[Rsiena-commits] r120 - in pkg: RSiena RSiena/R RSiena/data RSiena/inst/doc RSiena/man RSienaTest RSienaTest/R RSienaTest/data RSienaTest/doc RSienaTest/inst/doc RSienaTest/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Sep 20 19:21:02 CEST 2010 

Author: ripleyrm
Date: 2010-09-20 19:20:59 +0200 (Mon, 20 Sep 2010)
New Revision: 120

Modified:
   pkg/RSiena/DESCRIPTION
   pkg/RSiena/R/phase3.r
   pkg/RSiena/R/print01Report.r
   pkg/RSiena/R/sienaDataCreate.r
   pkg/RSiena/R/simstatsc.r
   pkg/RSiena/changeLog
   pkg/RSiena/data/allEffects.csv
   pkg/RSiena/inst/doc/s_man400.pdf
   pkg/RSiena/man/RSiena-package.Rd
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/effects.r
   pkg/RSienaTest/R/phase3.r
   pkg/RSienaTest/R/print01Report.r
   pkg/RSienaTest/R/sienaDataCreate.r
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/data/allEffects.csv
   pkg/RSienaTest/doc/Siena_algorithms4.tex
   pkg/RSienaTest/doc/s_man400.tex
   pkg/RSienaTest/inst/doc/s_man400.pdf
   pkg/RSienaTest/man/RSiena-package.Rd
Log:
Bug fixes

Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/DESCRIPTION	2010-09-20 17:20:59 UTC (rev 120)
@@ -1,8 +1,8 @@
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.11.119
-Date: 2010-08-21
+Version: 1.0.11.120
+Date: 2010-09-20
 Author: Various
 Depends: R (>= 2.9.0), xtable
 Imports: Matrix

Modified: pkg/RSiena/R/phase3.r
===================================================================
--- pkg/RSiena/R/phase3.r	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/R/phase3.r	2010-09-20 17:20:59 UTC (rev 120)
@@ -313,7 +313,7 @@
     if (!x$maxlike && z$cconditional)
         Report(c('basic rate parameter',
                  c('', 's')[as.integer(z$observations > 2) + 1],
-                 ' as well as \n'), outf)
+                 ' as well as \n'), sep='', outf)
     Report(c('convergence diagnostics, covariance and derivative matrices based on ',
              z$Phase3nits, ' iterations.\n\n'), sep='', outf)
     Report('Information for convergence diagnosis.\n', outf)

Modified: pkg/RSiena/R/print01Report.r
===================================================================
--- pkg/RSiena/R/print01Report.r	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/R/print01Report.r	2010-09-20 17:20:59 UTC (rev 120)
@@ -708,7 +708,7 @@
                                 nsmall=3, width=10), "\n"), outf)
             }
             Report('\n', outf)
-            Report(c(ifelse(nCovars == 1, "This ", "These"),
+            Report(c(ifelse(nCovars == 1, "This ", "These "),
                      "global mean value",
                      ifelse(nCovars == 1, " is ", "s are "),
                      "subtracted from the changing dyadic covariate",

Modified: pkg/RSiena/R/sienaDataCreate.r
===================================================================
--- pkg/RSiena/R/sienaDataCreate.r	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/R/sienaDataCreate.r	2010-09-20 17:20:59 UTC (rev 120)
@@ -1612,7 +1612,7 @@
                                                 dim3)
                 attr(newcovar, "range2") <- matrix(attr(const[[j]], "range2"),
                                                    ncol=dim3, nrow=2)
-                attr(newcovar, 'name') <- attr(const, "name")
+                attr(newcovar, 'name') <- attr(const[[j]], "name")
                 nVCovar <- nVCovar + 1
                 vars[[nVCovar]] <- newcovar
             }

Modified: pkg/RSiena/R/simstatsc.r
===================================================================
--- pkg/RSiena/R/simstatsc.r	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/R/simstatsc.r	2010-09-20 17:20:59 UTC (rev 120)
@@ -1760,6 +1760,7 @@
         basicEffects <- ff$basicEffects
         interactionEffects <- ff$interactionEffects
         nGroup <- ff$nGroup
+        types <- ff$types
     }
     ans <- .Call('effects', PACKAGE=pkgname, pData, basicEffects)
     pModel <- ans[[1]][[1]]

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/changeLog	2010-09-20 17:20:59 UTC (rev 120)
@@ -1,9 +1,23 @@
+2010-09-20 R-forge revision 120
+
+	* data/allEffects.csv: added alter average distance 2 effects for
+	behavior variables
+	* R/sienaDataCreate.r: fixed bug in names of dyadic covariates
+	when converted to varying covariates for groups
+	* R/getEffects.r: fixed bug in starting values for behavior
+	variables when all changes were in one direction
+	* R/phase3.r: minor correction to text in siena07 report.
+	* R/print01Report: minor correction to text.
+	* R/simstatsc.r (RSiena only): make sure types are available to
+	multiple processes.
+
+
 2010-08-21 R-forge revision 119
 
 	* R/sienaDataCreate.r: fix function comments so documentation
-	runs. 
+	runs.
 	* R/RSienaRDocumentation.r: minor source format changes.
-	
+
 2010-08-20 R-forge revision 118 RSienaTest only
 
 	* src/siena07internals.cpp, src/siena07models.cpp,

Modified: pkg/RSiena/data/allEffects.csv
===================================================================
--- pkg/RSiena/data/allEffects.csv	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/data/allEffects.csv	2010-09-20 17:20:59 UTC (rev 120)
@@ -17,6 +17,8 @@
 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
 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
 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
+behaviorOneModeObjective,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
+behaviorOneModeObjective,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
 behaviorOneModeObjective2,behavior xxxxxx: infl. one-sided ? x xxxxxx alter,beh. xxxxxx: infl. interaction? x xxxxxx alter,behInfl1sid,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
@@ -29,7 +31,7 @@
 behaviorBipartiteObjective,behavior xxxxxx dense triads <maybe wrong>,beh. xxxxxx dense triads <<<maybe wrong>>>,behDenseTriads,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 behaviorBipartiteObjective,behavior xxxxxx similarity in dense triads <maybe wrong>,beh. xxxxxx homogeneity of dense triads <<<maybe wrong>>>,simDenseTriads,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 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
-behaviorBipartiteObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
+behaviorBipartiteObjective,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
 behaviorBipartiteObjective,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
 behaviorBipartiteObjective2,behavior xxxxxx: infl. one-sided ? x xxxxxx alter,beh. xxxxxx: infl. interaction? x xxxxxx alter,behInfl1sid,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
@@ -44,8 +46,8 @@
 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,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,
@@ -72,12 +74,12 @@
 covarSymmetricObjective,same xxxxxx,same xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 covarSymmetricObjective,xxxxxx ego x xxxxxx alter,xxxxxx ego x xxxxxx alter,egoXAlt,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 covarSymmetricObjective,xxxxxx of indirect ties,xxxxxx of indirect ties,IndTies,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-covarSymmetricObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+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,
 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,
 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,
 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,
 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,",",0,0,objective,NA,NA,0,0,0,0,
+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,
 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,
 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,
 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,
@@ -90,7 +92,7 @@
 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,
 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,
 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,
-covarNonSymmetricObjective,xxxxxx alter at distance 2,xxxxxx alter at distance 2,altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+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,
 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,
 covarBehaviorInteractions,av.sim. x ,av.sim. x ,avSimX,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 covarBehaviorInteractions,tot. sim. x ,tot. sim. x ,totSimX,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
@@ -108,8 +110,8 @@
 nonSymmetricObjective,outdegree (density),Number of ties,density,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 nonSymmetricObjective,reciprocity,Number of reciprocated ties,recip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
 nonSymmetricObjective,transitive triplets,Number of transitive triplets,transTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-nonSymmetricObjective,transitive mediated triplets,Number of transitive triplets,transMedTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-nonSymmetricObjective,3-cycles,3-cycles,cycle3,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+nonSymmetricObjective,transitive mediated triplets,Number of transitive triplets,transMedTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
+nonSymmetricObjective,3-cycles,3-cycles,cycle3,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 nonSymmetricObjective,transitive ties,Number of ties with transitive closure,transTies,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 nonSymmetricObjective,betweenness,betweenness count,between,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 nonSymmetricObjective,balance,Amount of balance,balance,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
@@ -124,8 +126,8 @@
 nonSymmetricObjective,indegree - activity (sqrt),Sum of outdegrees x sqrt(indegree),inActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 nonSymmetricObjective,outdegree - activity,Sum of squared outdegrees,outAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
 nonSymmetricObjective,outdegree - activity (sqrt),Sum of outdegrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0
-nonSymmetricObjective,1/(outdegree + #),Sum 1/(outdegrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0
-nonSymmetricObjective,1/(outdegree+#)(outdegree+1+#),Sum 1/(outdegrees + #)(outdegrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0
+nonSymmetricObjective,1/(outdegree + #),Sum 1/(outdegrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+nonSymmetricObjective,1/(outdegree+#)(outdegree+1+#),Sum 1/(outdegrees + #)(outdegrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
 nonSymmetricObjective,out-out degree^(1/#) assortativity,Sum of out-out degree^(1/#) products,outOutAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,
 nonSymmetricObjective,out-in degree^(1/#) assortativity,Sum of out-in degree^(1/#) products,outInAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,
 nonSymmetricObjective,in-out degree^(1/#) assortativity,Sum of in-out degree^(1/#) products,inOutAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,
@@ -140,8 +142,8 @@
 symmetricObjective,degree of alter,Sum of squared degrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 symmetricObjective,sqrt degree of alter,Sum of degrees ,inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
 symmetricObjective,degree^(1.5),Sum of degrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-symmetricObjective,1/(degree + #),Sum 1/(degrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
-symmetricObjective,1/(degree+#)(degree+1+#),Sum 1/(degrees + #)(degrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+symmetricObjective,1/(degree + #),Sum 1/(degrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0
+symmetricObjective,1/(degree+#)(degree+1+#),Sum 1/(degrees + #)(degrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0
 symmetricObjective,degree^(1/#) assortativity,Sum of degree^(1/#) products,outOutAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0
 covarSymmetricRate,effect xxxxxx on rate,effect xxxxxx on rate,RateX,NA,xxxxxx,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,covariate,0,0,0,0
 covarNonSymmetricRate,effect xxxxxx on rate,Amount of change x xxxxxx,RateX,NA,xxxxxx,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,covariate,0,0,0,0

Modified: pkg/RSiena/inst/doc/s_man400.pdf
===================================================================
--- pkg/RSiena/inst/doc/s_man400.pdf	2010-08-21 17:17:59 UTC (rev 119)
+++ pkg/RSiena/inst/doc/s_man400.pdf	2010-09-20 17:20:59 UTC (rev 120)
@@ -247,295 +247,292 @@
 (Time heterogeneity in model parameters)
 endobj
 165 0 obj
+<< /S /GoTo /D (subsection.5.8) >>
+endobj
+168 0 obj
+(Limiting the maximum outdegree)
+endobj
+169 0 obj
 << /S /GoTo /D (section.6) >>
 endobj
-168 0 obj
+172 0 obj
 (Estimation)
 endobj
-169 0 obj
+173 0 obj
 << /S /GoTo /D (subsection.6.1) >>
 endobj
-172 0 obj
+176 0 obj
 (Algorithm)
 endobj
-173 0 obj
+177 0 obj
 << /S /GoTo /D (subsection.6.2) >>
 endobj
-176 0 obj
+180 0 obj
 (Output)
 endobj
-177 0 obj
+181 0 obj
 << /S /GoTo /D (subsubsection.6.2.1) >>
 endobj
-180 0 obj
+184 0 obj
 (Fixing parameters)
 endobj
-181 0 obj
+185 0 obj
 << /S /GoTo /D (subsubsection.6.2.2) >>
 endobj
-184 0 obj
+188 0 obj
 (Automatic fixing of parameters)
 endobj
-185 0 obj
+189 0 obj
 << /S /GoTo /D (subsubsection.6.2.3) >>
 endobj
-188 0 obj
+192 0 obj
 (Conditional and unconditional estimation)
 endobj
-189 0 obj
+193 0 obj
 << /S /GoTo /D (subsubsection.6.2.4) >>
 endobj
-192 0 obj
+196 0 obj
 (Required changes from conditional to unconditional estimation)
 endobj
-193 0 obj
+197 0 obj
 << /S /GoTo /D (section.7) >>
 endobj
-196 0 obj
+200 0 obj
 (Standard errors)
 endobj
-197 0 obj
+201 0 obj
 << /S /GoTo /D (section.8) >>
 endobj
-200 0 obj
+204 0 obj
 (Tests)
 endobj
-201 0 obj
+205 0 obj
 << /S /GoTo /D (subsection.8.1) >>
 endobj
-204 0 obj
+208 0 obj
 (Score-type tests)
 endobj
-205 0 obj
+209 0 obj
 << /S /GoTo /D (subsection.8.2) >>
 endobj
-208 0 obj
+212 0 obj
 (Example: one-sided tests, two-sided tests, and one-step estimates)
 endobj
-209 0 obj
+213 0 obj
 << /S /GoTo /D (subsubsection.8.2.1) >>
 endobj
-212 0 obj
+216 0 obj
 (Multi-parameter tests)
 endobj
-213 0 obj
+217 0 obj
 << /S /GoTo /D (subsection.8.3) >>
 endobj
-216 0 obj
+220 0 obj
 (Alternative application: convergence problems)
 endobj
-217 0 obj
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 120

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