[Rsiena-commits] r26 - in pkg: . RSienaTest RSienaTest/R RSienaTest/data RSienaTest/inst RSienaTest/man RSienaTest/src RSienaTest/src/data RSienaTest/src/model RSienaTest/src/model/effects RSienaTest/src/model/effects/generic RSienaTest/src/model/tables RSienaTest/src/model/variables RSienaTest/src/network RSienaTest/src/utils RSienaTest/src/win32 RSienaTest/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 2 05:31:32 CET 2009
Author: ripleyrm
Date: 2009-12-02 05:31:30 +0100 (Wed, 02 Dec 2009)
New Revision: 26
Added:
pkg/RSienaTest/
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/NAMESPACE
pkg/RSienaTest/R/
pkg/RSienaTest/R/RSienaRDocumentation.r
pkg/RSienaTest/R/Sienatest.r
pkg/RSienaTest/R/effects.r
pkg/RSienaTest/R/getTargets.r
pkg/RSienaTest/R/globals.r
pkg/RSienaTest/R/phase1.r
pkg/RSienaTest/R/phase2.r
pkg/RSienaTest/R/phase3.r
pkg/RSienaTest/R/print01Report.r
pkg/RSienaTest/R/print07Report.r
pkg/RSienaTest/R/printDataReport.r
pkg/RSienaTest/R/printInitialDescription.r
pkg/RSienaTest/R/robmon.r
pkg/RSienaTest/R/siena01.r
pkg/RSienaTest/R/siena07.r
pkg/RSienaTest/R/siena07gui.r
pkg/RSienaTest/R/sienaDataCreate.r
pkg/RSienaTest/R/sienaDataCreateFromSession.r
pkg/RSienaTest/R/sienaModelCreate.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/R/sienautils.r
pkg/RSienaTest/R/simstatsc.r
pkg/RSienaTest/R/zzz.R
pkg/RSienaTest/changeLog
pkg/RSienaTest/cleanup
pkg/RSienaTest/cleanup.win
pkg/RSienaTest/configure.win
pkg/RSienaTest/data/
pkg/RSienaTest/data/RSiena.rda
pkg/RSienaTest/data/allEffects.R
pkg/RSienaTest/data/allEffects.csv
pkg/RSienaTest/inst/
pkg/RSienaTest/inst/ilcampo.gif
pkg/RSienaTest/inst/sienascript
pkg/RSienaTest/man/
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/allEffects.Rd
pkg/RSienaTest/man/coCovar.Rd
pkg/RSienaTest/man/coDyadCovar.Rd
pkg/RSienaTest/man/getEffects.Rd
pkg/RSienaTest/man/installGui.Rd
pkg/RSienaTest/man/print01Report.Rd
pkg/RSienaTest/man/s501.Rd
pkg/RSienaTest/man/s502.Rd
pkg/RSienaTest/man/s503.Rd
pkg/RSienaTest/man/s50a.Rd
pkg/RSienaTest/man/siena01Gui.Rd
pkg/RSienaTest/man/siena07.Rd
pkg/RSienaTest/man/sienaCompositionChange.Rd
pkg/RSienaTest/man/sienaDataCreate.Rd
pkg/RSienaTest/man/sienaDataCreateFromSession.Rd
pkg/RSienaTest/man/sienaFit.Rd
pkg/RSienaTest/man/sienaGroupCreate.Rd
pkg/RSienaTest/man/sienaModelCreate.Rd
pkg/RSienaTest/man/sienaModelOptions.Rd
pkg/RSienaTest/man/sienaNet.Rd
pkg/RSienaTest/man/sienaNodeSet.Rd
pkg/RSienaTest/man/simstats0c.Rd
pkg/RSienaTest/man/tmp3.Rd
pkg/RSienaTest/man/tmp4.Rd
pkg/RSienaTest/man/varCovar.Rd
pkg/RSienaTest/man/varDyadCovar.Rd
pkg/RSienaTest/src/
pkg/RSienaTest/src/Makefile.profile
pkg/RSienaTest/src/Makefile.win
pkg/RSienaTest/src/Makevars
pkg/RSienaTest/src/data/
pkg/RSienaTest/src/data/ActorSet.cpp
pkg/RSienaTest/src/data/ActorSet.h
pkg/RSienaTest/src/data/BehaviorLongitudinalData.cpp
pkg/RSienaTest/src/data/BehaviorLongitudinalData.h
pkg/RSienaTest/src/data/ChangingCovariate.cpp
pkg/RSienaTest/src/data/ChangingCovariate.h
pkg/RSienaTest/src/data/ChangingDyadicCovariate.cpp
pkg/RSienaTest/src/data/ChangingDyadicCovariate.h
pkg/RSienaTest/src/data/ConstantCovariate.cpp
pkg/RSienaTest/src/data/ConstantCovariate.h
pkg/RSienaTest/src/data/ConstantDyadicCovariate.cpp
pkg/RSienaTest/src/data/ConstantDyadicCovariate.h
pkg/RSienaTest/src/data/Covariate.cpp
pkg/RSienaTest/src/data/Covariate.h
pkg/RSienaTest/src/data/Data.cpp
pkg/RSienaTest/src/data/Data.h
pkg/RSienaTest/src/data/DyadicCovariate.cpp
pkg/RSienaTest/src/data/DyadicCovariate.h
pkg/RSienaTest/src/data/DyadicCovariateValueIterator.cpp
pkg/RSienaTest/src/data/DyadicCovariateValueIterator.h
pkg/RSienaTest/src/data/ExogenousEvent.cpp
pkg/RSienaTest/src/data/ExogenousEvent.h
pkg/RSienaTest/src/data/LongitudinalData.cpp
pkg/RSienaTest/src/data/LongitudinalData.h
pkg/RSienaTest/src/data/NetworkLongitudinalData.cpp
pkg/RSienaTest/src/data/NetworkLongitudinalData.h
pkg/RSienaTest/src/data/OneModeNetworkLongitudinalData.cpp
pkg/RSienaTest/src/data/OneModeNetworkLongitudinalData.h
pkg/RSienaTest/src/model/
pkg/RSienaTest/src/model/EffectInfo.cpp
pkg/RSienaTest/src/model/EffectInfo.h
pkg/RSienaTest/src/model/EpochSimulation.cpp
pkg/RSienaTest/src/model/EpochSimulation.h
pkg/RSienaTest/src/model/Function.cpp
pkg/RSienaTest/src/model/Function.h
pkg/RSienaTest/src/model/Model.cpp
pkg/RSienaTest/src/model/Model.h
pkg/RSienaTest/src/model/SimulationActorSet.cpp
pkg/RSienaTest/src/model/SimulationActorSet.h
pkg/RSienaTest/src/model/State.cpp
pkg/RSienaTest/src/model/State.h
pkg/RSienaTest/src/model/StatisticCalculator.cpp
pkg/RSienaTest/src/model/StatisticCalculator.h
pkg/RSienaTest/src/model/effects/
pkg/RSienaTest/src/model/effects/AllEffects.h
pkg/RSienaTest/src/model/effects/AverageAlterEffect.cpp
pkg/RSienaTest/src/model/effects/AverageAlterEffect.h
pkg/RSienaTest/src/model/effects/AverageSimilarityEffect.cpp
pkg/RSienaTest/src/model/effects/AverageSimilarityEffect.h
pkg/RSienaTest/src/model/effects/BalanceEffect.cpp
pkg/RSienaTest/src/model/effects/BalanceEffect.h
pkg/RSienaTest/src/model/effects/BehaviorDependentBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorDependentBehaviorEffect.h
pkg/RSienaTest/src/model/effects/BehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorEffect.h
pkg/RSienaTest/src/model/effects/BehaviorMainBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorMainBehaviorEffect.h
pkg/RSienaTest/src/model/effects/BetweennessEffect.cpp
pkg/RSienaTest/src/model/effects/BetweennessEffect.h
pkg/RSienaTest/src/model/effects/ChangingCovariateBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/ChangingCovariateBehaviorEffect.h
pkg/RSienaTest/src/model/effects/ChangingCovariateMainBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/ChangingCovariateMainBehaviorEffect.h
pkg/RSienaTest/src/model/effects/ConstantCovariateBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/ConstantCovariateBehaviorEffect.h
pkg/RSienaTest/src/model/effects/ConstantCovariateMainBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/ConstantCovariateMainBehaviorEffect.h
pkg/RSienaTest/src/model/effects/CovariateAlterEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateAlterEffect.h
pkg/RSienaTest/src/model/effects/CovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateDependentNetworkEffect.h
pkg/RSienaTest/src/model/effects/CovariateEgoAlterEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateEgoAlterEffect.h
pkg/RSienaTest/src/model/effects/CovariateEgoEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateEgoEffect.h
pkg/RSienaTest/src/model/effects/CovariateIndirectTiesEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateIndirectTiesEffect.h
pkg/RSienaTest/src/model/effects/CovariateSimilarityEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateSimilarityEffect.h
pkg/RSienaTest/src/model/effects/DenseTriadsEffect.cpp
pkg/RSienaTest/src/model/effects/DenseTriadsEffect.h
pkg/RSienaTest/src/model/effects/DensityEffect.cpp
pkg/RSienaTest/src/model/effects/DensityEffect.h
pkg/RSienaTest/src/model/effects/DistanceTwoEffect.cpp
pkg/RSienaTest/src/model/effects/DistanceTwoEffect.h
pkg/RSienaTest/src/model/effects/DyadicCovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/DyadicCovariateDependentNetworkEffect.h
pkg/RSienaTest/src/model/effects/DyadicCovariateMainEffect.cpp
pkg/RSienaTest/src/model/effects/DyadicCovariateMainEffect.h
pkg/RSienaTest/src/model/effects/DyadicCovariateReciprocityEffect.cpp
pkg/RSienaTest/src/model/effects/DyadicCovariateReciprocityEffect.h
pkg/RSienaTest/src/model/effects/Effect.cpp
pkg/RSienaTest/src/model/effects/Effect.h
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/model/effects/EffectFactory.h
pkg/RSienaTest/src/model/effects/FourCyclesEffect.cpp
pkg/RSienaTest/src/model/effects/FourCyclesEffect.h
pkg/RSienaTest/src/model/effects/HigherCovariateEffect.cpp
pkg/RSienaTest/src/model/effects/HigherCovariateEffect.h
pkg/RSienaTest/src/model/effects/InInDegreeAssortativityEffect.cpp
pkg/RSienaTest/src/model/effects/InInDegreeAssortativityEffect.h
pkg/RSienaTest/src/model/effects/InOutDegreeAssortativityEffect.cpp
pkg/RSienaTest/src/model/effects/InOutDegreeAssortativityEffect.h
pkg/RSienaTest/src/model/effects/IndegreeActivityEffect.cpp
pkg/RSienaTest/src/model/effects/IndegreeActivityEffect.h
pkg/RSienaTest/src/model/effects/IndegreeEffect.cpp
pkg/RSienaTest/src/model/effects/IndegreeEffect.h
pkg/RSienaTest/src/model/effects/IndegreePopularityEffect.cpp
pkg/RSienaTest/src/model/effects/IndegreePopularityEffect.h
pkg/RSienaTest/src/model/effects/InverseOutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/InverseOutdegreeEffect.h
pkg/RSienaTest/src/model/effects/InverseSquaredOutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/InverseSquaredOutdegreeEffect.h
pkg/RSienaTest/src/model/effects/LinearShapeEffect.cpp
pkg/RSienaTest/src/model/effects/LinearShapeEffect.h
pkg/RSienaTest/src/model/effects/NetworkDependentBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/NetworkDependentBehaviorEffect.h
pkg/RSienaTest/src/model/effects/NetworkEffect.cpp
pkg/RSienaTest/src/model/effects/NetworkEffect.h
pkg/RSienaTest/src/model/effects/NetworkInteractionEffect.cpp
pkg/RSienaTest/src/model/effects/NetworkInteractionEffect.h
pkg/RSienaTest/src/model/effects/OutInDegreeAssortativityEffect.cpp
pkg/RSienaTest/src/model/effects/OutInDegreeAssortativityEffect.h
pkg/RSienaTest/src/model/effects/OutOutDegreeAssortativityEffect.cpp
pkg/RSienaTest/src/model/effects/OutOutDegreeAssortativityEffect.h
pkg/RSienaTest/src/model/effects/OutdegreeActivityEffect.cpp
pkg/RSienaTest/src/model/effects/OutdegreeActivityEffect.h
pkg/RSienaTest/src/model/effects/OutdegreeActivitySqrtEffect.cpp
pkg/RSienaTest/src/model/effects/OutdegreeActivitySqrtEffect.h
pkg/RSienaTest/src/model/effects/OutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/OutdegreeEffect.h
pkg/RSienaTest/src/model/effects/OutdegreePopularityEffect.cpp
pkg/RSienaTest/src/model/effects/OutdegreePopularityEffect.h
pkg/RSienaTest/src/model/effects/QuadraticShapeEffect.cpp
pkg/RSienaTest/src/model/effects/QuadraticShapeEffect.h
pkg/RSienaTest/src/model/effects/ReciprocityEffect.cpp
pkg/RSienaTest/src/model/effects/ReciprocityEffect.h
pkg/RSienaTest/src/model/effects/SameCovariateEffect.cpp
pkg/RSienaTest/src/model/effects/SameCovariateEffect.h
pkg/RSienaTest/src/model/effects/StructuralRateEffect.cpp
pkg/RSienaTest/src/model/effects/StructuralRateEffect.h
pkg/RSienaTest/src/model/effects/ThreeCyclesEffect.cpp
pkg/RSienaTest/src/model/effects/ThreeCyclesEffect.h
pkg/RSienaTest/src/model/effects/TotalSimilarityEffect.cpp
pkg/RSienaTest/src/model/effects/TotalSimilarityEffect.h
pkg/RSienaTest/src/model/effects/TransitiveMediatedTripletsEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveMediatedTripletsEffect.h
pkg/RSienaTest/src/model/effects/TransitiveTiesEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveTiesEffect.h
pkg/RSienaTest/src/model/effects/TransitiveTriadsEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveTriadsEffect.h
pkg/RSienaTest/src/model/effects/TransitiveTripletsEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveTripletsEffect.h
pkg/RSienaTest/src/model/effects/WWXClosureEffect.cpp
pkg/RSienaTest/src/model/effects/WWXClosureEffect.h
pkg/RSienaTest/src/model/effects/WXXClosureEffect.cpp
pkg/RSienaTest/src/model/effects/WXXClosureEffect.h
pkg/RSienaTest/src/model/effects/XWXClosureEffect.cpp
pkg/RSienaTest/src/model/effects/XWXClosureEffect.h
pkg/RSienaTest/src/model/effects/generic/
pkg/RSienaTest/src/model/effects/generic/AlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/AlterFunction.h
pkg/RSienaTest/src/model/effects/generic/BetweennessFunction.cpp
pkg/RSienaTest/src/model/effects/generic/BetweennessFunction.h
pkg/RSienaTest/src/model/effects/generic/ConstantFunction.cpp
pkg/RSienaTest/src/model/effects/generic/ConstantFunction.h
pkg/RSienaTest/src/model/effects/generic/DifferenceFunction.cpp
pkg/RSienaTest/src/model/effects/generic/DifferenceFunction.h
pkg/RSienaTest/src/model/effects/generic/EgoInDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/EgoInDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/EgoOutDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/EgoOutDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/GenericNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/generic/GenericNetworkEffect.h
pkg/RSienaTest/src/model/effects/generic/InDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/InStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InStarFunction.h
pkg/RSienaTest/src/model/effects/generic/InTieFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InTieFunction.h
pkg/RSienaTest/src/model/effects/generic/IntAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/IntAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/IntSqrtFunction.cpp
pkg/RSienaTest/src/model/effects/generic/IntSqrtFunction.h
pkg/RSienaTest/src/model/effects/generic/NetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/NetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/OutDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/OutTieFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutTieFunction.h
pkg/RSienaTest/src/model/effects/generic/ProductFunction.cpp
pkg/RSienaTest/src/model/effects/generic/ProductFunction.h
pkg/RSienaTest/src/model/effects/generic/ReciprocatedTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/ReciprocatedTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/TwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/TwoPathFunction.h
pkg/RSienaTest/src/model/tables/
pkg/RSienaTest/src/model/tables/BetweennessTable.cpp
pkg/RSienaTest/src/model/tables/BetweennessTable.h
pkg/RSienaTest/src/model/tables/Cache.cpp
pkg/RSienaTest/src/model/tables/Cache.h
pkg/RSienaTest/src/model/tables/ConfigurationTable.cpp
pkg/RSienaTest/src/model/tables/ConfigurationTable.h
pkg/RSienaTest/src/model/tables/CriticalInStarTable.cpp
pkg/RSienaTest/src/model/tables/CriticalInStarTable.h
pkg/RSienaTest/src/model/tables/EgocentricConfigurationTable.cpp
pkg/RSienaTest/src/model/tables/EgocentricConfigurationTable.h
pkg/RSienaTest/src/model/tables/NetworkCache.cpp
pkg/RSienaTest/src/model/tables/NetworkCache.h
pkg/RSienaTest/src/model/tables/TwoPathTable.cpp
pkg/RSienaTest/src/model/tables/TwoPathTable.h
pkg/RSienaTest/src/model/variables/
pkg/RSienaTest/src/model/variables/BehaviorVariable.cpp
pkg/RSienaTest/src/model/variables/BehaviorVariable.h
pkg/RSienaTest/src/model/variables/DependentVariable.cpp
pkg/RSienaTest/src/model/variables/DependentVariable.h
pkg/RSienaTest/src/model/variables/EffectValueTable.cpp
pkg/RSienaTest/src/model/variables/EffectValueTable.h
pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
pkg/RSienaTest/src/model/variables/NetworkVariable.h
pkg/RSienaTest/src/network/
pkg/RSienaTest/src/network/CommonNeighborIterator.cpp
pkg/RSienaTest/src/network/CommonNeighborIterator.h
pkg/RSienaTest/src/network/IncidentTieIterator.cpp
pkg/RSienaTest/src/network/IncidentTieIterator.h
pkg/RSienaTest/src/network/Network.cpp
pkg/RSienaTest/src/network/Network.h
pkg/RSienaTest/src/network/NetworkUtils.cpp
pkg/RSienaTest/src/network/NetworkUtils.h
pkg/RSienaTest/src/network/OneModeNetwork.cpp
pkg/RSienaTest/src/network/OneModeNetwork.h
pkg/RSienaTest/src/network/TieIterator.cpp
pkg/RSienaTest/src/network/TieIterator.h
pkg/RSienaTest/src/siena07.cpp
pkg/RSienaTest/src/utils/
pkg/RSienaTest/src/utils/NamedObject.cpp
pkg/RSienaTest/src/utils/NamedObject.h
pkg/RSienaTest/src/utils/Random.cpp
pkg/RSienaTest/src/utils/Random.h
pkg/RSienaTest/src/utils/SqrtTable.cpp
pkg/RSienaTest/src/utils/SqrtTable.h
pkg/RSienaTest/src/utils/Utils.cpp
pkg/RSienaTest/src/utils/Utils.h
pkg/RSienaTest/src/win32/
pkg/RSienaTest/src/win32/Makefile
pkg/RSienaTest/src/win32/siena.c
pkg/RSienaTest/src/win32/siena.ico
pkg/RSienaTest/src/win32/siena_rc.rc
pkg/RSienaTest/tests/
pkg/RSienaTest/tests/parallel.R
pkg/RSienaTest/tests/parallel.Rout.save
pkg/RSienaTest/tests/s50-network1.dat
pkg/RSienaTest/tests/s50-network2.dat
pkg/RSienaTest/tests/s50-network3.dat
pkg/RSienaTest/tests/s50.csv
pkg/RSienaTest/tests/s50_d1.net
pkg/RSienaTest/tests/s50_d2.net
pkg/RSienaTest/tests/s50_d3.net
pkg/RSienaTest/tests/s50e.csv
pkg/RSienaTest/tests/s50e.dat
pkg/RSienaTest/tests/s50paj.csv
Log:
User specified interactions
Added: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION (rev 0)
+++ pkg/RSienaTest/DESCRIPTION 2009-12-02 04:31:30 UTC (rev 26)
@@ -0,0 +1,17 @@
+Package: RSienaTest
+Type: Package
+Title: Siena - Simulation Investigation for Empirical Network Analysis
+Version: 1.0.9
+Date: 2009-12-01
+Author: Various
+Depends: R (>= 2.7.0), xtable
+Imports: Matrix
+Suggests: tcltk, rlecuyer, snow, network, codetools
+SystemRequirements: GNU make, tcl/tk 8.5, Tktable
+Maintainer: Ruth Ripley <ruth at stats.ox.ac.uk>
+Description: Fits models to longitudinal networks
+License: GPL (>=2)
+LazyLoad: yes
+LazyData: yes
+URL: http://www.stats.ox.ac.uk/~snijders/siena
+Packaged: 2009-12-01 16:33:21 UTC; ruth
Added: pkg/RSienaTest/NAMESPACE
===================================================================
--- pkg/RSienaTest/NAMESPACE (rev 0)
+++ pkg/RSienaTest/NAMESPACE 2009-12-02 04:31:30 UTC (rev 26)
@@ -0,0 +1,22 @@
+useDynLib(RSienaTest)
+export(coCovar, coDyadCovar, getEffects, model.create, print01Report,
+siena01Gui, siena07, sienaCompositionChange,
+sienaCompositionChangeFromFile, sienaDataCreate, sienaDataCreateFromSession,
+sienaGroupCreate, sienaModelCreate, sienaNet, sienaNodeSet, simstats0c, varCovar, varDyadCovar,
+ installGui)#, sienaTimeTest)
+
+import(Matrix)
+import(xtable)
+
+S3method(print, siena)
+S3method(print, sienaGroup)
+S3method(print, sienaFit)
+S3method(print, summary.sienaFit)
+S3method(print, sienaModel)
+S3method(summary, sienaFit)
+S3method(xtable, sienaFit)
+S3method(print, xtable.sienaFit)
+#S3method(print, sienaTimeTest)
+#S3method(summary, sienaTimeTest)
+#S3method(print, summary.sienaTimeTest)
+#S3method(plot, sienaTimeTest)
Added: pkg/RSienaTest/R/RSienaRDocumentation.r
===================================================================
--- pkg/RSienaTest/R/RSienaRDocumentation.r (rev 0)
+++ pkg/RSienaTest/R/RSienaRDocumentation.r 2009-12-02 04:31:30 UTC (rev 26)
@@ -0,0 +1,253 @@
+#/******************************************************************************
+# * SIENA: Simulation Investigation for Empirical Network Analysis
+# *
+# * Web: http://www.stats.ox.ac.uk/~snidjers/siena
+# *
+# * File: RSienaRDocumentation.r
+# *
+# * Description: This module contains the code for documenting the
+# * RSiena R source.
+# *****************************************************************************/
+##
+##@getInternals Documentation
+getInternals <- function()
+{
+ fnlist <- read.csv("RSienafnlist.csv", as.is=TRUE)
+ mylist <- ls(parent.frame())
+ ## print(mylist)
+ library(codetools)
+ mylist <- mylist[mylist %in% fnlist[, 3]]
+ mytt <- lapply(mylist, function(x)
+ {
+ x <- get(x, envir=parent.frame(3))
+ if (is.function(x))
+ {
+ tt <- findGlobals(x, merge=FALSE)[[1]]
+ tt2 <- findLocals(body(x))
+ tt <- c(tt, tt2)
+ tt[tt %in% fnlist[, 3]]
+ }
+ else
+ {
+ NULL
+ }
+ }
+ )
+ names(mytt) <- mylist
+ mytt
+}
+##@getRSienaDocumentation Documentation
+getRSienaRDocumentation <- function(Rdir)
+{
+ # library(xtable)
+ library(codetools)
+
+ thisdir <- getwd()
+ ## temporarily move directory
+ setwd(Rdir)
+
+ ## extract comment lines
+ shell('grep "##@" *.r *.R > comments.lis')
+ ## read them in
+ comms <- readLines('comments.lis')
+ ## remove the file
+ file.remove("comments.lis")
+ ## remove the shell line
+ comms <- comms[!grepl("comments.lis", comms)]
+ ## split off
+ mystr <- paste("##", "@", sep="")
+ comms1 <- strsplit(comms, mystr)
+ ## join up rest
+ comms2 <- do.call(rbind, comms1)
+ ## turn into dataframe
+ comms3 <- sapply(comms1, function(x)
+ {
+ tmp <- strsplit(x[2], " ")[[1]]
+ if (tmp[2] == "internal")
+ {
+ c(x[1], tmp[1], tmp[2], paste('internal to', tmp[3],
+ collapse=" "))
+ }
+ else
+ {
+ c(x[1], tmp[1], tmp[2], paste(tmp[-c(1,2)],
+ collapse=" "))
+ }
+ }
+ )
+ comms3 <- t(comms3)
+
+ ## get the calls (global)
+ codet <- lapply(comms3[,2], function(x)
+ {
+ x <- try(getFromNamespace(x, "RSiena"), silent=TRUE)
+ if (is.function(x))
+ {
+ tmp1 <- findGlobals(x, merge=FALSE)[[1]]
+ tmp2 <- findLocals(body(x))
+ tmp <- c(tmp1, tmp2)
+ }
+ else
+ tmp <- NULL
+ unique(as.vector(tmp[tmp %in% comms3[,2]]))
+ }
+ )
+ names(codet) <- comms3[, 2]
+
+ ## now the internal ones
+ ## find the list of files from comms3
+ ttmp <- unique(comms3[grepl("internal to", comms3[, 4]), 4])
+ ttmp <- sub("internal to ", "", ttmp)
+ ttmp2 <- comms3[match(ttmp, comms3[, 2]), 1]
+ ttmp2 <- sub(":", "", ttmp2)
+
+ ## write out the fnlist in the Rdir
+ write.csv(data.frame(comms3), "RSienafnlist.csv")
+ ## get the list of internals
+ tt <- lapply(1:length(ttmp), function(x, y, z)
+ {
+ yy <- y[x]
+ zz <- z[[x]]
+ yy <- getFromNamespace(yy, "RSiena")
+ targs <- formals(yy)
+ n <- length(targs)
+ myargs <- targs
+ for (i in 1:n)
+ myargs[[i]] <- 1
+ myargs['getDocumentation'] <- TRUE
+ do.call(yy, myargs)
+ }, y=ttmp, z=ttmp2)
+ names(tt) <- ttmp
+ ## remove the file
+ file.remove("RSienafnlist.csv")
+ ## reformat this
+ ttt <- lapply(1:length(tt), function(x,y)
+ {
+ yy <- y[[x]]
+ n <- length(y[[x]])
+ bb <- names(yy)
+ t1<- lapply(1:length(yy), function(x, b, a)
+ {
+ y <- a[[x]]
+ bb <- b[[x]]
+ n <- length(y)
+ if ( n > 0)
+ cbind( rep(bb, n), y)
+ else
+ c( bb, " ")
+ }, a=yy, b=bb)
+ t2 <- do.call(rbind,t1)
+ }, y=tt
+ )
+
+ tttt <- as.data.frame(do.call(rbind,ttt))
+ names(tttt) <- c('Function', 'Calls')
+
+ ## create an object that will tabify to the right output
+ tmp2 <- codet
+
+ tmp4 <- lapply(1 : length(tmp2), function(x, y, z, a)
+ {
+ n <- length(y[[x]])
+ if (n > 0)
+ {
+ cbind( rep(a[x, 1], n), rep(z[x], n), y[[x]], rep(a[x, 3], n),
+ rep(a[x, 4], n))
+ }
+ else
+ {
+ cbind(a[x, 1], z[x], " ", a[x, 3], a[x, 4])
+ }
+
+ }, y=tmp2, z=names(tmp2), a=comms3)
+
+ tmp5 <- do.call(rbind, tmp4)
+ tmp5 <- as.data.frame(tmp5, stringsAsFactors=FALSE)
+ names(tmp5) <- c('Source File', 'Function', 'Calls', 'Type', 'Notes')
+
+ ## now merge in the internals
+ tmp5bit <- tmp5[tmp5$Function %in%tttt$Function,]
+ tmerge <- merge(tmp5bit, tttt, by="Function")
+ tmerge <- tmerge[, -3]
+ tmerge <- tmerge[, c(2, 1, 5, 3, 4)]
+ names(tmerge)[3] <- "Calls"
+ tmp5new <- rbind(tmp5[!tmp5$Function %in% tttt$Function,], tmerge)
+ tmp55 <- split(tmp5new, tmp5new$Function)
+
+ ## same for called by
+ tmp6 <- lapply(1 : length(tmp2), function(x, y, z)
+ {
+ n <- length(y[[x]])
+ if (n > 0)
+ {
+ cbind( rep(z[x], n), y[[x]] )
+ }
+ else
+ {
+ cbind(z[x], " ")
+ }
+
+ }, y=tmp2, z=names(tmp2))
+
+ tmp7 <- do.call(rbind, tmp6)
+
+ tmp7 <- as.data.frame(tmp7, stringsAsFactors=FALSE)
+ names(tmp7) <- c( 'Called from', 'Function')
+
+ tmp7 <- tmp7[order(tmp7[,2],tmp7[,1]), ]
+
+ tttt7 <- tttt
+ names(tttt7) <- c("Called from", "Function")
+ tttt7 <- tttt7[order(tttt7[,2],tttt7[,1]), ]
+
+ tmp7bit <- tmp7[tmp7$Function %in% tttt7$Function, ]
+
+ tmp7new <- merge(tmp7, tttt7, by=c("Function", "Called from"), all=TRUE)
+
+ tmp7new <- tmp7new[order(tmp7new[,1], tmp7new[,2]),]
+
+ tmp77new <- split(tmp7new, tmp7new$Function)
+
+ tmp77new <- tmp77new[-1]
+
+ ## create desired output format
+ tmp11 <- lapply(1:length(names(tmp55)), function(x,y,z)
+ {
+ thisone <- names(tmp55)[x]
+ yy <- y[[thisone]]
+ zz <- z[[thisone]]
+ d <- max(nrow(yy), nrow(zz))
+ fn <- yy$Function[1]
+ src<- yy$`Source File`[1]
+ type<- yy$Type[1]
+ notes<- yy$Notes[1]
+ if (!is.null(zz))
+ {
+ called <- c(zz[,2], rep(' ', d-nrow(zz)))
+ }
+ else
+ {
+ called <- rep(' ', d)
+ }
+ tmp <- data.frame(src=rep(src,d),
+ fun=rep(fn, d),
+ type=rep(type, d),
+ notes=rep(notes, d),
+ calls=c(yy[,3], rep(' ', d-nrow(yy))),
+ called=called, stringsAsFactors=FALSE)
+ tmp
+ }, y=tmp55, z=tmp77new)
+ ## join into a data frame
+ tmp12 <- do.call(rbind, tmp11)
+ names(tmp12)[2] <- "Function"
+
+ tmp12 <- tmp12[order(tmp12[, "type"], row.names(tmp12)), ]
+ tmp12 <- tmp12[, c(3, 2, 5, 6, 4, 1)]
+ ff <- xtable(tmp12)
+ ## go back to start directory
+ setwd(thisdir)
+ print(ff, tabular.environment="longtable",
+ file="RSienaRDocumentation.tex", floating=FALSE)
+
+ write.csv(tmp12, "RSienaRDocumentation.csv")
+}
Added: pkg/RSienaTest/R/Sienatest.r
===================================================================
--- pkg/RSienaTest/R/Sienatest.r (rev 0)
+++ pkg/RSienaTest/R/Sienatest.r 2009-12-02 04:31:30 UTC (rev 26)
@@ -0,0 +1,233 @@
+#/******************************************************************************
+# * SIENA: Simulation Investigation for Empirical Network Analysis
+# *
+# * Web: http://www.stats.ox.ac.uk/~snidjers/siena
+# *
+# * File: Sienatest.r
+# *
+# * Description: This module contains the function for instability analysis and
+# * score tests.
+# *
+# *****************************************************************************/
+##@InstabilityAnalysis siena07 Not currently used
+InstabilityAnalysis<- function(z)
+{
+ ##I think this is not correct, because of scaling. cond number of var matrix of X
+ ## can be obtained via svd(data) (which is stored in z$sf). Square of ratio
+ ## of smallest to largest singular value.
+ Report('Instability Analysis\n')
+ pp<- length(z$diver)
+ constant<- z$diver
+ test<- z$test
+ covtheta<- z$covtheta
+ covZ<- z$msf
+ covth<- covtheta[!(test|constant),!(test|constant)]
+ covth<- MatrixNorm(covth)
+ eigenv<- eigen(covth,symmetric=TRUE)$values
+ ma<- max(eigenv)
+ mi<- min(eigenv)
+ if (mi!=0)
+ cond.n <- ma/mi
+ Report('Instability analysis\n',lf)
+ Report('--------------------\n\n',lf)
+ Report('Variance-covariance matrix of parameter estimates',lf)
+ ##if (global boolean1 )
+ ## Report(' (without coordinates that are kept constant):\n',lf)
+ ##else
+ Report(c(':\n\nCondition number = ',format(cond.n,width=4,nsmall=4,digits=1),
+ ' \n\n'),sep='',lf)
+ Report(c('Eigen Values ',format(eigenv,width=6,nsmall=6,digits=1)),lf)
+ Report('\n\n',lf)
+ covZ<- MatrixNorm(covZ)
+ eigenvZ<-eigen(covZ,symmetric=TRUE)$values
+ ma<- max(eigenvZ)
+ mi<- min(eigenvZ)
+ if (mi!=0)
+ cond.n <- ma/mi
+ Report('Variance-covariance matrix of X',lf)
+ Report(c(':\n\nCondition number = ',format(cond.n,width=4,nsmall=4,digits=1),
+ ' \n\n'),sep='',lf)
+ Report(c('Eigen Values ',format(eigenvZ,width=6,nsmall=6,digits=1)),lf)
+ Report(c('\n\n',date(),'\n'),sep='',lf)
+ mysvd<- svd(z$sf)$d
+ ma<- max(mysvd)
+ mi<- min(mysvd)
+ cond.n<- (ma/mi)^2
+ Report(c(':\n\nCondition number2 = ',format(cond.n,width=4,nsmall=4,digits=1),
+ ' \n\n'),sep='',lf)
+ Report(c('Singular Values ',format(mysvd,width=6,nsmall=6,digits=1)),lf)
+ Report(c('\n\n',date(),'\n'),sep='',lf)
+}
+
+##@MatrixNorm siena07 Not currently used. May be incorrect.
+MatrixNorm<- function(mat)
+{
+ tmp<- apply(mat,2,function(x)x/sqrt(crossprod(x)))
+ ##or sweep(mat,2,apply(mat,2,function(x)x/sqrt(crossprod(x))
+ tmp
+}
+##@TestOutput siena07 Print report
+TestOutput <- function(z, x)
+{
+ testn <- sum(z$test)
+ # browser()
+ if (testn)
+ {
+ if (x$maxlike)
+ Heading(2, outf,'Score test <c>')
+ else
+ Heading(2, outf, 'Generalised score test <c>')
+ Report('Testing the goodness-of-fit of the model restricted by\n',outf)
+ j<- 0
+ for (k in 1:z$pp)
+ if (z$test[k])
+ {
+ j<- j+1
+ Report(c(' (',j,') ',format(paste(z$effects$type[k],': ',
+ z$effects$effectName[k],
+ sep=''),
+ width=50),' = ',
+ sprintf("%8.4f",z$theta[k]),'\n'),
+ sep = '', outf)
+ }
+ Report('_________________________________________________\n',outf)
+ Report(' ',outf)
+ Report(' \n',outf)
+ if (testn > 1)
+ Report('Joint test:\n-----------\n',outf)
+ Report(c(' c = ',sprintf("%8.4f", z$testresOverall),
+ ' d.f. = ',j,' p-value '),sep='',outf)
+ pvalue <- 1-pchisq(z$testresOverall,j)
+ if (pvalue < 0.0001)
+ Report('< 0.0001',outf)
+ else
+ Report(c('= ',sprintf("%8.4f",pvalue)), sep = '', outf)
+ if (testn==1)
+ Report(c('\n one-sided (normal variate): ',
+ sprintf("%8.4f",z$testresulto[1])), sep = '', outf)
+ if (testn> 1)
+ {
+ Report('\n\n',outf)
+ for (k in 1:j)
+ {
+ Report(c('(',k,') tested separately:\n'),sep='',outf)
+ Report('-----------------------\n',outf)
+ Report(' - two-sided:\n',outf)
+ Report(c(' c = ', sprintf("%8.4f", z$testresult[k]),
+ ' d.f. = 1 p-value '), sep = '', outf)
+ pvalue<- 1-pchisq(z$testresult[k],1)
+ if (pvalue < 0.0001)
+ Report('< 0.0001\n',outf)
+ else
+ Report(c('= ', sprintf("%8.4f", pvalue), '\n'), sep = '',
+ outf)
+ Report(c(' - one-sided (normal variate): ',
+ sprintf("%8.4f", z$testresulto[k])), sep = '', outf)
+ if (k<j)
+ Report('\n\n',outf)
+ }
+ }
+ Report(' \n_________________________________________________\n\n',outf)
+ Report('One-step estimates: \n\n',outf)
+ for (i in 1 : z$pp)
+ {
+ onestepest<- z$oneStep[i]+z$theta[i]
+ Report(c(format(paste(z$effects$type[i],': ',
+ z$effects$effectName[i], sep = ''),
+ width=50),
+ sprintf("%8.4f", onestepest), '\n'), sep = '', outf)
+ }
+ Report('\n',outf)
+ }
+}
+##@ScoreTest siena07 Do score tests
+ScoreTest<- function(pp, dfra, msf, fra, test, maxlike)
+{
+ testresult<- rep(NA, pp) ##for chisq per parameter
+ testresulto <- rep(NA, pp) ##for one-sided tests per parameter
+ ##first the general one
+ ans <- EvaluateTestStatistic(maxlike, test, dfra, msf, fra)
+ testresOverall <- ans$cvalue
+ covMatrix <- ans$covMatrix
+ if (sum(test) == 1)
+ {
+ testresulto[1] <- ans$oneSided
+ }
+ else
+ {
+ ## single df tests
+ use <- !test
+ k <- 0
+ for (i in 1:pp)
+ {
+ if (test[i])
+ {
+ k <- k+1
+ use[i] <- TRUE
+ ans <- EvaluateTestStatistic(maxlike, test[use], dfra[use, use],
+ msf[use, use], fra[use])
+ testresult[k] <- ans$cvalue
+ testresulto[k] <- ans$oneSided
+ use[i] <- FALSE
+ }
+ }
+ }
+ ##onestep estimator
+ if (maxlike)
+ dfra2 <- dfra + msf
+ else
+ dfra2 <- dfra
+ dinv2 <- solve(dfra2)
+ oneStep<- -dinv2 %*% fra
+ list(testresult=testresult, testresulto=testresulto,
+ testresOverall=testresOverall, covMatrix=covMatrix,
+ oneStep=oneStep, dinv2= dinv2, dfra2=dfra2)
+}
+##@EvaluateTestStatistic siena07 Calculate score test statistics
+EvaluateTestStatistic<- function(maxlike, test, dfra, msf, fra)
+{
+ ##uses local arrays set up in the calling procedure
+ d11 <- dfra[!test,!test,drop=FALSE]
+ d22 <- dfra[test,test,drop=FALSE]
+ d21 <- dfra[test,!test,drop=FALSE]
+ d12 <- t(d21)
+ sigma11 <- msf[!test,!test,drop=FALSE]
+ sigma22<- msf[test,test,drop=FALSE]
+ sigma12 <- msf[!test,test,drop=FALSE]
+ sigma21<- t(sigma12)
+ z1 <- fra[!test]
+ z2 <- fra[test]
+ id11 <- solve(d11)
+ rg<- d21%*%id11
+ if (!maxlike)
+ {
+ ##orthogonalise deviation vector
+ ov<- z2-rg%*%z1
+ ##compute var(ov) = sigma22- (d21%*%id11) %*%sigma12 -
+ ## sigma21 %*% t(id11)%*% t(d21) +
+ ## d21%*%id11 %*% sigma11 %*% t(id11) %*% t(d21)
+ v2<- sigma21 - rg%*%sigma11
+ v6<- v2 %*% t(id11) %*% t(d21)
+ v9<- sigma22 - rg %*% sigma12 -v6
+ }
+ else
+ {
+ ov <- -z2
+ v9 <- d22 - rg %*% d12
+ }
+ vav<- solve(v9) ## vav is the inverse variance matrix of ov
+ cvalue <- t(ov) %*% vav %*% ov
+ if (cvalue < 0) cvalue <- 0
+ if (sum(test)==1)
+ {
+ if (vav>0)
+ oneSided <- ov * sqrt(vav)
+ else
+ oneSided <- 0
+ if (!maxlike) oneSided<- - oneSided
+ ## change the sign for intuition for users
+ }
+ else
+ oneSided <- 0
+ list(cvalue=cvalue, oneSided=oneSided, covMatrix=v9)
+}
Added: pkg/RSienaTest/R/effects.r
===================================================================
--- pkg/RSienaTest/R/effects.r (rev 0)
+++ pkg/RSienaTest/R/effects.r 2009-12-02 04:31:30 UTC (rev 26)
@@ -0,0 +1,1278 @@
+#/******************************************************************************
+# * SIENA: Simulation Investigation for Empirical Network Analysis
+# *
+# * Web: http://www.stats.ox.ac.uk/~snidjers/siena
+# *
+# * File: effects.r
+# *
+# * Description: This module contains the code for the creation of the
+# * effects object to go with a Siena data object or group object.
+# *****************************************************************************/
+##@getEffects DataCreate
+getEffects<- function(x, nintn = 10, getDocumentation=FALSE)
+{
+ ##@duplicateDataFrameRow internal getEffects Put period numbers in
+ duplicateDataFrameRow <- function(x, n)
+ {
+ tmp <- NULL
+ for (i in 1:n)
+ {
+ xx <- x
+ xx[, c("effectName", "functionName", "period")] <-
+ sub("nnnnnn", periodNos[i], xx[, c("effectName", "functionName",
+ "period")])
+ tmp <- rbind(tmp, xx)
+ }
+ tmp
+ }
+ ##@substituteNames internal getEffects replace xxxxxx, yyyyyy, zzzzzz
+ substituteNames <- function(nameVectors, xName=NULL, yName=NULL, zName=NULL)
+ {
+ effects <- nameVectors[, c("effectName", "functionName",
+ "interaction1", "interaction2")]
+ if (!is.null(xName))
+ {
+ effects <- sapply(effects, function(x)
+ gsub("xxxxxx", xName, x))
+ }
+ if (!is.null(yName))
+ {
+ effects <- sapply(effects, function(x)
+ gsub("yyyyyy", yName, x))
+ }
+ if (!is.null(zName))
+ {
+ effects <- sapply(effects, function(x)
+ gsub("zzzzzz", zName, x))
+ }
+ nameVectors[, c("effectName", "functionName",
+ "interaction1", "interaction2")] <- effects
+ nameVectors
+ }
+ ##@createEffects internal getEffects Extract required rows and change text
+ createEffects <- function(effectGroup, xName=NULL, yName=NULL)
+ {
+ effects <- allEffects[allEffects$effectGroup == effectGroup, ]
+ if (nrow(effects) == 0)
+ {
+ stop("empty effect group")
+ }
+ if (any(is.na(effects$effectName)))
+ {
+ stop("missing effect name")
+ }
+ effects <- substituteNames(effects, xName, yName)
+ effects
+ }
+ ##@networkRateEffects internal getEffects create a set of rate effects
+ networkRateEffects <- function(depvar, varname, symmetric, bipartite)
+ {
+ if (symmetric)
+ {
+ rateEffects <- createEffects("symmetricRate", varname)
+ }
+ else if (bipartite)
+ {
+ rateEffects <- createEffects("bipartiteRate", varname)
+ }
+ else
+ {
+ rateEffects <- createEffects("nonSymmetricRate", varname)
+ }
+ if (observations == 1)
+ {
+ rateEffects <- rateEffects[-2, ] ## remove the extra period
+ }
+ else
+ {
+ ## get correct number of rows
+ rateEffects <- rbind(duplicateDataFrameRow(rateEffects[2, ],
+ observations),
+ rateEffects[-c(1, 2), ])
+ }
+ rateEffects
+ }
+ ##@oneModeNet internal getEffects
+ oneModeNet <- function(depvar, varname)
+ {
+ symmetric <- attr(depvar, "symmetric")
+ nodeSet <- attr(depvar, 'nodeSet')
+
+ rateEffects <- networkRateEffects(depvar, varname, symmetric=symmetric,
+ bipartite=FALSE)
+
+ if (symmetric)
+ {
+ objEffects <- createEffects("symmetricObjective", varname)
+ }
+ else
+ {
+ objEffects <- createEffects("nonSymmetricObjective", varname)
+ }
+ for (j in seq(along = xx$dycCovars))
+ {
+ if (attr(xx$dycCovars[[j]], 'nodeSet')[1] == nodeSet)
+ {
+ objEffects <- rbind(objEffects,
+ createEffects("dyadObjective",
+ names(xx$dycCovars)[j]))
+ }
+ }
+ for (j in seq(along = xx$dyvCovars))
+ {
+ if (attr(xx$dyvCovars[[j]], 'nodeSet')[1] == nodeSet)
+ {
+ objEffects <- rbind(objEffects,
+ createEffects("dyadObjective",
+ names(xx$dyvCovars)[j]))
+ }
+ }
+ for (j in seq(along = xx$cCovars))
+ {
+ if (attr(xx$cCovars[[j]], 'nodeSet') == nodeSet)
+ {
+ tmp <- covarOneModeEff(names(xx$cCovars)[j],
+ attr(xx$cCovars[[j]], 'poszvar'),
+ attr(xx$cCovars[[j]], 'moreThan2'),
+ symmetric)
+ objEffects <- rbind(objEffects, tmp$objEff)
+ rateEffects <- rbind(rateEffects, tmp$rateEff)
+ }
+ }
+ for (j in seq(along=xx$depvars))
+ {
+ if (types[j] == 'behavior' &&
+ attr(xx$depvars[[j]], 'nodeSet') == nodeSet)
+ {
+ tmp <- covarOneModeEff(names(xx$depvars)[j],
+ poszvar=TRUE,
+ attr(xx$depvars[[j]], 'moreThan2'),
+ symmetric)
+ objEffects <- rbind(objEffects, tmp$objEff)
+ rateEffects <- rbind(rateEffects, tmp$rateEff)
+ }
+ }
+ for (j in seq(along=xx$vCovars))
+ {
+ if (attr(xx$vCovars[[j]], 'nodeSet') == nodeSet)
+ {
+ tmp <- covarOneModeEff(names(xx$vCovars)[j],
+ attr(xx$vCovars[[j]], 'poszvar'),
+ attr(xx$vCovars[[j]], 'moreThan2'),
+ symmetric)
+ objEffects <- rbind(objEffects,tmp$objEff)
+ rateEffects<- rbind(rateEffects,tmp$rateEff)
+ }
+ }
+
+### not sure we need this: if so then check relevant combinations of nodesets
+ if (length(xx$cCovars) + length(xx$vCovars) +
+ length(xx$dycCovars) + length(xx$dyvCovars) +
+ length(types=='behavior') > 0)
+ {
+ interaction <- createEffects("unspecifiedNetInteraction")
+ objEffects <- rbind(objEffects, interaction[rep(1, nintn), ])
+ }
+
+ for (j in seq(along=xx$depvars))
+ {
+ otherName <- names(xx$depvars)[j]
+ if (types[j] == 'oneMode' &&
+ attr(xx$depvars[[j]], 'nodeSet') == nodeSet &&
+ varname != otherName)
+ {
+ if (attr(xx$depvars[[j]], "symmetric"))
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("nonSymmetricSymmetricObjective",
+ otherName))
+ }
+ else
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("nonSymmetricNonSymmetricObjective",
+ otherName))
+ }
+ }
+ if (types[j] == 'bipartite' &&
+ (attr(xx$depvars[[j]], 'nodeSet')[1] == nodeSet))
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("nonSymmetricBipartiteObjective",
+ otherName))
+ }
+ if (types[j] != "behavior" && varname != otherName)
+ {
+ for (k in seq(along=xx$cCovars))
+ {
+ if (attr(xx$cCovars[[k]], 'nodeSet') == nodeSet)
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("covarNetNetObjective",
+ otherName, names(xx$cCovars)[k]))
+ }
+ }
+ for (k in seq(along=xx$vCovars))
+ {
+ if (attr(xx$vCovars[[k]], 'nodeSet') == nodeSet)
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("covarNetNetObjective",
+ otherName, names(xx$vCovars)[k]))
+ }
+ }
+ for (k in seq(along=xx$depvars))
+ {
+ if (types[j] == 'behavior' &&
+ attr(xx$depvars[[j]], 'nodeSet') == nodeSet)
+ {
+ objEffects <-
+ rbind(objEffects,
+ createEffects("covarNetNetObjective",
+ otherName,
+ names(xx$depvars)[k]))
+ }
+ }
+
+ }
+ }
+ if ((nOneModes + nBipartites) > 1) ## add the network name
+ {
+ objEffects$functionName <- paste(varname, ': ',
+ objEffects$functionName, sep = '')
+ objEffects$effectName <- paste(varname, ': ',
+ objEffects$effectName, sep = '')
+ }
+ ## now create the real effects, extra rows for endowment effects etc
+ objEffects <- createObjEffectList(objEffects, varname)
+ rateEffects <- createRateEffectList(rateEffects, varname)
+
+ ## replace the text for endowment effects
+ tmp <- objEffects$functionName[objEffects$type =='endow']
+ tmp <- paste('Lost ties:', tmp)
+ objEffects$functionName[objEffects$type == 'endow'] <- tmp
+
+ ## get starting values
+ starts <- getNetworkStartingVals(depvar)
+
+ ##set defaults
+ rateEffects[1:noPeriods, "include"] <- TRUE
+ rateEffects[1:noPeriods, "initialValue"] <- starts$startRate
+ rateEffects$basicRate[1:observations] <- TRUE
+
+ objEffects$untrimmedValue <- rep(0, nrow(objEffects))
+ if (attr(depvar,'symmetric'))
+ {
+ objEffects[objEffects$effectName == "degree (density)" &
+ objEffects$type == "eval",
+ c('include', "initialValue", "untrimmedValue")] <-
+ list(TRUE, starts$degree, starts$untrimmed)
+ objEffects[objEffects$effectName=='transitive triads' &
+ objEffects$type=='eval','include'] <- TRUE
+ }
+ else
+ {
+ if (!(attr(depvar,'allUpOnly') || attr(depvar, 'allDownOnly')))
+ {
+ objEffects[objEffects$effectName =='outdegree (density)'&
+ objEffects$type == 'eval',
+ c('include', "initialValue", "untrimmedValue")] <-
+ list(TRUE, starts$degree, starts$untrimmed)
+ }
+ else
+ {
+ objEffects <-
+ objEffects[!objEffects$shortName == "density", ]
+ }
+ objEffects[objEffects$effectName == 'reciprocity'&
+ objEffects$type == 'eval','include'] <- TRUE
+ }
+ rateEffects$basicRate[1:observations] <- TRUE
+ list(effects=rbind(rateEffects = rateEffects, objEffects = objEffects),
+ starts=starts)
+ }
+
+ ##@behaviornet internal getEffects
+ behaviorNet <- function(depvar, varname)
+ {
+ nodeSet <- attr(depvar,'nodeSet')
+
+ rateEffects <- createEffects("behaviorRate", varname)
+ if (observations == 1)
+ {
+ rateEffects <- rateEffects[-2, ] ## remove the extra period
+ }
+ else
+ {
+ ## get correct number of rows
+ rateEffects <- rbind(duplicateDataFrameRow(rateEffects[2, ],
+ observations),
+ rateEffects[-c(1, 2), ])
+ }
+
+ objEffects <- createEffects("behaviorObjective", varname)
+
+ for (j in seq(along=xx$depvars))
+ {
+ if (types[j] == 'oneMode' &&
+ attr(xx$depvars[[j]], 'nodeSet') == nodeSet)
+ {
+ objEffects <- rbind(objEffects,
+ createEffects("behaviorOneModeObjective",
+ varname, names(xx$depvars)[j]))
+ rateEffects <- rbind(rateEffects,
+ createEffects("behaviorOneModeRate",
+ varname, names(xx$depvars)[j]))
+ }
+ if (types[j] == 'bipartite' &&
+ (attr(xx$depvars[[j]], 'nodeSet')[1] == nodeSet))
+ {
+ objEffects <- rbind(objEffects,
+ createEffects("behaviorBipartiteObjective",
+ varname, names(xx$depvars)[j]))
+ rateEffects <- rbind(rateEffects,
+ createEffects("behaviorBipartiteRate",
+ varname, names(xx$depvars)[j]))
+ }
+ }
+
+ for (j in seq(along = xx$cCovars))
+ {
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 26
More information about the Rsiena-commits
mailing list