[Rsiena-commits] r94 - in pkg: RSiena RSiena/src RSienaTest RSienaTest/src

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Jun 4 14:33:48 CEST 2010 

Author: ripleyrm
Date: 2010-06-04 14:33:47 +0200 (Fri, 04 Jun 2010)
New Revision: 94

Added:
   pkg/RSiena/src/Makevars.win
   pkg/RSienaTest/src/Makevars.win
Removed:
   pkg/RSiena/src/Makefile.win
   pkg/RSienaTest/src/Makefile.win
Modified:
   pkg/RSiena/changeLog
   pkg/RSiena/src/Makevars
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/src/Makevars
Log:
Makefile changes, changelog

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSiena/changeLog	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,5 +1,107 @@
-2020-04-28 R-forge revision 84
+2010-06-04 R-forge revision 94 
 
+	* src/Makefile.win replaced by src/Makevars.win. Amended
+	src/Makevars.
+	
+2010-06-04 R-forge revision 93 (RSienaTest only)
+
+	* R/effectsMethods.r: fix to print.sienaEffects for empty object
+	* R/globals.r: make silent parameter suppress all screen output
+	* R/maxlikec.r, R/phase1.r, src/model/ml/many, 
+	doc/Siena_algorithms4.tex : maximum likelihood 
+	* inst/examples/algorithms.r, inst/examples/runalg.r, R/phase2.r,
+	R/phase3.r, R/simstatsc.r, src/model/EpochSimulation.cpp,
+	src/model/EpochSimulation.h, src/model/Model.cpp,
+	src/model/Model.h, src/model/ml/many, doc/RSienaDeveloper.tex: 
+	algorithms
+	* R/sienaDataCreate.r: calculate
+	similarity mean for alters, reverted revision 88
+	* R/sienaeffects.r, man/includeEffects.Rd, man/includeInteraction.Rd,
+	man/setEffect.Rd: reverted revision 88, added timedummy to
+	setEffect, allow includeInteraction to set include to FALSE as
+	well as TRUE.
+	* R/sienaprint.r: fixed bug if used time dummies: use requested
+	effects not effects object. Also fix for added lines in
+	print.sienaFit, which were wrong if there were a large number of
+	effects. 
+	* R/sienaTimeTest.r: added include parameter to includeTimeDummy,
+	and print out changed lines. Changed header comment.
+	* R/simstatsc.r: error message if use composition change with
+	bipartite networks (temporary, till I fix this!). Added similarity
+	mean for alters. Fix to treatment of missings in sparse bipartite
+	networks. 
+	* src/model/EpochSimulation.cpp: fix to error message if unlikely
+	to terminate the epoch.
+	* tests/parallel.R, parallel.Rout.save: change in line number of effect
+	* man/plot.sienaTimeTest.Rd, man/sienaTimeTest.Rd, 
+	man/includeTimeDummy.Rd: split the help file into three. 
+	
+2010-06-04 R-forge revision 92 (RSienaTest only)
+
+	* data/allEffects.csv, R/effects.r, src/siena07.cpp,
+	src/model/effects/allEffects.h, 
+	src/model/effects/EffectFactory.cpp,
+	src/model/effects/BehaviorEffect.cpp, 
+	src/model/effects/BehaviorEffect.h, 
+	src/model/effects/AltersCovariateAverageEffect.cpp, 
+	src/model/effects/AltersCovariateAverageEffect.h, 
+	src/model/effects/CovariateandNetworkBehaviorEffect.cpp, 
+	src/model/effects/CovariateandNetworkBehaviorEffect.h, 
+	src/model/effects/CovariateDependentNetworkEffect.cpp,
+	src/model/effects/CovariateDependentNetworkEffect.h,
+	src/model/effects/CovariateDistance2AlterEffect.h,
+	src/model/effects/CovariateDistance2AlterEffect.cpp,
+	src/model/effects/CovariateDistance2AlterEffect.h,
+	src/model/effects/CovariateDistance2NetworkEffect.cpp,
+	src/model/effects/CovariateDistance2NetworkEffect.h,
+	src/model/effects/CovariateDistance2SimilarityEffect.cpp,
+	src/model/effects/CovariateDistance2SimilarityEffect.h,
+	src/data/Covariate.cpp, src/data/Covariate.h,
+	src/data/BehaviorLongitudinalData.cpp, 
+	src/data/BehaviorLongitudinalData.h,
+	src/model/variables/BehaviorVariable.cpp, 
+	src/model/variables/BehaviorVariable.h, 
+	src/model/variables/DependentVariable.h, 
+	src/model/variables/NetworkVariable.cpp, 
+	src/model/variables/NetworkVariable.h: new average alter effects
+	
+2010-05-30 R-forge revision 91 (RSienaTest only)
+
+	* Changelog: Updated changelog!
+
+2010-05-29 R-forge revision 90 (RSienaTest only)
+
+	* man/s_man400.tex, RSiena.bib. Added Tom's changes to manual
+	and sorted out corrupted characters from previous update.
+	
+2010-05-29 R-forge revision 89 (RSienaTest only)
+
+	* R/sienaTimeTest.r, R/sienaeffects.r, man/sienaTimeTest.Rd,
+	man/includeEffects.Rd, doc/s_man400.tex, RSiena.bib: new option to
+	control orthogonalization in sienaTimeTest, 
+	add parameters to includeEffects, documentation update.
+	
+2010-02-28 R-forge revision 88 (RSienaTest only)
+
+	* R/sienaTimeTest.r, sienaDataCreate.r, simstatsc.r, 
+	man/sienaTimeTest.Rd: TimeDummies for RateX effects (constant
+	covariate only!).	
+
+2010-05-27 R-forge revision 87 (RSienaTest only)
+
+	* R/sienaTimeTest.r: fix to plot.sienaTimeTest
+	
+2010-05-23 R-forge revision 86 (RSienaTest only)
+
+	* R/sienaTimeTest.r, man/sienaTimeTest.Rd, NAMESPACE: 
+	new function: includeTimeDummy, fix naming in plot.sienaTimeTest
+	
+2010-05-22 R-forge revision 85 (RSienaTest only)
+	
+	* R/sienaTimeTest.r: fix for unconditional estimation
+	
+2010-04-28 R-forge revision 84
+
 	* src/many: removed <R.h> and adjusted other header files
 	* man/iwlms.Rd: (RSienaTest only) eol-style property set.
 	* doc/RSienaDeveloper.tex: notes about headers and R/C

Deleted: pkg/RSiena/src/Makefile.win
===================================================================
--- pkg/RSiena/src/Makefile.win	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSiena/src/Makefile.win	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,43 +0,0 @@
-#-*- Makefile -*-
-#
-
-include $(R_HOME)/etc$(R_ARCH)/Makeconf
-
-#RHOME = d:/R/R-2.9.0/
-#RHOME = c:/progra~1/R/R-2.9.0/
-#RHOME = c:/R/R-2.9.0/
-.PHONY: all libs execs
-
-SOURCES=$(wildcard data/*.cpp utils/*.cpp utils/random.h model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp network/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
-EXTRAS=$(foreach i,$(SOURCES),$(basename $i).o)
-
-PKG_LIBS=-L. -lSn
-PKG_CPPFLAGS=-I.
-
-SHLIB = RSiena.dll
-SHLIB_LD = $(CXX)
-
-ifeq ($(strip $(WIN)),64)
-EXECS =
-else
-EXECS = execs
-endif
-
-all: libs $(SHLIB) $(EXECS)
-libs: libSn.a
-
-libSn.a: $(EXTRAS)
-	 $(AR) cr libSn.a $(EXTRAS)
-
-RSiena.dll: siena07.o libSn.a
-
-siena.exe:
-	@(cd win32; make all)
-
-execs:
-	@(cd win32; make install)
-
-
-clean:
-	@rm -f RSiena.dll libSn.a $(EXTRAS) siena07.o
-	@(cd win32; make clean)

Modified: pkg/RSiena/src/Makevars
===================================================================
--- pkg/RSiena/src/Makevars	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSiena/src/Makevars	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,9 +1,14 @@
-SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
-OBJECTS = siena07.o $(foreach i,$(SOURCES),$(basename $i).o)
+SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/*/*.cpp model/*/*/*.cpp)
+
+OBJECTS = siena07.o $(SOURCES:.cpp=.o)
+
 PKG_CPPFLAGS=-I.
+
 # PKG_CXXFLAGS=-fno-omit-frame-pointer
 
-all: clean $(SHLIB)
+all: $(SHLIB)
 
+$(OBJECTS): clean
+
 clean:
 	@rm -f $(OBJECTS)

Added: pkg/RSiena/src/Makevars.win
===================================================================
--- pkg/RSiena/src/Makevars.win	                        (rev 0)
+++ pkg/RSiena/src/Makevars.win	2010-06-04 12:33:47 UTC (rev 94)
@@ -0,0 +1,10 @@
+SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
+
+OBJECTS = siena07.o $(SOURCES:.cpp=.o)
+
+PKG_CPPFLAGS=-I.
+
+all: $(SHLIB)
+
+clean:
+	@rm -f $(SHLIB) $(OBJECTS)


Property changes on: pkg/RSiena/src/Makevars.win
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSienaTest/changeLog	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,12 +1,105 @@
-2010-05-30 R-forge revision 91
-	* Updated changelog!
+2010-06-04 R-forge revision 94 
+
+	* src/Makefile.win replaced by src/Makevars.win. Amended
+	src/Makevars.
 	
-2010-05-30 R-forge revisions 84-89
-	* Added includeTimeDummy function
-	* Added sienaTimeTest functionality
-	* Support for RateX timedummy effects
-	* Added documentation to manual on sienaTimeTest
+2010-06-04 R-forge revision 93 (RSienaTest only)
+
+	* R/effectsMethods.r: fix to print.sienaEffects for empty object
+	* R/globals.r: make silent parameter suppress all screen output
+	* R/maxlikec.r, R/phase1.r, src/model/ml/many, 
+	doc/Siena_algorithms4.tex : maximum likelihood 
+	* inst/examples/algorithms.r, inst/examples/runalg.r, R/phase2.r,
+	R/phase3.r, R/simstatsc.r, src/model/EpochSimulation.cpp,
+	src/model/EpochSimulation.h, src/model/Model.cpp,
+	src/model/Model.h, src/model/ml/many, doc/RSienaDeveloper.tex: 
+	algorithms
+	* R/sienaDataCreate.r: calculate
+	similarity mean for alters, reverted revision 88
+	* R/sienaeffects.r, man/includeEffects.Rd, man/includeInteraction.Rd,
+	man/setEffect.Rd: reverted revision 88, added timedummy to
+	setEffect, allow includeInteraction to set include to FALSE as
+	well as TRUE.
+	* R/sienaprint.r: fixed bug if used time dummies: use requested
+	effects not effects object. Also fix for added lines in
+	print.sienaFit, which were wrong if there were a large number of
+	effects. 
+	* R/sienaTimeTest.r: added include parameter to includeTimeDummy,
+	and print out changed lines. Changed header comment.
+	* R/simstatsc.r: error message if use composition change with
+	bipartite networks (temporary, till I fix this!). Added similarity
+	mean for alters. Fix to treatment of missings in sparse bipartite
+	networks. 
+	* src/model/EpochSimulation.cpp: fix to error message if unlikely
+	to terminate the epoch.
+	* tests/parallel.R, parallel.Rout.save: change in line number of effect
+	* man/plot.sienaTimeTest.Rd, man/sienaTimeTest.Rd, 
+	man/includeTimeDummy.Rd: split the help file into three. 
 	
+2010-06-04 R-forge revision 92 (RSienaTest only)
+
+	* data/allEffects.csv, R/effects.r, src/siena07.cpp,
+	src/model/effects/allEffects.h, 
+	src/model/effects/EffectFactory.cpp,
+	src/model/effects/BehaviorEffect.cpp, 
+	src/model/effects/BehaviorEffect.h, 
+	src/model/effects/AltersCovariateAverageEffect.cpp, 
+	src/model/effects/AltersCovariateAverageEffect.h, 
+	src/model/effects/CovariateandNetworkBehaviorEffect.cpp, 
+	src/model/effects/CovariateandNetworkBehaviorEffect.h, 
+	src/model/effects/CovariateDependentNetworkEffect.cpp,
+	src/model/effects/CovariateDependentNetworkEffect.h,
+	src/model/effects/CovariateDistance2AlterEffect.h,
+	src/model/effects/CovariateDistance2AlterEffect.cpp,
+	src/model/effects/CovariateDistance2AlterEffect.h,
+	src/model/effects/CovariateDistance2NetworkEffect.cpp,
+	src/model/effects/CovariateDistance2NetworkEffect.h,
+	src/model/effects/CovariateDistance2SimilarityEffect.cpp,
+	src/model/effects/CovariateDistance2SimilarityEffect.h,
+	src/data/Covariate.cpp, src/data/Covariate.h,
+	src/data/BehaviorLongitudinalData.cpp, 
+	src/data/BehaviorLongitudinalData.h,
+	src/model/variables/BehaviorVariable.cpp, 
+	src/model/variables/BehaviorVariable.h, 
+	src/model/variables/DependentVariable.h, 
+	src/model/variables/NetworkVariable.cpp, 
+	src/model/variables/NetworkVariable.h: new average alter effects
+	
+2010-05-30 R-forge revision 91 (RSienaTest only)
+
+	* Changelog: Updated changelog!
+
+2010-05-29 R-forge revision 90 (RSienaTest only)
+
+	* man/s_man400.tex, RSiena.bib. Added Tom's changes to manual
+	and sorted out corrupted characters from previous update.
+	
+2010-05-29 R-forge revision 89 (RSienaTest only)
+
+	* R/sienaTimeTest.r, R/sienaeffects.r, man/sienaTimeTest.Rd,
+	man/includeEffects.Rd, doc/s_man400.tex, RSiena.bib: new option to
+	control orthogonalization in sienaTimeTest, 
+	add parameters to includeEffects, documentation update.
+	
+2010-02-28 R-forge revision 88 (RSienaTest only)
+
+	* R/sienaTimeTest.r, sienaDataCreate.r, simstatsc.r, 
+	man/sienaTimeTest.Rd: TimeDummies for RateX effects (constant
+	covariate only!).	
+
+2010-05-27 R-forge revision 87 (RSienaTest only)
+
+	* R/sienaTimeTest.r: fix to plot.sienaTimeTest
+	
+2010-05-23 R-forge revision 86 (RSienaTest only)
+
+	* R/sienaTimeTest.r, man/sienaTimeTest.Rd, NAMESPACE: 
+	new function: includeTimeDummy, fix naming in plot.sienaTimeTest
+	
+2010-05-22 R-forge revision 85 (RSienaTest only)
+	
+	* R/sienaTimeTest.r: fix for unconditional estimation
+	
 2010-04-28 R-forge revision 84
 
 	* src/many: removed <R.h> and adjusted other header files

Deleted: pkg/RSienaTest/src/Makefile.win
===================================================================
--- pkg/RSienaTest/src/Makefile.win	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSienaTest/src/Makefile.win	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,43 +0,0 @@
-#-*- Makefile -*-
-#
-
-include $(R_HOME)/etc$(R_ARCH)/Makeconf
-
-#RHOME = d:/R/R-2.9.0/
-#RHOME = c:/progra~1/R/R-2.9.0/
-#RHOME = c:/R/R-2.9.0/
-.PHONY: all libs execs
-
-SOURCES=$(wildcard data/*.cpp utils/*.cpp utils/random.h model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp network/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
-EXTRAS=$(foreach i,$(SOURCES),$(basename $i).o)
-
-PKG_LIBS=-L. -lSn
-PKG_CPPFLAGS=-I.
-
-SHLIB = RSienaTest.dll
-SHLIB_LD = $(CXX)
-
-ifeq ($(strip $(WIN)),64)
-EXECS =
-else
-EXECS = execs
-endif
-
-all: libs $(SHLIB) $(EXECS)
-libs: libSn.a
-
-libSn.a: $(EXTRAS)
-	 $(AR) cr libSn.a $(EXTRAS)
-
-RSienaTest.dll: siena07.o libSn.a
-
-siena.exe:
-	@(cd win32; make all)
-
-execs:
-	@(cd win32; make install)
-
-
-clean:
-	@rm -f RSienaTest.dll libSn.a $(EXTRAS) siena07.o
-	@(cd win32; make clean)

Modified: pkg/RSienaTest/src/Makevars
===================================================================
--- pkg/RSienaTest/src/Makevars	2010-06-04 12:25:08 UTC (rev 93)
+++ pkg/RSienaTest/src/Makevars	2010-06-04 12:33:47 UTC (rev 94)
@@ -1,9 +1,14 @@
-SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
-OBJECTS = siena07.o $(foreach i,$(SOURCES),$(basename $i).o)
+SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/*/*.cpp model/*/*/*.cpp)
+
+OBJECTS = siena07.o $(SOURCES:.cpp=.o)
+
 PKG_CPPFLAGS=-I.
+
 # PKG_CXXFLAGS=-fno-omit-frame-pointer
 
-all: clean $(SHLIB)
+all: $(SHLIB)
 
+$(OBJECTS): clean
+
 clean:
 	@rm -f $(OBJECTS)

Added: pkg/RSienaTest/src/Makevars.win
===================================================================
--- pkg/RSienaTest/src/Makevars.win	                        (rev 0)
+++ pkg/RSienaTest/src/Makevars.win	2010-06-04 12:33:47 UTC (rev 94)
@@ -0,0 +1,10 @@
+SOURCES=$(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/effects/*.cpp model/tables/*.cpp model/variables/*.cpp model/effects/generic/*.cpp model/ml/*.cpp model/filters/*.cpp)
+
+OBJECTS = siena07.o $(SOURCES:.cpp=.o)
+
+PKG_CPPFLAGS=-I.
+
+all: $(SHLIB)
+
+clean:
+	@rm -f $(SHLIB) $(OBJECTS)


Property changes on: pkg/RSienaTest/src/Makevars.win
___________________________________________________________________
Added: svn:eol-style
   + native

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