetaCompare.out
Modified:
   pkg/RSiena/DESCRIPTION
   pkg/RSiena/R/effects.r
   pkg/RSiena/R/effectsDocumentation.r
   pkg/RSiena/changeLog
   pkg/RSiena/data/allEffects.csv
   pkg/RSiena/inst/doc/RSiena_Manual.pdf
   pkg/RSiena/man/RSiena-package.Rd
   pkg/RSiena/src/data/BehaviorLongitudinalData.cpp
   pkg/RSiena/src/model/EpochSimulation.cpp
   pkg/RSiena/src/model/Model.cpp
   pkg/RSiena/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
   pkg/RSiena/src/model/ml/Chain.cpp
   pkg/RSiena/src/model/ml/MLSimulation.cpp
   pkg/RSiena/src/model/variables/DependentVariable.cpp
   pkg/RSiena/src/model/variables/EffectValueTable.h
   pkg/RSiena/tests/parallel.Rout.save
   pkg/RSiena/tests/scriptfile.Rout.save
   pkg/RSiena/tests/scripts.Rout.save
   pkg/RSienaTest/.Rbuildignore
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/effects.r
   pkg/RSienaTest/R/effectsDocumentation.r
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/data/allEffects.csv
   pkg/RSienaTest/doc/RSienaDeveloper.tex
   pkg/RSienaTest/doc/RSiena_Manual.tex
   pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
   pkg/RSienaTest/man/RSiena-package.Rd
   pkg/RSienaTest/src/data/BehaviorLongitudinalData.cpp
   pkg/RSienaTest/src/model/EpochSimulation.cpp
   pkg/RSienaTest/src/model/StatisticCalculator.h
   pkg/RSienaTest/src/model/effects/DiffusionRateEffect.cpp
   pkg/RSienaTest/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
   pkg/RSienaTest/src/model/ml/Chain.cpp
   pkg/RSienaTest/src/model/ml/MLSimulation.cpp
   pkg/RSienaTest/src/model/variables/DependentVariable.cpp
   pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
   pkg/RSienaTest/tests/parallel.Rout.save
   pkg/RSienaTest/tests/scriptfile.Rout.save
   pkg/RSienaTest/tests/scripts.Rout.save
Log:
Testing system, bug fixes

Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/DESCRIPTION	2012-03-25 15:42:52 UTC (rev 208)
@@ -1,8 +1,8 @@
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.207
-Date: 2012-03-21
+Version: 1.0.12.208
+Date: 2012-03-25
 Author: Various
 Depends: R (>= 2.10.0)
 Imports: Matrix

Modified: pkg/RSiena/R/effects.r
===================================================================
--- pkg/RSiena/R/effects.r	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/R/effects.r	2012-03-25 15:42:52 UTC (rev 208)
@@ -384,16 +384,32 @@
                 attr(xx$depvars[[j]], "nodeSet") == nodeSet)
             {
 				depvarname <- names(xx$depvars)[j]
-                tmpObjEffects <-
-					createEffects("behaviorOneModeObjective",
-								  varname, depvarname, name=varname,
-								  groupName=groupName, group=group,
-								  netType=netType)
-				tmpRateEffects <-
-					createEffects("behaviorOneModeRate",
-								  varname, depvarname, name=varname,
-								  groupName=groupName, group=group,
-								  netType=netType)
+				if (attr(xx$depvars[[j]], "symmetric"))
+				{
+					tmpObjEffects <-
+						createEffects("behaviorSymmetricObjective",
+									  varname, depvarname, name=varname,
+									  groupName=groupName, group=group,
+									  netType=netType)
+					tmpRateEffects <-
+						createEffects("behaviorSymmetricRate",
+									  varname, depvarname, name=varname,
+									  groupName=groupName, group=group,
+									  netType=netType)
+				}
+				else
+				{
+					tmpObjEffects <-
+						createEffects("behaviorOneModeObjective",
+									  varname, depvarname, name=varname,
+									  groupName=groupName, group=group,
+									  netType=netType)
+					tmpRateEffects <-
+						createEffects("behaviorOneModeRate",
+									  varname, depvarname, name=varname,
+									  groupName=groupName, group=group,
+									  netType=netType)
+				}
 				if ((nOneModes + nBipartites) > 1) ## add the network name
 				{
 					tmpObjEffects$functionName <-
@@ -812,12 +828,12 @@
                                          netType=netType)
         }
 
-       covRateEffects <- createEffects("covarBehaviorRate", varname, covarname,
+        covRateEffects <- createEffects("covarBehaviorRate", varname, covarname,
                                         name=name,
                                         groupName=groupName, group=group,
-                                         netType=netType)
+                                        netType=netType)
         ## if we have a real covariate, need to add other effects for every
-        ## approriate network
+        ## appropriate network
         if (!same)
         {
             for (j in seq(along=xx$depvars))
@@ -825,24 +841,24 @@
                 if (types[j] == 'oneMode' &&
                     attr(xx$depvars[[j]], 'nodeSet') == nodeSet)
                 {
-					newEffects <-
-						createEffects("covarBehaviorNetObjective", varname,
-									  covarname, names(xx$depvars)[j],
-									  groupName=groupName, group=group,
-									  netType=netType, name=name)
+                    newEffects <-
+                        createEffects("covarBehaviorNetObjective", varname,
+                                      covarname, names(xx$depvars)[j],
+                                      groupName=groupName, group=group,
+                                      netType=netType, name=name)
 
                     covObjEffects <- rbind(covObjEffects, newEffects)
 				}
                 if ((types[j] == "bipartite" &&
-                        attr(xx$depvars[[j]], 'nodeSet')[2] == nodeSet))
+                     attr(xx$depvars[[j]], 'nodeSet')[2] == nodeSet))
                 {
-  					newEffects <-
-						createEffects("covarBehaviorBipartiteObjective", varname,
-									  covarname, names(xx$depvars)[j],
-									  groupName=groupName, group=group,
-									  netType=netType, name=name)
-                  covObjEffects <- rbind(covObjEffects, newEffects)
-				}
+                    newEffects <-
+                        createEffects("covarBehaviorBipartiteObjective", varname,
+                                      covarname, names(xx$depvars)[j],
+                                      groupName=groupName, group=group,
+                                      netType=netType, name=name)
+                    covObjEffects <- rbind(covObjEffects, newEffects)
+                }
             }
         }
 

Modified: pkg/RSiena/R/effectsDocumentation.r
===================================================================
--- pkg/RSiena/R/effectsDocumentation.r	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/R/effectsDocumentation.r	2012-03-25 15:42:52 UTC (rev 208)
@@ -35,6 +35,7 @@
 
                  "behaviorRate",
                  "behaviorOneModeRate",
+				 "behaviorSymmetricRate",
                  "behaviorBipartiteRate",
                  "covarBehaviorRate",
 
@@ -63,6 +64,7 @@
 
                  "behaviorObjective",
                  "behaviorOneModeObjective",
+                 "behaviorSymmetricObjective",
                  "behaviorBipartiteObjective",
                  "covarBehaviorObjective",
                  "unspecifiedBehaviorInteraction")

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/changeLog	2012-03-25 15:42:52 UTC (rev 208)
@@ -1,3 +1,34 @@
+2012-03-25 R-forge revision 208
+
+	* src/data/BehaviorLongitudinalData.cpp: fix memory leak
+	* src/model/effects/generic/CovariateDistance2NetworkFunction.cpp:
+	fix memory leak
+	* src/model/variables/NetworkVariable.cpp: fix bug in endowment
+	and creation effect scores for no change.
+	* data/allEffects.csv, R/effects.r, R/effectsDocumentation.r:
+	split behavior network effects between symmetric and other networks.
+	* src/model/model.cpp (RSiena only),
+	src/model/variables/DependentVariable.cpp,
+	src/model/variables/EffectValueTable.h (RSiena only): added
+	comments, formatting
+	* src/model/effects/DiffusionRateEffect.cpp: bug fix (RSienaTest
+	only)
+	* doc/RSienaDeveloper.tex: updated doc (RSienaTest only)
+	* doc/MCMCandRM.pdf: added
+	* tests/effectsTest.R, tests/sampson.r, testrefs/*,
+	.Rbuildignore: new testing files added, not to be included in tar
+	ball. (RSienaTest only)
+	* inst/examples/Sampson_t2.txt, inst/examples/Sampson_t3.txt,
+	inst/examples/Sampson_t4.txt, inst/examples/vtextexoreal.dat:
+	added.
+	* src/effects.r: correct bug causing crash with sparse matrices
+	with changes all in one direction.
+	* src/model/EpochSimulation.cpp: added comments
+	* src/model/ml/MLSimulation.cpp: correct test when storing
+	rejection numbers.
+	* src/model/StatisticCalculator.h: formatting (RSienaTest only)
+	* src/model/ml/chain.cpp: initialize finalReciprocalRate explicitly.
+
 2012-03-21 R-forge revision 207 (RSienaTest only)
 	* siena07internals.cpp, DependentVariable.h,
 	DependentVariable.cpp: changed calculation of scores for diffusion

Modified: pkg/RSiena/data/allEffects.csv
===================================================================
--- pkg/RSiena/data/allEffects.csv	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/data/allEffects.csv	2012-03-25 15:42:52 UTC (rev 208)
@@ -17,6 +17,22 @@
 behaviorOneModeObjective,behavior xxxxxx similarity in dense triads <maybe wrong>,beh. xxxxxx homogeneity of dense triads <<<maybe wrong>>>,simDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK
 behaviorOneModeObjective,behavior xxxxxx reciprocated degree,beh. xxxxxx reciprocated degrees,recipDeg,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
 behaviorOneModeObjective,behavior xxxxxx ave. sim. x popularity ego,beh. xxxxxx ave. sim. x indegrees ego,avSimPopEgo,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx average similarity,beh. xxxxxx average similarity,avSim,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx total similarity,beh. xxxxxx total similarity,totSim,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx degree,beh. xxxxxx outdegrees,outdeg,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx isolate,beh. xxxxxx isolate,isolate,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx ave. sim. x reciprocity,beh. xxxxxx ave. similarity x reciprocity,avSimRecip,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx tot. sim. x reciprocity,beh. xxxxxx tot. similarity x reciprocity,totSimRecip,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx ave. sim. x popularity alter,beh. xxxxxx ave. sim. x indegrees(one-sided),avSimPopAlt,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx tot. sim. x popularity alter,beh. xxxxxx tot. sim. x indegrees(one-sided),totSimPopAlt,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx x popularity alter,beh. xxxxxx x indegrees(one-sided),popAlt,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx ave. sim. x rec. x pop. (alter),beh. xxxxxx ave. sim. x rec. x i.d.(one-sided),avSimRecPop,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx tot. sim. x rec. x pop. (alter),beh. xxxxxx tot. sim. x rec. x i.d.(one-sided),totSimRecPop,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+behaviorSymmetricObjective,behavior xxxxxx average alter,beh. xxxxxx average alters,avAlt,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx average rec. alters,beh. xxxxxx average rec. alters,avRecAlt,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx dense triads <maybe wrong>,beh. xxxxxx dense triads <<<maybe wrong>>>,behDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx similarity in dense triads <maybe wrong>,beh. xxxxxx homogeneity of dense triads <<<maybe wrong>>>,simDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK
+behaviorSymmetricObjective,behavior xxxxxx ave. sim. x popularity ego,beh. xxxxxx ave. sim. x indegrees ego,avSimPopEgo,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 behaviorBipartiteObjective,behavior xxxxxx average similarity,beh. xxxxxx average similarity,avSim,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 behaviorBipartiteObjective,behavior xxxxxx total similarity,beh. xxxxxx total similarity,totSim,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 behaviorBipartiteObjective,behavior xxxxxx outdegree,beh. xxxxxx outdegrees,outdeg,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
@@ -30,22 +46,23 @@
 behaviorBipartiteObjective,behavior xxxxxx ave. sim. x popularity ego,beh. xxxxxx ave. sim. x indegrees ego,avSimPopEgo,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 behaviorObjective,behavior xxxxxx linear shape,beh. xxxxxx cent. sum,linear,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK
 behaviorObjective,behavior xxxxxx quadratic shape,beh. xxxxxx sum of cent. squares,quad,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-behaviorRate,rate xxxxxx period 1,Amount of behavioral change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0
-behaviorRate,rate xxxxxx (period nnnnnn),Amount of behavioral change in period nnnnnn on xxxxxx,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0
-behaviorOneModeRate,outdegree effect on rate xxxxxx,Amount of change on xxxxxx x outdegree,outRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-behaviorOneModeRate,indegree effect on rate xxxxxx,Amount of change on xxxxxx x indegree,inRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-behaviorOneModeRate,reciprocated effect on rate xxxxxx,Amount of change on xxxxxx x reciprocity,recipRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-behaviorBipartiteRate,outdegree effect on rate xxxxxx,Amount of change on xxxxxx x outdegree,outRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-behaviorBipartiteRate,reciprocated effect on rate xxxxxx,Amount of change on xxxxxx x reciprocity,recipRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-nonSymmetricRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0
-nonSymmetricRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0
-nonSymmetricRate,outdegree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-nonSymmetricRate,indegree effect on rate xxxxxx,Amount of change x indegrees,inRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-nonSymmetricRate,reciprocity effect on rate xxxxxx,Amount of change x reciprocity,recipRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-nonSymmetricRate,effect 1/outdegree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
-bipartiteRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0
-bipartiteRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0
-bipartiteRate,outdegree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0
+behaviorRate,rate xxxxxx period 1,Amount of behavioral change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
+behaviorRate,rate xxxxxx (period nnnnnn),Amount of behavioral change in period nnnnnn on xxxxxx,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
+behaviorOneModeRate,outdegree effect on rate xxxxxx,Amount of change on xxxxxx x outdegree,outRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+behaviorOneModeRate,indegree effect on rate xxxxxx,Amount of change on xxxxxx x indegree,inRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+behaviorOneModeRate,reciprocated effect on rate xxxxxx,Amount of change on xxxxxx x reciprocity,recipRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+behaviorSymmetricRate,degree effect on rate xxxxxx,Amount of change on xxxxxx x degree,outRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+behaviorBipartiteRate,outdegree effect on rate xxxxxx,Amount of change on xxxxxx x outdegree,outRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+behaviorBipartiteRate,reciprocated effect on rate xxxxxx,Amount of change on xxxxxx x reciprocity,recipRate,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+nonSymmetricRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
+nonSymmetricRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
+nonSymmetricRate,outdegree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+nonSymmetricRate,indegree effect on rate xxxxxx,Amount of change x indegrees,inRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+nonSymmetricRate,reciprocity effect on rate xxxxxx,Amount of change x reciprocity,recipRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+nonSymmetricRate,effect 1/outdegree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+bipartiteRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
+bipartiteRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
+bipartiteRate,outdegree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
 bipartiteRate,effect 1/outdegree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
 symmetricRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
 symmetricRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
@@ -66,13 +83,11 @@
 covarSymmetricObjective,same xxxxxx,same xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarSymmetricObjective,xxxxxx ego x xxxxxx alter,xxxxxx ego x xxxxxx alter,egoXaltX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarSymmetricObjective,xxxxxx of indirect ties,xxxxxx of indirect ties,IndTies,FALSE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
-covarSymmetricObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
+covarSymmetricObjective,xxxxxx alter at distance 2 (#),xxxxxx alter at distance 2 (#),altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
 covarSymmetricObjective,xxxxxx similarity at distance 2,xxxxxx similarity at distance 2,simDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarBipartiteObjective,xxxxxx alter,Sum of indegrees x xxxxxx,altX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarBipartiteObjective,xxxxxx squared alter,Sum of indegrees x squared xxxxxx,altSqX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarBipartiteObjective,xxxxxx ego,Sum of outdegrees x xxxxxx,egoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego
-covarBipartiteObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
-covarBipartiteObjective,xxxxxx similarity at distance 2,xxxxxx similarity at distance 2,simDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,xxxxxx alter,Sum of indegrees x xxxxxx,altX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,xxxxxx squared alter,Sum of indegrees x squared xxxxxx,altSqX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,xxxxxx ego,Sum of outdegrees x xxxxxx,egoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego
@@ -84,7 +99,7 @@
 covarNonSymmetricObjective,xxxxxx ego x xxxxxx alter x recipr.,Sum xxxxxx ego x xxxxxx rec.alter,egoXaltXRecip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,higher xxxxxx,ego > alter for xxxxxx,higher,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,xxxxxx of indirect ties,Sum xxxxxx of indirect ties,IndTies,FALSE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
-covarNonSymmetricObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
+covarNonSymmetricObjective,xxxxxx alter at distance 2 (#),xxxxxx alter at distance 2 (#),altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
 covarNonSymmetricObjective,xxxxxx similarity at distance 2,xxxxxx similarity at distance 2,simDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 covarBehaviorNetObjective,behavior xxxxxx: av.sim. (zzzzzz) x yyyyyy,beh. xxxxxx av.sim. (zzzzzz) x yyyyyy,avSimEgoX,TRUE,yyyyyy,zzzzzz,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 covarBehaviorNetObjective,behavior xxxxxx: tot. sim. (zzzzzz) x yyyyyy ,beh xxxxxx tot. sim. (zzzzzz) x yyyyyy,totSimEgoX,TRUE,yyyyyy,zzzzzz,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
@@ -181,5 +196,5 @@
 nonSymmetricBipartiteObjective,from xxxxxx agreement,"mixed triplets XWW, W = xxxxxx",from,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 bipartiteBipartiteObjective,outdegree^(1/#) xxxxxx activity,sum outd. x degree^(1/#) xxxxxx,outActIntn,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,dyadic
 covarNetNetObjective,from xxxxxx agr. x same yyyyyy,"m.tr. XWW, W = xxxxxx, same yyyyyy",covNetNet,TRUE,xxxxxx,yyyyyy,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
-covarNetNetObjective,yyyyyy alter at distance 2 on xxxxxx,yyyyyy alter at distance 2 on xxxxxx,altDist2W,TRUE,xxxxxx,yyyyyy,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+covarNetNetObjective,yyyyyy alter at distance 2 on xxxxxx (#),yyyyyy alter at distance 2 on xxxxxx (#),altDist2W,TRUE,xxxxxx,yyyyyy,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
 covarNetNetObjective,yyyyyy similarity at distance 2 on xxxxxx,yyyyyy similarity at distance 2 on xxxxxx,simDist2W,TRUE,xxxxxx,yyyyyy,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,

Modified: pkg/RSiena/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSiena/inst/doc/RSiena_Manual.pdf	2012-03-21 14:40:31 UTC (rev 207)
+++ pkg/RSiena/inst/doc/RSiena_Manual.pdf	2012-03-25 15:42:52 UTC (rev 208)
@@ -44,21 +44,18 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 208

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