[Rsiena-commits] r295 - in pkg/RSienaTest: . inst/unitTests src src/lib
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 23 16:11:29 CEST 2016
Author: fschoenen
Date: 2016-07-23 16:11:28 +0200 (Sat, 23 Jul 2016)
New Revision: 295
Added:
pkg/RSienaTest/Makefile
pkg/RSienaTest/src/sources.list
Removed:
pkg/RSienaTest/src/lib/RNGStreams/
Modified:
pkg/RSienaTest/.Rbuildignore
pkg/RSienaTest/.Rinstignore
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/configure
pkg/RSienaTest/configure.ac
pkg/RSienaTest/configure.win
pkg/RSienaTest/inst/unitTests/effect.persistence.test.R
pkg/RSienaTest/inst/unitTests/model.persistence.test.R
pkg/RSienaTest/src/Makevars.in
Log:
buildsystem
buildsystem: added Makefile and src/sources.list
unitTests: removed sink('/dev/null')
Modified: pkg/RSienaTest/.Rbuildignore
===================================================================
--- pkg/RSienaTest/.Rbuildignore 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/.Rbuildignore 2016-07-23 14:11:28 UTC (rev 295)
@@ -1,18 +1,17 @@
^doc
-src/SienaProfile.cpp
-src/SienaProfile.o
-src/SienaProfile.exe
+^RSienaTest_.*\.tar\.gz
+
+Makefile
+
+src/Makefile.profile
+src/SienaProfile\..*
+
src/RMath.dll
src/libpgSn.a
-src/Makefile.profile
+
tests/testrefs
tests/effectsTest.R
tests/slowtest.R
tests/sampson.r
-inst/.*[.]log
-inst/.*[.]bbl
-inst/.*[.]blg
-inst/.*[.]aux
-inst/.*[.]out
-inst/.*[.]toc
-inst/.*[.]bak
+
+inst/.*\.(log|bbl|blg|aux|out|toc|bak)
Modified: pkg/RSienaTest/.Rinstignore
===================================================================
--- pkg/RSienaTest/.Rinstignore 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/.Rinstignore 2016-07-23 14:11:28 UTC (rev 295)
@@ -1,11 +1 @@
-inst/.*[.]tex
-inst/.*[.]png
-inst/.*[.]jpg
-inst/.*[.]bib
-inst/.*[.]log
-inst/.*[.]bbl
-inst/.*[.]blg
-inst/.*[.]aux
-inst/.*[.]out
-inst/.*[.]toc
-inst/.*[.]bak
+inst/.*\.(tex|png|jpg|bib)
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/DESCRIPTION 2016-07-23 14:11:28 UTC (rev 295)
@@ -1,8 +1,8 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-294
-Date: 2016-05-25
+Version: 1.1-295
+Date: 2016-07-23
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger
Depends: R (>= 2.15.0), utils
Imports: Matrix, tcltk, lattice, parallel, MASS, RUnit, methods
Added: pkg/RSienaTest/Makefile
===================================================================
--- pkg/RSienaTest/Makefile (rev 0)
+++ pkg/RSienaTest/Makefile 2016-07-23 14:11:28 UTC (rev 295)
@@ -0,0 +1,116 @@
+# Build System
+#
+# With the introduction of MPI and therfore the need of autoconf things got
+# little more complicated. This is a Makefile providing simple targets. Short
+# run down of the manual build system:
+#
+# 1. Running `autoconf` transforms 'configure.ac' to 'configure'. The
+# configure.ac/configure.win files contain the logic for MPI discovery.
+#
+# 2. Calling `R CMD INSTALL {pkg}` will run configure and make.
+#
+# 2.1 `configure` builds the 'Makevars' file from the 'Makevars.in' template
+# replacing Variables enclosed in '@'. This includes compiler and linker
+# flags (@PKG_CPPFLAGS@, @PKG_LIBS@) as well as the list of source files
+# (@PKG_SOURCES@) which is stored in the 'src/sources.list' file and
+# generated by this 'Makefile'.
+
+# High level targets for this file:
+#
+# clean
+# Remove temporary files.
+# build, check, install
+# Correspond the to `R CMD *` versions.
+# test_capture, test
+# Trigger the regression testing. regsave captures the state, regtest
+# tests against the saved state.
+
+# Parse DESCRIPTION file.
+PKG_VERSION := $(shell grep -i ^version DESCRIPTION | cut -d\ -f2-)
+PKG_REVISION := $(shell echo $(PKG_VERSION) | cut -d- -f2-)
+PKG_NAME := $(shell grep -i ^package DESCRIPTION | cut -d\ -f2-)
+PKG_DATE := $(shell grep -i ^date DESCRIPTION | cut -d\ -f2-)
+PKG_TARBALL := $(PKG_NAME)_$(PKG_VERSION).tar.gz
+PKG_IMPORTS := $(shell grep -i ^imports DESCRIPTION | cut -d\ -f2-)
+PKG_SUGGESTS := $(shell grep -i ^suggests DESCRIPTION | cut -d\ -f2-)
+
+# Actual source information.
+# SRC_REVISION := $(shell svn info --show-item revision)
+SRC_LIST = src/sources.list
+
+# Top level source files containing the R binding.
+SRC_BINDING = \
+ RInterface.cpp \
+ RUtil.cpp \
+ siena07internals.cpp \
+ siena07models.cpp \
+ siena07setup.cpp \
+ siena07utilities.cpp
+
+# Folders in src/ needed entirely.
+SRC_MODULES = data Eigen estimator logger model network sim utils
+
+# R command settings.
+R = R
+R_RUN = $(R) -e
+R_BUILD = $(R) CMD build
+R_CHECK = $(R) CMD check --as-cran
+R_INSTALL = $(R) CMD INSTALL
+
+.PHONY:
+all: clean check
+
+.PHONY:
+clean:
+# ifeq ($(OS),Windows_NT)
+# sh ./cleanup.win
+# else
+# ./cleanup
+# endif
+ -rm -rf $(PKG_NAME).Rcheck
+ -rm -f $(PKG_TARBALL)
+
+.PHONY:
+check: $(PKG_TARBALL)
+ $(R_CHECK) $<
+
+.PHONY:
+install: $(PKG_TARBALL)
+ $(R_INSTALL) $<
+
+.PHONY:
+build: $(PKG_TARBALL)
+$(PKG_TARBALL): configure $(SRC_LIST)
+ $(R_BUILD) .
+
+.PHONY:
+commitchecks: # test
+ # test $(PKG_REVISION) -eq $$(($(SRC_REVISION)+1)) # DESCRIPTION revision
+ test $(PKG_DATE) = $$(date -I) # DESCRIPTION date
+ chmod a+x configure cleanup # script permissions
+
+configure: configure.ac
+ autoconf
+
+# build the list of source files
+$(SRC_LIST): $(shell find src -iname '*.cpp')
+ echo -n "$(SRC_BINDING)" >$@
+ cd src && find $(SRC_MODULES) -iname '*.cpp' -printf ' %p' >>$(@:src/%=%)
+
+# dependencies
+.PHONY:
+install_dep:
+ $(R_RUN) "options(repos='http://stat.ethz.ch/CRAN');\
+ pkgs <- c(strsplit('$(PKG_IMPORTS)', ', '), strsplit('$(PKG_SUGGESTS)', ', '));\
+ for (pkg in pkgs) install.packages(pkg)"
+
+# regression tests
+.PHONY:
+test_capture:
+ cd inst/unitTests && \
+ $(R_RUN) "require($(PKG_NAME)); record_values <- T; RSienaTest:::run_tests(dir='.')"
+
+.PHONY:
+test:
+ cd inst/unitTests && \
+ $(R_RUN) "require($(PKG_NAME)); RSienaTest:::run_tests(dir='.')"
Property changes on: pkg/RSienaTest/Makefile
___________________________________________________________________
Added: svn:mime-type
+ text/plain;charset=UTF-8
Added: svn:eol-style
+ native
Modified: pkg/RSienaTest/configure
===================================================================
--- pkg/RSienaTest/configure 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/configure 2016-07-23 14:11:28 UTC (rev 295)
@@ -622,6 +622,7 @@
ac_subst_vars='LTLIBOBJS
PKG_LIBS
PKG_CPPFLAGS
+PKG_SOURCES
ORTED
LIBOBJS
EGREP
@@ -2241,7 +2242,7 @@
-# Checks {{{1
+# Checks (autoscan) {{{1
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -4130,7 +4131,7 @@
done
-# Args {{{1
+# Args (mpi discovery) {{{1
MPI=yes
# Check whether --with-mpi-include-path was given.
@@ -4630,8 +4631,12 @@
PKG_LIBS=
fi
+PKG_SOURCES=$(cat src/sources.list)
+
+
+
ac_config_files="$ac_config_files src/Makevars"
cat >confcache <<\_ACEOF
Modified: pkg/RSienaTest/configure.ac
===================================================================
--- pkg/RSienaTest/configure.ac 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/configure.ac 2016-07-23 14:11:28 UTC (rev 295)
@@ -1,6 +1,20 @@
# vim:fdm=marker:
-# Based on the autoconf.ac from the Rmpi package.
-# Process this file with autoconf to produce a configure script.
+
+# Based on the autoconf.ac from the Rmpi package
+# <http://www.stats.uwo.ca/faculty/yu/Rmpi/>. Run `autoconf` to produce the
+# 'configure' script.
+
+# - Run with automatic detection: `R CMD INSTALL {pkg}`
+
+# - Run with a prefix folder. Subfolders will be searched for binarys.
+# `R CMD INSTALL {pkg} --configure-args=--with-mpi=/path/to/location`
+
+# - Fully specify paths and type.
+# `R CMD INSTALL {pkg} --configure-args=" \\
+# --with-Rmpi-include=/path/to/mpi_include_dir \\
+# --with-Rmpi-libpath=/path/to/mpi_lib_dir \\
+# --with-Rmpi-type={OPENMPI,MPICH,MPICH2,LAM}"`
+
AC_PREREQ([2.69])
AC_INIT([RSienaTest], 1.1-289)
AC_CONFIG_SRCDIR([src])
@@ -275,6 +289,10 @@
PKG_LIBS=
fi
+PKG_SOURCES=$(cat src/sources.list)
+
+AC_SUBST(PKG_SOURCES)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(PKG_LIBS)
+
AC_OUTPUT(src/Makevars)
Modified: pkg/RSienaTest/configure.win
===================================================================
--- pkg/RSienaTest/configure.win 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/configure.win 2016-07-23 14:11:28 UTC (rev 295)
@@ -66,8 +66,11 @@
*) echo "No MPI Installation found. Compiling without MPI support." >&2 ;;
esac
+PKG_SOURCES="$(cat src/sources.list)"
+
# Take care that variables do not contain '\' backslashes or '#' hashes!
sed "
+s#@PKG_SOURCES@#$PKG_SOURCES#;
s#@PKG_LIBS@#$PKG_LIBS#;
s#@PKG_CPPFLAGS@#$PKG_CPPFLAGS#" \
src/Makevars.in >src/Makevars.win
Modified: pkg/RSienaTest/inst/unitTests/effect.persistence.test.R
===================================================================
--- pkg/RSienaTest/inst/unitTests/effect.persistence.test.R 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/inst/unitTests/effect.persistence.test.R 2016-07-23 14:11:28 UTC (rev 295)
@@ -76,80 +76,92 @@
test.effect.symmetric.objective <- function() {
group <- 'symmetricObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
data <- sienaDataCreate(net)
eff <- all_non_gmm_effects(data, group)
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
test.effect.non.symmetric.objective <- function() {
group <- 'nonSymmetricObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
data <- sienaDataCreate(net)
eff <- all_non_gmm_effects(data, group)
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
test.effect.covar.symmetric.objective <- function() {
group <- 'covarSymmetricObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
atr <- varCovar(s50a)
data <- sienaDataCreate(net, atr)
eff <- all_non_gmm_effects(data, group, interaction1='atr')
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
test.effect.covar.non.symmetric.objective <- function() {
group <- 'covarNonSymmetricObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
atr <- varCovar(s50a)
data <- sienaDataCreate(net, atr)
eff <- all_non_gmm_effects(data, group, interaction1='atr')
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
test.effect.behavior.objective <- function() {
group <- 'behaviorObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
atr <- sienaDependent(s50a, type='behavior')
data <- sienaDataCreate(atr)
eff <- all_non_gmm_effects(data, group)
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
ignored.effect.behavior.one.mode.objective <- function() {
group <- 'behaviorOneModeObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
atr <- sienaDependent(s50a, type='behavior')
data <- sienaDataCreate(net, atr)
eff <- all_non_gmm_effects(data, group, interaction1='net')
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
ignored.effect.objective.gmm.onemode <- function() {
- # sink('/dev/null')
+ # sink(NULL)
group <- 'gmm.nonSymmetricObjective'
if (skip_recording(group)) return()
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
@@ -176,7 +188,7 @@
ignored.effect.non.symmetric.symmetric.objective <- function() {
group <- 'nonSymmetricSymmetricObjective'
if (skip_recording(group)) return()
- # sink('/dev/null')
+ # sink(NULL)
net1 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
net2 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
data <- sienaDataCreate(net1, net2)
@@ -189,7 +201,8 @@
ignored.effect.covar.net.net.objective <- function() {
group <- 'covarNetNetObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net1 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
net2 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
atr <- varCovar(s50a)
@@ -197,13 +210,15 @@
eff <- all_non_gmm_effects(data, group, interaction1='atr', interaction2='net2')
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
ignored.effect.triple.network.objective <- function() {
group <- 'tripleNetworkObjective'
if (skip_recording(group)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net1 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
net2 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
net3 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
@@ -211,5 +226,6 @@
eff <- all_non_gmm_effects(data, group, interaction1='net2', interaction2='net3')
ans <- run_effect_test_model(data, eff)
sink()
+ close(dn)
check_model_persistence(group, ans)
}
Modified: pkg/RSienaTest/inst/unitTests/model.persistence.test.R
===================================================================
--- pkg/RSienaTest/inst/unitTests/model.persistence.test.R 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/inst/unitTests/model.persistence.test.R 2016-07-23 14:11:28 UTC (rev 295)
@@ -13,13 +13,15 @@
fn_name <- paste('test.model', name, value, paste(names(list(...)), sep='_'), sep='.')
assign(fn_name, function() {
if (skip_recording(fn_name)) return()
- sink('/dev/null')
+ dn <- textConnection(NULL, 'w')
+ sink(dn)
net <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
data <- sienaDataCreate(net)
eff <- getEffects(data)
eff <- includeEffects(eff, transTrip)
ans <- siena07(model, data=data, effects=eff, batch=T)
sink()
+ close(dn)
check_model_persistence(fn_name, ans)
}, envir=test_environment)
})()
Modified: pkg/RSienaTest/src/Makevars.in
===================================================================
--- pkg/RSienaTest/src/Makevars.in 2016-05-28 21:22:05 UTC (rev 294)
+++ pkg/RSienaTest/src/Makevars.in 2016-07-23 14:11:28 UTC (rev 295)
@@ -1,26 +1,15 @@
# -*- Makefile -*-
# vim:ft=make:
-# library root path
-DEPENDENCIES = lib
-
-# currently unused
-# RNGSTREAMS = $(DEPENDENCIES)/RNGStreams
-# RNGSTREAMS_CPP = -I$(RNGSTREAMS)
-
-# template lib, only includes needed
-EIGEN = $(DEPENDENCIES)/Eigen
+EIGEN = lib/Eigen
EIGEN_CPP = -I$(EIGEN)
OBJECTS = $(SOURCES:.cpp=.o)
+SOURCES = @PKG_SOURCES@
-# 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')
-
PKG_CPPFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -I. $(RNGSTREAMS_CPP) $(EIGEN_CPP) @PKG_CPPFLAGS@
# -UNDEBUG -DR_LEGACY -DPROFILER
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(ARCHLIB) @PKG_LIBS@
-# $(LAPACK_LIBS) $(BLAS_LIBS) -lprofiler -ltcmalloc
+# -lprofiler -ltcmalloc
all: $(SHLIB)
Added: pkg/RSienaTest/src/sources.list
===================================================================
--- pkg/RSienaTest/src/sources.list (rev 0)
+++ pkg/RSienaTest/src/sources.list 2016-07-23 14:11:28 UTC (rev 295)
@@ -0,0 +1 @@
+RInterface.cpp RUtil.cpp siena07internals.cpp siena07models.cpp siena07setup.cpp siena07utilities.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 Eigen/RLegacy.cpp estimator/components/PeriodWiseScoreCollector.cpp estimator/components/TimesCollector.cpp estimator/components/StatisticCollector.cpp estimator/components/ScoreCollector.cpp estimator/components/NSimCollector.cpp estimator/components/ParameterSum.cpp estimator/components/PeriodWiseStatisticsCollector.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 logger/Priority.cpp logger/formatter/MPIAwareFormatter.cpp logger/LogEntry.cpp logger/appender/FileAppender.cpp logger/appender/AppenderPool.cpp 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/DyadicCovariateAndNetworkBehaviorEffect.cpp model/effects/OutdegreeActivitySqrtEffect.cpp model/effects/CovariateSimmelianAlterEffect.cpp model/effects/LinearShapeEffect.cpp model/effects/Effect.cpp model/effects/SimmelianEffect.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/DyadicCovariateAvAltEffect.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/CovariateDiffEgoEffect.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/SimilarityWEffect.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/SameCovariateInStarFunction.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/SameCovariateOutStarFunction.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/CovariateEgoSquaredEffect.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/FourCyclesEffect.cpp model/effects/AverageSimmelianAlterEffect.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/CovariateDiffEffect.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 network/NetworkUtils.cpp network/CommonNeighborIterator.cpp network/layers/DistanceTwoLayer.cpp network/Network.cpp network/iterators/GeneralTieIterator.cpp network/iterators/AdvUnionTieIterator.cpp network/Simmelian.cpp network/OneModeNetwork.cpp network/IncidentTieIterator.cpp network/TieIterator.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 utils/debugging/StopWatch.cpp utils/debugging/ApproxSize.cpp utils/Utils.cpp utils/NamedObject.cpp utils/Random.cpp utils/SqrtTable.cpp
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