[Rsiena-commits] r291 - in pkg/RSienaTest: . src src/data src/estimator/update/step src/model src/model/effects src/model/effects/generic src/model/ml src/model/tables src/model/variables src/network/iterators src/sim src/utils
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 3 20:08:25 CET 2016
Author: fschoenen
Date: 2016-02-03 20:08:24 +0100 (Wed, 03 Feb 2016)
New Revision: 291
Modified:
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/src/Makevars.in
pkg/RSienaTest/src/data/BehaviorLongitudinalData.h
pkg/RSienaTest/src/data/ChangingDyadicCovariate.cpp
pkg/RSienaTest/src/data/ChangingDyadicCovariate.h
pkg/RSienaTest/src/data/ConstantDyadicCovariate.cpp
pkg/RSienaTest/src/data/ConstantDyadicCovariate.h
pkg/RSienaTest/src/data/Covariate.cpp
pkg/RSienaTest/src/data/Data.cpp
pkg/RSienaTest/src/data/Data.h
pkg/RSienaTest/src/data/DyadicCovariateValueIterator.cpp
pkg/RSienaTest/src/data/DyadicCovariateValueIterator.h
pkg/RSienaTest/src/data/NetworkConstraint.cpp
pkg/RSienaTest/src/data/NetworkConstraint.h
pkg/RSienaTest/src/data/NetworkLongitudinalData.cpp
pkg/RSienaTest/src/data/NetworkLongitudinalData.h
pkg/RSienaTest/src/estimator/update/step/UpdateStep.cpp
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/Model.cpp
pkg/RSienaTest/src/model/Model.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/BalanceEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorEffect.h
pkg/RSienaTest/src/model/effects/CovariateAndNetworkBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateDependentBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateIndirectTiesEffect.cpp
pkg/RSienaTest/src/model/effects/DenseTriadsEffect.cpp
pkg/RSienaTest/src/model/effects/DiffusionRateEffect.cpp
pkg/RSienaTest/src/model/effects/DiffusionRateEffect.h
pkg/RSienaTest/src/model/effects/DistanceTwoEffect.cpp
pkg/RSienaTest/src/model/effects/DyadicCovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/FourCyclesEffect.cpp
pkg/RSienaTest/src/model/effects/InStructuralEquivalenceEffect.cpp
pkg/RSienaTest/src/model/effects/InverseOutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/InverseSquaredOutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/IsolateNetEffect.cpp
pkg/RSienaTest/src/model/effects/MixedNetworkEffect.h
pkg/RSienaTest/src/model/effects/NetworkDependentBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/NetworkEffect.h
pkg/RSienaTest/src/model/effects/RecipdegreeActivityEffect.cpp
pkg/RSienaTest/src/model/effects/RecipdegreePopularityEffect.cpp
pkg/RSienaTest/src/model/effects/StructuralRateEffect.cpp
pkg/RSienaTest/src/model/effects/TruncatedOutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/TwoNetworkDependentBehaviorEffect.cpp
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/CovariateDistance2AlterNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2NetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateMixedNetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateMixedNetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateNetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateNetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariatePredicate.h
pkg/RSienaTest/src/model/effects/generic/DoubleOutActFunction.cpp
pkg/RSienaTest/src/model/effects/generic/DoubleOutActFunction.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/EqualCovariatePredicate.cpp
pkg/RSienaTest/src/model/effects/generic/EqualCovariatePredicate.h
pkg/RSienaTest/src/model/effects/generic/GwespFunction.cpp
pkg/RSienaTest/src/model/effects/generic/GwespFunction.h
pkg/RSienaTest/src/model/effects/generic/HomCovariateMixedTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/HomCovariateMixedTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/InDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/InJaccardFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InJaccardFunction.h
pkg/RSienaTest/src/model/effects/generic/InStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InStarFunction.h
pkg/RSienaTest/src/model/effects/generic/InStarsTimesDegreesFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InStarsTimesDegreesFunction.h
pkg/RSienaTest/src/model/effects/generic/InTieFunction.cpp
pkg/RSienaTest/src/model/effects/generic/InTieFunction.h
pkg/RSienaTest/src/model/effects/generic/MissingCovariatePredicate.cpp
pkg/RSienaTest/src/model/effects/generic/MissingCovariatePredicate.h
pkg/RSienaTest/src/model/effects/generic/MixedInStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedInStarFunction.h
pkg/RSienaTest/src/model/effects/generic/MixedNetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedNetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/MixedOutStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedOutStarFunction.h
pkg/RSienaTest/src/model/effects/generic/MixedThreeCyclesFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedThreeCyclesFunction.h
pkg/RSienaTest/src/model/effects/generic/MixedTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/NetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/NetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/OneModeNetworkAlterFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OneModeNetworkAlterFunction.h
pkg/RSienaTest/src/model/effects/generic/OutActDistance2Function.cpp
pkg/RSienaTest/src/model/effects/generic/OutActDistance2Function.h
pkg/RSienaTest/src/model/effects/generic/OutDegreeFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutDegreeFunction.h
pkg/RSienaTest/src/model/effects/generic/OutJaccardFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutJaccardFunction.h
pkg/RSienaTest/src/model/effects/generic/OutStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutStarFunction.h
pkg/RSienaTest/src/model/effects/generic/OutTieFunction.cpp
pkg/RSienaTest/src/model/effects/generic/OutTieFunction.h
pkg/RSienaTest/src/model/effects/generic/ReciprocatedTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/ReciprocatedTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/ReverseTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/ReverseTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/SameCovariateInTiesFunction.cpp
pkg/RSienaTest/src/model/effects/generic/SameCovariateInTiesFunction.h
pkg/RSienaTest/src/model/effects/generic/SameCovariateMixedTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/SameCovariateMixedTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/SameCovariateTwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/SameCovariateTwoPathFunction.h
pkg/RSienaTest/src/model/effects/generic/TwoPathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/TwoPathFunction.h
pkg/RSienaTest/src/model/ml/Chain.cpp
pkg/RSienaTest/src/model/ml/Chain.h
pkg/RSienaTest/src/model/ml/MLSimulation.cpp
pkg/RSienaTest/src/model/ml/MLSimulation.h
pkg/RSienaTest/src/model/ml/MiniStep.cpp
pkg/RSienaTest/src/model/ml/MiniStep.h
pkg/RSienaTest/src/model/tables/Cache.cpp
pkg/RSienaTest/src/model/tables/Cache.h
pkg/RSienaTest/src/model/variables/BehaviorVariable.cpp
pkg/RSienaTest/src/model/variables/DependentVariable.cpp
pkg/RSienaTest/src/model/variables/DependentVariable.h
pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
pkg/RSienaTest/src/model/variables/NetworkVariable.h
pkg/RSienaTest/src/network/iterators/GeneralTieIterator.cpp
pkg/RSienaTest/src/network/iterators/GeneralTieIterator.h
pkg/RSienaTest/src/network/iterators/UnionTieIterator.h
pkg/RSienaTest/src/siena07internals.cpp
pkg/RSienaTest/src/siena07internals.h
pkg/RSienaTest/src/siena07utilities.h
pkg/RSienaTest/src/sim/MetropolisHastingsSimulation.h
pkg/RSienaTest/src/sim/Simulation.h
pkg/RSienaTest/src/sim/StatisticsSimulation.h
pkg/RSienaTest/src/utils/NamedObject.h
pkg/RSienaTest/src/utils/Random.h
Log:
include order; removed `using namespace`
Modified: pkg/RSienaTest/ChangeLog
===================================================================
--- pkg/RSienaTest/ChangeLog 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/ChangeLog 2016-02-03 19:08:24 UTC (rev 291)
@@ -1,3 +1,8 @@
+2016-02-03 R-Forge Revision 291
+Changes in RSienaTest:
+ * Fixed include order.
+ * Removed `using namespace` from all headers.
+
2016-01-31 R-Forge Revision 290
Changes in RSiena and RSienaTest:
* New effects FBDeg, FRDeg, BRDeg (RFDeg was mentioned earlier
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/DESCRIPTION 2016-02-03 19:08:24 UTC (rev 291)
@@ -1,8 +1,8 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-290
-Date: 2016-01-31
+Version: 1.1-291
+Date: 2016-02-03
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger
Depends: R (>= 2.15.0), utils
Imports: Matrix, tcltk, lattice, parallel, MASS, RUnit
Modified: pkg/RSienaTest/src/Makevars.in
===================================================================
--- pkg/RSienaTest/src/Makevars.in 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/Makevars.in 2016-02-03 19:08:24 UTC (rev 291)
@@ -14,287 +14,10 @@
OBJECTS = $(SOURCES:.cpp=.o)
-# the following works but is GNU make (check --as-cran warning), and depends
-# on find
-# SOURCES = $(shell find ...) or $(wildcard *.cpp)
-SOURCES = $(shell find model estimator network logger Eigen sim utils data -name '*.cpp') $(shell find -maxdepth 1 -name '*.cpp')
+# The following works but is GNU make (check --as-cran warning), and depends on find.
+SOURCES = $(wildcard *.cpp) \
+ $(shell find model estimator network logger Eigen sim utils data -name '*.cpp')
-# :r !find src -name '*.cpp' | sed -n 's/$/ \\/;s/^src\//\t/p'
-
-# SOURCES = \
-# model/ml/BehaviorChange.cpp \
-# model/ml/Chain.cpp \
-# model/ml/NetworkChange.cpp \
-# model/ml/MiniStep.cpp \
-# model/ml/Option.cpp \
-# model/ml/MLSimulation.cpp \
-# model/variables/DiffusionEffectValueTable.cpp \
-# model/variables/EffectValueTable.cpp \
-# model/variables/BehaviorVariable.cpp \
-# model/variables/NetworkVariable.cpp \
-# model/variables/DependentVariable.cpp \
-# model/EpochSimulation.cpp \
-# model/effects/OutOutDegreeAssortativityEffect.cpp \
-# model/effects/ReciprocatedSimilarityEffect.cpp \
-# model/effects/AverageInAlterEffect.cpp \
-# model/effects/NetworkEffect.cpp \
-# model/effects/EffectFactory.cpp \
-# model/effects/DyadicCovariateDependentNetworkEffect.cpp \
-# model/effects/InteractionCovariateEffect.cpp \
-# model/effects/ReciprocalDegreeBehaviorEffect.cpp \
-# model/effects/OutdegreeActivityEffect.cpp \
-# model/effects/TransitiveTriadsEffect.cpp \
-# model/effects/RecipdegreePopularityEffect.cpp \
-# model/effects/SimilarityEffect.cpp \
-# model/effects/IsolateNetEffect.cpp \
-# model/effects/DenseTriadsBehaviorEffect.cpp \
-# model/effects/AverageAlterInDist2Effect.cpp \
-# model/effects/AverageAlterEffect.cpp \
-# model/effects/TruncatedOutdegreeEffect.cpp \
-# model/effects/OutdegreeActivitySqrtEffect.cpp \
-# model/effects/LinearShapeEffect.cpp \
-# model/effects/Effect.cpp \
-# model/effects/InStructuralEquivalenceEffect.cpp \
-# model/effects/IsolateEffect.cpp \
-# model/effects/HomCovariateActivityEffect.cpp \
-# model/effects/NetworkDependentBehaviorEffect.cpp \
-# model/effects/BetweennessEffect.cpp \
-# model/effects/CovariateIndirectTiesEffect.cpp \
-# model/effects/QuadraticShapeEffect.cpp \
-# model/effects/SameCovariateActivityEffect.cpp \
-# model/effects/IndegreeEffect.cpp \
-# model/effects/AltersInDist2CovariateAverageEffect.cpp \
-# model/effects/AverageAlterDist2Effect.cpp \
-# model/effects/PopularityAlterEffect.cpp \
-# model/effects/WXXClosureEffect.cpp \
-# model/effects/AltersCovariateAvSimEffect.cpp \
-# model/effects/XWXClosureEffect.cpp \
-# model/effects/IndegreePopularityEffect.cpp \
-# model/effects/AltersCovariateAvAltEffect.cpp \
-# model/effects/InverseSquaredOutdegreeEffect.cpp \
-# model/effects/InverseOutdegreeEffect.cpp \
-# model/effects/CovariateAndNetworkBehaviorEffect.cpp \
-# model/effects/CovariateAlterEffect.cpp \
-# model/effects/SimilarityTransitiveTripletsEffect.cpp \
-# model/effects/SameCovariateTransitiveTripletsEffect.cpp \
-# model/effects/AlterCovariateActivityEffect.cpp \
-# model/effects/IndegreeActivityEffect.cpp \
-# model/effects/HomCovariateTransitiveTripletsEffect.cpp \
-# model/effects/HigherCovariateEffect.cpp \
-# model/effects/SameCovariateEffect.cpp \
-# model/effects/AltersDist2CovariateAverageEffect.cpp \
-# model/effects/DistanceTwoEffect.cpp \
-# model/effects/DoubleInPopEffect.cpp \
-# model/effects/DoubleRecDegreeBehaviorEffect.cpp \
-# model/effects/OutdegreePopularityEffect.cpp \
-# model/effects/generic/ProductFunction.cpp \
-# model/effects/generic/InTieFunction.cpp \
-# model/effects/generic/EqualCovariatePredicate.cpp \
-# model/effects/generic/HomCovariateMixedTwoPathFunction.cpp \
-# model/effects/generic/CovariateDistance2SimilarityNetworkFunction.cpp \
-# model/effects/generic/SameCovariateTwoPathFunction.cpp \
-# model/effects/generic/OutStarFunction.cpp \
-# model/effects/generic/InDegreeFunction.cpp \
-# model/effects/generic/EgoInDegreeFunction.cpp \
-# model/effects/generic/OutTieFunction.cpp \
-# model/effects/generic/CovariateDistance2InAlterNetworkFunction.cpp \
-# model/effects/generic/DifferenceFunction.cpp \
-# model/effects/generic/MixedOutStarFunction.cpp \
-# model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.cpp \
-# model/effects/generic/CovariateMixedNetworkAlterFunction.cpp \
-# model/effects/generic/InJaccardFunction.cpp \
-# model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp \
-# model/effects/generic/OutActDistance2Function.cpp \
-# model/effects/generic/TwoPathFunction.cpp \
-# model/effects/generic/GenericNetworkEffect.cpp \
-# model/effects/generic/MissingCovariatePredicate.cpp \
-# model/effects/generic/CovariatePredicate.cpp \
-# model/effects/generic/IntAlterFunction.cpp \
-# model/effects/generic/SameCovariateInTiesFunction.cpp \
-# model/effects/generic/BetweennessFunction.cpp \
-# model/effects/generic/EgoOutDegreeFunction.cpp \
-# model/effects/generic/OutJaccardFunction.cpp \
-# model/effects/generic/SumFunction.cpp \
-# model/effects/generic/ReciprocatedTwoPathFunction.cpp \
-# model/effects/generic/ConditionalFunction.cpp \
-# model/effects/generic/MixedThreeCyclesFunction.cpp \
-# model/effects/generic/CovariateDistance2NetworkFunction.cpp \
-# model/effects/generic/AlterFunction.cpp \
-# model/effects/generic/IntSqrtFunction.cpp \
-# model/effects/generic/MixedNetworkAlterFunction.cpp \
-# model/effects/generic/MixedInStarFunction.cpp \
-# model/effects/generic/OutDegreeFunction.cpp \
-# model/effects/generic/SameCovariateMixedTwoPathFunction.cpp \
-# model/effects/generic/InStarsTimesDegreesFunction.cpp \
-# model/effects/generic/ConstantFunction.cpp \
-# model/effects/generic/MixedTwoPathFunction.cpp \
-# model/effects/generic/ReverseTwoPathFunction.cpp \
-# model/effects/generic/AlterPredicate.cpp \
-# model/effects/generic/CovariateNetworkAlterFunction.cpp \
-# model/effects/generic/GwespFunction.cpp \
-# model/effects/generic/NetworkAlterFunction.cpp \
-# model/effects/generic/DoubleOutActFunction.cpp \
-# model/effects/generic/OneModeNetworkAlterFunction.cpp \
-# model/effects/generic/InStarFunction.cpp \
-# model/effects/TransitiveMediatedTripletsEffect.cpp \
-# model/effects/TransitiveTiesEffect.cpp \
-# model/effects/ReciprocityEffect.cpp \
-# model/effects/MaxAlterEffect.cpp \
-# model/effects/DenseTriadsSimilarityEffect.cpp \
-# model/effects/RecipdegreeActivityEffect.cpp \
-# model/effects/TransitiveTripletsEffect.cpp \
-# model/effects/OutdegreeEffect.cpp \
-# model/effects/CovariateDependentNetworkEffect.cpp \
-# model/effects/WWXClosureEffect.cpp \
-# model/effects/CovariateDependentBehaviorEffect.cpp \
-# model/effects/OutInDegreeAssortativityEffect.cpp \
-# model/effects/DyadicCovariateReciprocityEffect.cpp \
-# model/effects/AntiIsolateEffect.cpp \
-# model/effects/NetworkInteractionEffect.cpp \
-# model/effects/InInDegreeAssortativityEffect.cpp \
-# model/effects/AltersCovariateAverageEffect.cpp \
-# model/effects/DyadicCovariateMainEffect.cpp \
-# model/effects/CovariateSimmelianAlterEffect.cpp \
-# model/effects/FourCyclesEffect.cpp \
-# model/effects/CovariateEgoAlterEffect.cpp \
-# model/effects/InIsolateDegreeEffect.cpp \
-# model/effects/ThreeCyclesEffect.cpp \
-# model/effects/TwoNetworkDependentBehaviorEffect.cpp \
-# model/effects/BalanceEffect.cpp \
-# model/effects/CovariateEgoEffect.cpp \
-# model/effects/DenseTriadsEffect.cpp \
-# model/effects/JumpCovariateTransitiveTripletsEffect.cpp \
-# model/effects/AverageReciprocatedAlterEffect.cpp \
-# model/effects/DoubleDegreeBehaviorEffect.cpp \
-# model/effects/StructuralRateEffect.cpp \
-# model/effects/BehaviorInteractionEffect.cpp \
-# model/effects/TransitiveReciprocatedTriplets2Effect.cpp \
-# model/effects/CovariateSimilarityEffect.cpp \
-# model/effects/InAltersCovariateAverageEffect.cpp \
-# model/effects/BehaviorEffect.cpp \
-# model/effects/MixedNetworkEffect.cpp \
-# model/effects/TransitiveReciprocatedTripletsEffect.cpp \
-# model/effects/DiffusionRateEffect.cpp \
-# model/effects/IsolatePopEffect.cpp \
-# model/effects/DensityEffect.cpp \
-# model/effects/InOutDegreeAssortativityEffect.cpp \
-# model/effects/DoubleOutActEffect.cpp \
-# model/effects/MainCovariateEffect.cpp \
-# model/effects/AltersCovariateTotSimEffect.cpp \
-# model/EffectInfo.cpp \
-# model/State.cpp \
-# model/filters/PermittedChangeFilter.cpp \
-# model/filters/LowerFilter.cpp \
-# model/filters/DisjointFilter.cpp \
-# model/filters/NetworkDependentFilter.cpp \
-# model/filters/HigherFilter.cpp \
-# model/filters/AtLeastOneFilter.cpp \
-# model/Function.cpp \
-# model/Model.cpp \
-# model/StatisticCalculator.cpp \
-# model/tables/EgocentricConfigurationTable.cpp \
-# model/tables/NetworkCache.cpp \
-# model/tables/ConfigurationTable.cpp \
-# model/tables/MixedConfigurationTable.cpp \
-# model/tables/Cache.cpp \
-# model/tables/BetweennessTable.cpp \
-# model/tables/TwoPathTable.cpp \
-# model/tables/TwoNetworkCache.cpp \
-# model/tables/CriticalInStarTable.cpp \
-# model/tables/MixedTwoPathTable.cpp \
-# model/tables/MixedEgocentricConfigurationTable.cpp \
-# model/SimulationActorSet.cpp \
-# model/settings/PrimarySetting.cpp \
-# model/settings/Setting.cpp \
-# model/settings/MeetingSetting.cpp \
-# model/settings/SettingsFactory.cpp \
-# model/settings/GeneralSetting.cpp \
-# model/settings/ComposableSetting.cpp \
-# model/settings/DyadicSetting.cpp \
-# model/settings/UniversalSetting.cpp \
-# model/settings/SettingInfo.cpp \
-# estimator/components/TimesCollector.cpp \
-# estimator/components/StatisticCollector.cpp \
-# estimator/components/ScoreCollector.cpp \
-# estimator/components/NSimCollector.cpp \
-# estimator/components/ParameterSum.cpp \
-# estimator/listener/EstimatorListener.cpp \
-# estimator/update/autocorrelation/MinMaxACStopCondition.cpp \
-# estimator/update/autocorrelation/AutoCorrelator.cpp \
-# estimator/update/autocorrelation/MaxACStopCondition.cpp \
-# estimator/update/step/GMMDiagonalStep.cpp \
-# estimator/update/step/normalization/StepNormalization.cpp \
-# estimator/update/step/normalization/SDStepNormalization.cpp \
-# estimator/update/step/GMMFullStep.cpp \
-# estimator/update/step/UpdateStep.cpp \
-# estimator/update/StopCondition.cpp \
-# estimator/update/UpdateController.cpp \
-# estimator/Controller.cpp \
-# estimator/GMMEstimator.cpp \
-# estimator/derivative/FiniteDifference.cpp \
-# estimator/derivative/Differentiation.cpp \
-# estimator/derivative/DifferentiationController.cpp \
-# estimator/derivative/ScoreDeviation.cpp \
-# estimator/derivative/MLDifferentiation.cpp \
-# estimator/test/StaticController.cpp \
-# estimator/SienaFit.cpp \
-# siena07models.cpp \
-# network/NetworkUtils.cpp \
-# network/CommonNeighborIterator.cpp \
-# network/layers/DistanceTwoLayer.cpp \
-# network/Network.cpp \
-# network/iterators/SingleIterator.cpp \
-# network/iterators/UnionTieIterator.cpp \
-# network/iterators/FilteredIterator.cpp \
-# network/iterators/IntVecIterator.cpp \
-# network/iterators/IntDoubleMapIterator.cpp \
-# network/Simmelian.cpp \
-# network/OneModeNetwork.cpp \
-# network/IncidentTieIterator.cpp \
-# network/TieIterator.cpp \
-# logger/Priority.cpp \
-# logger/formatter/MPIAwareFormatter.cpp \
-# logger/LogEntry.cpp \
-# logger/appender/FileAppender.cpp \
-# logger/appender/AppenderPool.cpp \
-# siena07internals.cpp \
-# siena07utilities.cpp \
-# Eigen/RLegacy.cpp \
-# RUtil.cpp \
-# sim/Simulation.cpp \
-# sim/modificator/ResultModificator.cpp \
-# sim/modificator/MeanStatisticsCalculator.cpp \
-# sim/modificator/DolbyModificator.cpp \
-# sim/listener/ResultListener.cpp \
-# sim/listener/Result.cpp \
-# sim/mpi/MPICommunicator.cpp \
-# sim/mpi/MPIStatisticsSimulation.cpp \
-# sim/StatisticsSimulation.cpp \
-# sim/MetropolisHastingsSimulation.cpp \
-# siena07setup.cpp \
-# utils/debugging/StopWatch.cpp \
-# utils/debugging/ApproxSize.cpp \
-# utils/Utils.cpp \
-# utils/NamedObject.cpp \
-# utils/Random.cpp \
-# utils/SqrtTable.cpp \
-# data/ChangingDyadicCovariate.cpp \
-# data/ConstantDyadicCovariate.cpp \
-# data/OneModeNetworkLongitudinalData.cpp \
-# data/DyadicCovariateValueIterator.cpp \
-# data/LongitudinalData.cpp \
-# data/NetworkLongitudinalData.cpp \
-# data/ExogenousEvent.cpp \
-# data/Covariate.cpp \
-# data/DyadicCovariate.cpp \
-# data/BehaviorLongitudinalData.cpp \
-# data/ChangingCovariate.cpp \
-# data/Data.cpp \
-# data/NetworkConstraint.cpp \
-# data/ActorSet.cpp \
-# data/ConstantCovariate.cpp \
-# RInterface.cpp
-
PKG_CPPFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -I. $(RNGSTREAMS_CPP) $(EIGEN_CPP) @PKG_CPPFLAGS@
# -UNDEBUG -DR_LEGACY -DPROFILER
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(ARCHLIB) @PKG_LIBS@
Modified: pkg/RSienaTest/src/data/BehaviorLongitudinalData.h
===================================================================
--- pkg/RSienaTest/src/data/BehaviorLongitudinalData.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/BehaviorLongitudinalData.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -91,7 +91,7 @@
// lobservedDistributions[observation][value] stores the frequency of
// the given value at the given observation.
- map<int, double> * lobservedDistributions;
+ std::map<int, double> * lobservedDistributions;
};
}
Modified: pkg/RSienaTest/src/data/ChangingDyadicCovariate.cpp
===================================================================
--- pkg/RSienaTest/src/data/ChangingDyadicCovariate.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/ChangingDyadicCovariate.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -14,6 +14,8 @@
#include "data/ActorSet.h"
#include "data/DyadicCovariateValueIterator.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/ChangingDyadicCovariate.h
===================================================================
--- pkg/RSienaTest/src/data/ChangingDyadicCovariate.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/ChangingDyadicCovariate.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -16,8 +16,6 @@
#include <set>
#include "DyadicCovariate.h"
-using namespace std;
-
namespace siena
{
@@ -52,38 +50,38 @@
bool excludeMissings) const;
DyadicCovariateValueIterator columnValues(int j, int observation,
bool excludeMissings) const;
- const map <int, double> & rRowValues(int i, int observation) const;
+ const std::map <int, double> & rRowValues(int i, int observation) const;
private:
// A row based representation of non-zero values of the covariate.
// The value at observation k for a pair (i,j) is stored in
// lpRowValues[k][i][j].
- map<int, double> ** lpRowValues;
+ std::map<int, double> ** lpRowValues;
// A column based representation of non-zero values of the covariate.
// The value at observation k for a pair (i,j) is stored in
// lpColumnValues[k][j][i].
- map<int, double> ** lpColumnValues;
+ std::map<int, double> ** lpColumnValues;
// A row based representation of missing values. Actor j belongs to
// lpRowMissings[k][i] if and only if the covariate value for the pair
// (i,j) is missing at observation k.
- set<int> ** lpRowMissings;
+ std::set<int> ** lpRowMissings;
// A column based representation of missing values. Actor i belongs to
// lpColumnMissings[k][j] if and only if the covariate value for the pair
// (i,j) is missing at observation k.
- set<int> ** lpColumnMissings;
+ std::set<int> ** lpColumnMissings;
// The number of observations
int lobservationCount;
// empty set
- set <int> * lpEmptySet;
+ std::set<int> * lpEmptySet;
};
}
Modified: pkg/RSienaTest/src/data/ConstantDyadicCovariate.cpp
===================================================================
--- pkg/RSienaTest/src/data/ConstantDyadicCovariate.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/ConstantDyadicCovariate.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -13,6 +13,8 @@
#include "data/ActorSet.h"
#include "data/DyadicCovariateValueIterator.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/ConstantDyadicCovariate.h
===================================================================
--- pkg/RSienaTest/src/data/ConstantDyadicCovariate.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/ConstantDyadicCovariate.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -16,8 +16,6 @@
#include <set>
#include "DyadicCovariate.h"
-using namespace std;
-
namespace siena
{
@@ -49,30 +47,26 @@
void missing(int i, int j, bool flag);
DyadicCovariateValueIterator rowValues(int i) const;
DyadicCovariateValueIterator columnValues(int j) const;
- const map <int, double> & rRowValues(int i) const;
+ const std::map<int, double> & rRowValues(int i) const;
private:
// A row based representation of non-zero values of the covariate.
// The value for a pair (i,j) is stored in lpRowValues[i][j].
+ std::map<int, double> * lpRowValues;
- map<int, double> * lpRowValues;
-
// A column based representation of non-zero values of the covariate.
// The value for a pair (i,j) is stored in lpColumnValues[j][i].
+ std::map<int, double> * lpColumnValues;
- map<int, double> * lpColumnValues;
-
// A row based representation of missing values. Actor j belongs to
// lpRowMissings[i] if and only if the covariate value for the pair
// (i,j) is missing.
+ std::set<int> * lpRowMissings;
- set<int> * lpRowMissings;
-
// A column based representation of missing values. Actor i belongs to
// lpColumnMissings[j] if and only if the covariate value for the pair
// (i,j) is missing.
-
- set<int> * lpColumnMissings;
+ std::set<int> * lpColumnMissings;
};
}
Modified: pkg/RSienaTest/src/data/Covariate.cpp
===================================================================
--- pkg/RSienaTest/src/data/Covariate.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/Covariate.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -9,9 +9,10 @@
* Covariate class.
*****************************************************************************/
+#include "Covariate.h"
#include <cmath>
-#include "Covariate.h"
+using namespace std;
namespace siena
{
Modified: pkg/RSienaTest/src/data/Data.cpp
===================================================================
--- pkg/RSienaTest/src/data/Data.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/Data.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -21,6 +21,8 @@
#include "data/ChangingDyadicCovariate.h"
#include "data/ExogenousEvent.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/Data.h
===================================================================
--- pkg/RSienaTest/src/data/Data.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/Data.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -17,8 +17,6 @@
#include <string>
#include "data/NetworkConstraint.h"
-using namespace std;
-
namespace siena
{
@@ -131,10 +129,10 @@
// Network constraints
- const NetworkConstraint * addNetworkConstraint(string networkName1,
- string networkName2,
+ const NetworkConstraint * addNetworkConstraint(std::string networkName1,
+ std::string networkName2,
NetworkConstraintType type);
- const vector<const NetworkConstraint *> & rNetworkConstraints() const;
+ const std::vector<const NetworkConstraint *> & rNetworkConstraints() const;
private:
// The number of observations
@@ -171,7 +169,7 @@
// Network constraints like higher(network1,network2),
// disjoint(network1,network2), etc.
- vector<const NetworkConstraint *> lnetworkConstraints;
+ std::vector<const NetworkConstraint *> lnetworkConstraints;
};
Modified: pkg/RSienaTest/src/data/DyadicCovariateValueIterator.cpp
===================================================================
--- pkg/RSienaTest/src/data/DyadicCovariateValueIterator.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/DyadicCovariateValueIterator.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -12,6 +12,8 @@
#include "DyadicCovariateValueIterator.h"
#include "utils/Utils.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/DyadicCovariateValueIterator.h
===================================================================
--- pkg/RSienaTest/src/data/DyadicCovariateValueIterator.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/DyadicCovariateValueIterator.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -15,8 +15,6 @@
#include <map>
#include <set>
-using namespace std;
-
namespace siena
{
@@ -38,21 +36,21 @@
void next();
private:
- DyadicCovariateValueIterator(map<int, double> & rValues,
- set<int> & rMissings);
+ DyadicCovariateValueIterator(std::map<int, double> & rValues,
+ std::set<int> & rMissings);
void skipMissings();
// Points to the current element in the map of values
- map<int, double>::const_iterator lcurrent;
+ std::map<int, double>::const_iterator lcurrent;
// Points to the end of the map of values
- map<int, double>::const_iterator lend;
+ std::map<int, double>::const_iterator lend;
// Points to the current element in the set of missing values
- set<int>::const_iterator lmissingCurrent;
+ std::set<int>::const_iterator lmissingCurrent;
// Points to the end of the set of missing values
- set<int>::const_iterator lmissingEnd;
+ std::set<int>::const_iterator lmissingEnd;
};
}
Modified: pkg/RSienaTest/src/data/NetworkConstraint.cpp
===================================================================
--- pkg/RSienaTest/src/data/NetworkConstraint.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/NetworkConstraint.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -11,6 +11,8 @@
#include "NetworkConstraint.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/NetworkConstraint.h
===================================================================
--- pkg/RSienaTest/src/data/NetworkConstraint.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/NetworkConstraint.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -14,8 +14,6 @@
#include <string>
-using namespace std;
-
namespace siena
{
@@ -40,20 +38,20 @@
class NetworkConstraint
{
public:
- NetworkConstraint(string networkName1,
- string networkName2,
+ NetworkConstraint(std::string networkName1,
+ std::string networkName2,
NetworkConstraintType type);
- inline string networkName1() const;
- inline string networkName2() const;
+ inline std::string networkName1() const;
+ inline std::string networkName2() const;
inline NetworkConstraintType type() const;
private:
// The name of the first network involved in this constraint
- string lnetworkName1;
+ std::string lnetworkName1;
// The name of the second network involved in this constraint
- string lnetworkName2;
+ std::string lnetworkName2;
// The type of the constraint
NetworkConstraintType ltype;
@@ -67,7 +65,7 @@
/**
* Returns the name of the first network variable involved in this constraint.
*/
-string NetworkConstraint::networkName1() const
+std::string NetworkConstraint::networkName1() const
{
return this->lnetworkName1;
}
@@ -76,7 +74,7 @@
/**
* Returns the name of the second network variable involved in this constraint.
*/
-string NetworkConstraint::networkName2() const
+std::string NetworkConstraint::networkName2() const
{
return this->lnetworkName2;
}
Modified: pkg/RSienaTest/src/data/NetworkLongitudinalData.cpp
===================================================================
--- pkg/RSienaTest/src/data/NetworkLongitudinalData.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/NetworkLongitudinalData.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -17,6 +17,8 @@
#include "network/IncidentTieIterator.h"
#include "data/ActorSet.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/data/NetworkLongitudinalData.h
===================================================================
--- pkg/RSienaTest/src/data/NetworkLongitudinalData.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/data/NetworkLongitudinalData.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -80,8 +80,8 @@
bool oneModeNetwork() const;
const std::vector<SettingInfo> & rSettingNames() const;
- void addSettingName(const string id, const string settingType,
- const string covarName, const Permission_Type permType);
+ void addSettingName(const std::string id, const std::string settingType,
+ const std::string covarName, const Permission_Type permType);
private:
// The set of actors receiving the ties of the network
@@ -130,7 +130,7 @@
bool loneMode;
// vector of setting names for this network
- vector<SettingInfo> lsettingNames;
+ std::vector<SettingInfo> lsettingNames;
};
}
Modified: pkg/RSienaTest/src/estimator/update/step/UpdateStep.cpp
===================================================================
--- pkg/RSienaTest/src/estimator/update/step/UpdateStep.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/estimator/update/step/UpdateStep.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -9,6 +9,7 @@
#include "UpdateStep.h"
+using namespace std;
using namespace Eigen;
namespace siena {
Modified: pkg/RSienaTest/src/model/EffectInfo.cpp
===================================================================
--- pkg/RSienaTest/src/model/EffectInfo.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/model/EffectInfo.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -11,6 +11,8 @@
#include "EffectInfo.h"
+using namespace std;
+
namespace siena
{
Modified: pkg/RSienaTest/src/model/EffectInfo.h
===================================================================
--- pkg/RSienaTest/src/model/EffectInfo.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/model/EffectInfo.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -14,8 +14,6 @@
#include <string>
-using namespace std;
-
namespace siena
{
@@ -26,17 +24,17 @@
class EffectInfo
{
public:
- EffectInfo(string variableName,
- string effectName,
- string effectType,
+ EffectInfo(std::string variableName,
+ std::string effectName,
+ std::string effectType,
double parameter,
double internalEffectParameter,
- string interactionName1,
- string interactionName2,
- string rateType);
- EffectInfo(string variableName,
- string effectName,
- string effectType,
+ std::string interactionName1,
+ std::string interactionName2,
+ std::string rateType);
+ EffectInfo(std::string variableName,
+ std::string effectName,
+ std::string effectType,
double parameter,
const EffectInfo * pEffect1,
const EffectInfo * pEffect2,
@@ -44,29 +42,29 @@
void parameter(double value);
- string variableName() const;
- string effectName() const;
- string effectType() const;
+ std::string variableName() const;
+ std::string effectName() const;
+ std::string effectType() const;
double parameter() const;
double internalEffectParameter() const;
- string interactionName1() const;
- string interactionName2() const;
- string rateType() const;
+ std::string interactionName1() const;
+ std::string interactionName2() const;
+ std::string rateType() const;
const EffectInfo * pEffectInfo1() const;
const EffectInfo * pEffectInfo2() const;
const EffectInfo * pEffectInfo3() const;
private:
// The name of the variable this effect is associated with
- string lvariableName;
+ std::string lvariableName;
// A short name of the effect used to identify the semantics
// of this effect
- string leffectName;
+ std::string leffectName;
// The type of the effect ("rate", "eval", or "endow")
- string leffectType;
+ std::string leffectType;
// The multiplicative weight in the respective function
double lparameter;
@@ -77,15 +75,15 @@
// The name of a variable or covariate this effect is interacting with,
// if applicable
- string linteractionName1;
+ std::string linteractionName1;
// The name of the other interaction variable or covariate, if the
// effect has two such interactions
- string linteractionName2;
+ std::string linteractionName2;
// Distinguishes between structural rate effects and covariate rate effects
- string lrateType;
+ std::string lrateType;
// The interacting effect descriptions.
// Undefined for non-interaction effects.
Modified: pkg/RSienaTest/src/model/EpochSimulation.cpp
===================================================================
--- pkg/RSienaTest/src/model/EpochSimulation.cpp 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/model/EpochSimulation.cpp 2016-02-03 19:08:24 UTC (rev 291)
@@ -41,9 +41,11 @@
#include "model/ml/Chain.h"
#include "model/ml/MiniStep.h"
+using namespace std;
using namespace siena::logger;
namespace siena {
+
SEXP getMiniStepList(const MiniStep& miniStep, int period);
SEXP getMiniStepDF(const MiniStep& miniStep);
Modified: pkg/RSienaTest/src/model/EpochSimulation.h
===================================================================
--- pkg/RSienaTest/src/model/EpochSimulation.h 2016-02-01 16:56:52 UTC (rev 290)
+++ pkg/RSienaTest/src/model/EpochSimulation.h 2016-02-03 19:08:24 UTC (rev 291)
@@ -17,8 +17,6 @@
#include <string>
#include "data/Data.h"
-using namespace std;
-
namespace siena
{
@@ -48,117 +46,116 @@
class EpochSimulation
{
public:
- EpochSimulation(Data * pData, Model * pModel);
- virtual ~EpochSimulation();
+ EpochSimulation(Data * pData, Model * pModel);
+ virtual ~EpochSimulation();
- void initialize(int period);
+ void initialize(int period);
- // Method of moments related
- void runEpoch(int period);
+ // Method of moments related
+ void runEpoch(int period);
- // Accessors
+ // Accessors
+ const Data * pData() const;
+ const Model * pModel() const;
+ const DependentVariable * pVariable(std::string name) const;
+ const std::vector<DependentVariable *> & rVariables() const;
+ const SimulationActorSet * pSimulationActorSet(
+ const ActorSet * pOriginalActorSet) const;
+ int period() const;
+ double time() const;
+ Cache * pCache() const;
- const Data * pData() const;
- const Model * pModel() const;
- const DependentVariable * pVariable(string name) const;
- const vector<DependentVariable *> & rVariables() const;
- const SimulationActorSet * pSimulationActorSet(
- const ActorSet * pOriginalActorSet) const;
- int period() const;
- double time() const;
- Cache * pCache() const;
+ // Scores
- // Scores
-
- double score(const EffectInfo * pEffect) const;
- void score(const EffectInfo * pEffect, double value);
- map<const EffectInfo *, double>
+ double score(const EffectInfo * pEffect) const;
+ void score(const EffectInfo * pEffect, double value);
+ std::map<const EffectInfo *, double>
derivative(const EffectInfo * pEffect1) const;
double derivative(const EffectInfo * pEffect1,
- const EffectInfo * pEffect2) const;
+ const EffectInfo * pEffect2) const;
void derivative(const EffectInfo * pEffect1, const EffectInfo * pEffect2,
- double value);
+ double value);
Chain * pChain();
void pChain(Chain * pChain);
void clearChain();
void updateParameters(int period);
- double calculateLikelihood() const;
+ double calculateLikelihood() const;
void simpleRates(bool flag);
bool simpleRates() const;
double lnFactorial(int a) const;
protected:
- void calculateRates();
- double totalRate() const;
- DependentVariable * chooseVariable() const;
- int chooseActor(const DependentVariable * pVariable) const;
+ void calculateRates();
+ double totalRate() const;
+ DependentVariable * chooseVariable() const;
+ int chooseActor(const DependentVariable * pVariable) const;
- // A vector of dependent variables with their current values
- vector<DependentVariable *> lvariables;
+ // A vector of dependent variables with their current values
+ std::vector<DependentVariable *> lvariables;
private:
- void runStep();
- void drawTimeIncrement();
- bool reachedCompositionChange() const;
- void makeNextCompositionChange();
+ void runStep();
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 291
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