2010-08-21 R-forge revision 119

	* R/sienaDataCreate.r: fix function comments so documentation
	runs. 
	* R/RSienaRDocumentation.r: minor source format changes.
	
2010-08-20 R-forge revision 118 RSienaTest only

	* src/siena07internals.cpp, src/siena07models.cpp,
	src/siena07setup.cpp, src/siena07utilities.cpp,
	src/siena07internals.h, src/siena07models.h,
	src/siena07setup.h, src/siena07utilities.h: set eol style
	* doc/config.dox: added doxygen configuration file

2010-08-20 R-forge revision 117 RSienaTest only

	* doc/RSiena.bib, s_man400.tex, Siena_algorithms4.tex,
	simstats0c.tex: documentation updates
	* inst/examples/algorithms.r: improvements!
	* R/initialiseFRAN.r, R/simstatsc.r: removed initialise function
	to separate source file
	* src/siena07.cpp deleted
	* src/siena07internals.cpp, src/siena07models.cpp,
	src/siena07setup.cpp, src/siena07utilities.cpp,
	src/siena07internals.h, src/siena07models.h,
	src/siena07setup.h, src/siena07utilities.h: replacements for
	siena07.cpp
	* R/bayes.r, R/maxlikec.r, R/phase1.r, R/robmon.r, R/siena07.r,
	src/many, man/siena07.Rd : ML changes (in progress)
	* src/model/variables/DependentVariable.cpp,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/DependentVariable.h,
	src/model/variables/NetworkVariable.h: symmetric networks (in progress)

2010-08-20 R-forge revision 116 RSiena only

	* R/simstatsc.r: forgotten part of previous change to print.

2010-08-20 R-forge revision 115

	* R/siena08.r: correct p-values on report.
	* R/sienaprint.r: correct print layout in special cases
	* R/sienaDataCreate.r: changes for ML (in progress)

2010-07-19 R-forge revision 114

	* R/print01Report.r: fix bug in names of multiple behavior
	variables on siena01 report.
	* R/print07Report.r, R/sienaprint.r: remove references to data in
	printing, as object gets too large.

2010-07-10 R-forge revision 113

	* src/model/variables/NetworkVariable.cpp: bug fix for endowment
	effects, since a recent change
	* src/model/ml/NetworkChange: bug fix, could not return bipartite
	simulations.
	* src/siena07.cpp, src/model/Model.h, src/model/Model.cpp,
	src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h,
	R/simstatsc.r, R/sienaDataCreate.r, R/sienaModelCreate.r: adaptive
	permutation length and probabilities for missings for ML
	(in progress still!)
	* src/model/ml/Chain.cpp: removed structural links from initial
	chain (ML)

2010-07-04 R-forge revision 112

	* R/sienautils.r: fix bug with groups and constant dyadic
	covariates with only 2 periods. (Introduced in revision 109!)

2010-07-03 R-forge revision 111

	* src/siena07.cpp, src/model/ml/Chain.cpp,
	src/model/ml/MLSimulation.cpp, src/model/ml/Option.cpp,
	src/model/ml/MLSimulation.h, src/model/ml/Option.h,
	R/phase1.r, R/sienaModelCreate.r, R/simstatsc.r, R/maxlike.r,
	man/sienaModelCreate.Rd: ML changes
	* src/model/variables/NetworkVariable.cpp,
        doc/simstats0c.tex (RSienaTest only): added option of
	no change for bipartite networks.
	* doc/RSienaDeveloper.tex (RSienaTest only): added some details
	about C++ and Doxygen.

2010-06-25 R-forge revision 110

	* man/coDyadCovar.Rd, man/varDyadCovar.Rd: added sparse parameter
	to documentation.

2010-06-25 R-forge revision 109

	* data/allEffects.csv, R/effects.r: removed inappropriate dyadic
	covariate effects for bipartite networks.
	* src/model/variables/NetworkVariable.cpp: correct distance
	accumulation for symmetric networks with conditional estimation
	* R/sienaModelCreate.r: add default variable for cond=TRUE
	* R/sienaprint.r: add Score test results to summary.sienaFit
	* R/simstatsc.r: remove data object from stored f again (still on z)
	* src/data/ChangingDyadicCovariate.cpp,
	src/data/ChangingDyadicCovariate.h,
	src/model/effects/DyadicCovariateDependentNetworkEffect.cpp,
	src/model/effects/DyadicCovariateDependentNetworkEffect.h
	src/model/effects/DyadicCovariateMainEffect.cpp,
	src/model/effects/DyadicCovariateReciprocityEffect.cpp,
	src/model/effects/EffectFactory.cpp,
	src/model/effects/NetworkEffect.cpp,
	R/sienaDataCreate.r, R/sienaDataCreateFromSession,
	R/print01Report.r, R/sienautils.r,
	R/simstatsc.r, man/coDyadCovar.Rd, man/varDyadCovar.Rd:
	dyadic covariates now deal correctly with missing values and can
	be sparse matrices.

2010-06-21 R-forge revision 108

	* doc/RSienaDeveloper.tex: added note about Rd2dvi.
	* data/allEffects.csv, R/effects.r, R/sienaDataCreate.r,
	src/data/BehaviorLongitudinalData.cpp, BehaviorLongitudinalData.h,
	src/data/Covariate.cpp, src/data/Covariate.h,
	src/model/effects/AllEffects.h, src/model/effects/BehaviorEffect.cpp,
	src/model/effects/BehaviorEffect.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.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/model/effects/EffectFactory.cpp,
	src/model/variables/BehaviorVariable.cpp,
	src/model/variables/BehaviorVariable.h,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h, src/siena07.cpp,
	tests/parallel.R, tests/parallel.Rout.save
	: (RSiena only) covariate-at-distance-2 effects
	* man/coDyadCovar.Rd, man/siena01Gui.Rd, man/sienaDataCreate.Rd,
	man/sienaDataCreateFromSession.Rd, man/sienaNet.Rd,
	man/sienaNodeSet.Rd, man/sienaTimeTest.Rd, man/simstats0c.Rd,
	man/varDyadCovar.Rd: minor edits
	* R/effectsDocumentation.r: bug caused by insertion of timeDummy
	column
	* R/effectsMethods.r, man/print.sienaEffects.Rd: more fixes for
	empty cases, new argument to allow printing of all lines.
	* man/siena07.Rd, sienaModelCreate.Rd: major edits.
	* R/bayes.r: defer the plots till later
	* R/globals.r (RSiena only): allow use of Report with no file,
	suppress everything with silent.
	* R/maxlikec.r, R/phase1.r, phase2.r, phase3.r,
	src/model/EpochSimulation.cpp,
	src/model/EpochSimulation.h, src/model/ml/BehaviorChange.cpp,
	src/model/ml/BehaviorChange.h, src/model/ml/Chain.cpp,
	src/model/ml/Chain.h, src/model/ml/MiniStep.cpp,
	src/model/ml/MiniStep.h, src/model/MLSimulation.cpp,
	src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h,
	src/model/Model.cpp, src/model/Model.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, src/siena07.cpp:
	(RSiena only): 	minor changes for ML or algorithms
	* src/model/EpochSimulation.cpp: (RSiena only)
	corrected error message if unlikely to terminate epoch.
	* inst/doc/effects.pdf: updated list, after correcting bug
	* R/print01Report.r: fix bug with more than 2 groups
	* R/printInitialDescription.r: fix bug with 8 waves
	* R/sienaDataCreate.r: make covariate-at-dist-2 effects work for
	groups and for bipartites, multiple networks, behavior variables
	with missing values...
	* R/simstatsc.r: fix bug in naming user defined dyadic interactions.
	* R/sienaTimeTest.r: (RSiena only) make RateX effects work with varying
	covariates too.

2010-06-21 R-forge revision 107 RSienaTest only

	* NAMESPACE, R/sienaTimeTest.r, man/includeTimeDummy.Rd,
	man/sienaTimeTest.Rd, man/plot.sienaTimeTest.Rd, man/setEffect.Rd,
	CHANGELOG, doc/s_man400.tex : Reinstated includeTimeDummy.

2010-06-18 R-forge revision 106

	* DESCRIPTION: new version numbers: added 105 to end.

2010-06-18 R-forge revision 105

	* R/siena01.r: bug fix: call edit.data.frame directly to avoid the edit
	method of sienaEffects objects.

2010-06-10 R-forge revision 104 RSiena

	* doc/s_man400.tex: Updated RSiena manual script as per
	Tom's request.

2010-06-08 R-forge revision 103 RSienaTest only

	* man/sienaTimeTest.Rd, man/setEffect.Rd,
	CHANGELOG, doc/s_man400.tex: get through checks

2010-06-08 R-forge revision 102 RSienaTest only

	* NAMESPACE, R/sienaTimeTest.r, man/includeTimeDummy.Rd,
	man/sienaTimeTest.Rd, man/plot.sienaTimeTest.Rd, man/setEffect.Rd,
	CHANGELOG, doc/s_man400.tex: Deleted includeTimeDummy.

2010-06-08 R-forge revision 101 RSienaTest only

	* R/sienaTimeTest.r: added changing covariate functionality to
	sienaTimeFix for RateX effects.

2010-06-08 R-forge revision 100

	* Changelog, doc/s_man400.tex: fixed incorrect revision numbers.

2010-06-08 R-forge revision 99

	* R/simstatsc.r: fixed bug that bipartite networks not allowed 'loops'

2010-06-08 R-forge revision 98

	* R/simstatsc.r: constant dyadic covariates with missing values
	should now work correctly, varying ones do not fail, but the
	centering and filling in of missing values for these is still to
	be sorted out. Also treatment of bipartite nets with composition
	change has been corrected. (Previously missings were not processed
	correctly if a sparse-matrix format network (even after the
	previous change!) and composition change was ignored for all
	bipartite networks.)

	* doc/RSiena.bib: additions.

2010-06-04 R-forge revision 97

	* NAMESPACE: added forgotten includeTimeDummy

2010-06-04 R-forge revision 96 (RSiena mainly)

	* R/sienaTimeTest.r, R/sienaeffects.r, man/sienaTimeTest.rd,
	man/includeTimeDummy.rd, man/includeEffects.Rd, man/setEffects.Rd,
	man/plot.sienaTimeTest.rd, man/inlcudeInteraction.Rd :
	as for revisions 85-89, 93 for RSienaTest
	* R/effects.r: bug fixes as in revision 92
	* R/effectsMethods.r: bug fixes as in revision 93
	* R/sienaPrint.r: bug fixes as in revision 93
	* R/simstatsc.r: bug fixes as in revision 93

2010-06-04 R-forge revision 95

	* .Rbuildignore: added Makefile.profile to suppress warning
	* R/phase2.r: removed stray RSiena:::
	* doc/s_man400.tex: updated changelog

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 interactions or time dummies
	present: 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
	* R/effects.r: fixed bugs for more than two groups and no 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.

2010-05-28 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
	interface. (RSienatest only)

2010-04-25 R-forge revision 83

	* R/effectsMethods.r: fix bug introduced trying to pass checks

2010-04-24 R-forge revision 82

	* R/effectsMethods.r, man/print.sienaEffects.Rd,
	man/edit.sienaEffects.Rd, NAMESPACE: print, summary and edit
	methods for sienaEffects objects.

2010-04-24 R-forge revision 81

	* src/model/effects/structuralRateEffect.cpp: fix crash caused by
	size of effect table for bipartite networks.
	* R/bayes.r, src/siena07.cpp, src/model/ml/MLSimulation.cpp,
	src/model/ml/MLsimulation.h, src/model/model.cpp,
	src/model/model.h, src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h, src/utils/Random.cpp,
	src/utils/Random.h: New function bayes and supporting methods.
	* R/phase3.r, R/simstatsc.r: changes for ML
	* R/simstatscr, src/siena07.cpp, src/model/EpochSimulation.cpp,
	src/model/variables/BehaviorVariable.cpp,
	src/model/variables/NetworkVariable.cpp
	src/model/EpochSimulation.h:
	create and return chain after MOM simulation
	* src/model/EpochSimulation.cpp: added trap to stop conditional
	estimation after 1000000 steps.
	* src/model/ml/chains.cpp, src/model/ml/chains.h,
	src/model/ml/MiniStep.cpp, src/model/ml/MiniStep.h,
	src/siena07.cpp: print utilities for
	chains. create an R dataframe from a ministep. Print list of CCP's
	* src/model/ml/MLSimulation.cpp, src/model/model/cpp,
	src/model/model.h: changes for ML
	* src/model/variables/BehaviorVariable.cpp: fixed ambiguous call
	to abs: need cstdlib as well as cmath. Possibly to do with
	NO_C_HEADERS.

2010-04-14 R-forge revision 80

	* R/sienaTimeTest.r, man/sienaTimeTest.Rd. corrected default
	plevels for plot
	* RSienaTest only NAMESPACE: corrected package name

2010-04-13 R-forge revision 79

	* R/sienaTimeTest.r, man/sienaTimeTest.Rd, data/allEffects.csv,
	R/simstatsc.r, man/allEffects.Rd, man/getEffects.Rd:
	new function sienaTimeTest.

2010-04-12 R-forge revision 78

	* R/sienaeffects.r, man/includeEffects.Rd,
	man/includeInteraction.Rd, man/setEffects.Rd: allow character or
	non character input of effect names.
	* R/siena01.r: include effectNumber, effect1, effect2, effect3 in
	display of included effects.
	* R/print01Report.r: ignore diagonal missing values in total count

2010-04-12 R-forge revision 77 (RSiena only)

	* inst/examples/many, man/coDyadCovar.Rd: added new line to end.
	* data/allEffects.csv: remove trailing blanks
	* man/includeEffects.Rd, man/siena07.Rd, R/siena07.r,
	R/sienaDataCreateFromSession.r: minor formatting
	* R/sienaModelCreate.R, man/sienaModelCreate.Rd: changes to storage of
	function to be used, additions of ML parameters.
	* R/globals.r: changed matrix print to stop using scientific
	notation
	* R/phase1.r: changed dfra to use for loops rather than apply's to
	save memory
	* R/maxlike.r, phase1.r, phase2.r, phase3.r, robmon.r: new function
	makeZsmall, minor changes for maxlike.
	* R/print01Report.r: fix bug which did not find whether symmetric
	correctly.
	* R/printInitialDescription.r: fix bug to printout of average
	degrees.
	* R/siena01.r: fix bug: the save function did not keep the model options
	* R/sienaDataCreate.r: changes to attributes concerning missing
	values. Remove warning in checkConstraints with bipartite networks.
	* R/sienaPrint.r: fix to text re rates for conditional simulation
	* R/simstatsc.r: changes for maxlike
	* tests/parallel.Rout.save: updated test output.

2010-04-12 R-forge revision 76 (RSienaTest only)

	* src/data/ActorSet.cpp,
	src/model/effects/AverageReciprocatedAlterEffect.cpp,
	src/model/effects/ReciprocalDegreeBehaviorEffect.cpp,
	src/model/variables/BehaviorVariable.cpp,
	src/model/variables/EffectValueTable.cpp,
	src/network/OneModeNetwork.cpp,src/utils/SqrtTable.cpp:
	changes for Solaris compiling.
	* inst/examples/many, man/coDyadCovar.Rd: added new line to end.
	* data/allEffects.csv: remove trailing blanks
	* doc/RSiena.bib, doc/s_man400.tex: changes to manual
	* man/includeEffects.Rd, man/siena07.Rd, R/siena07.r,
	R/sienaDataCreateFromSession.r: minor formatting
	* R/sienaModelCreate.R, man/sienaModelCreate.Rd: changes to storage of
	function to be used, additions of ML parameters.
	* R/globals.r: changed matrix print to stop using scientific
	notation
	* R/phase1.r: changed dfra to use for loops rather than apply's to
	save memory
	* R/maxlike.r, phase1.r, phase2.r, phase3.r, robmon.r: new function
	makeZsmall, minor changes for maxlike.
	* R/iwlsm.r, maxlikecalc.r, siena08.r: added eolstyle native
	* R/print01Report.r: fix bug which did not find whether symmetric
	correctly.
	* R/printInitialDescription.r: fix bug to printout of average
	degrees.
	* R/siena01.r: fix bug: the save function did not keep the model options
	* R/sienaDataCreate.r: changes to attributes concerning missing
	values. Remove warning in checkConstraints with bipartite networks.
	* R/sienaPrint.r: fix to text re rates for conditional simulation
	* R/simstatsc.r: changes for maxlike, also changes to use of
	previous values
	* R/maxlikec.r: new function for maximum likelihood, corresponding
	to simstatsc.r
	* src/model/Model.cpp, Model.h, ml/MLSimulation.cpp,
	ml/MLSimulation.h, ml/NetworkChange.cpp, ml/NetworkChange.h,
	variables/DependentVariable.cpp, variables/DependentVariable.h,
	variables/NetworkVariable.cpp, variables/NetworkVariable.h,
	siena07.cpp: changes for max like.
	* tests/parallel.Rout.save: updated test output.
	* R/phase2.r: fixed bug, could not use multiple processors with
	only one effect

2010-03-31 R-forge revision 75

	* R/getEffects.r: fix bug causing crash with Dyadic covariates and
	bipartite networks

2010-03-30 R-forge revision 74 (RSiena only)

	* R/print01Report.r: change to text about missing values
	* inst/doc/s_man400.pdf: updated manual

2010-03-30 R-forge revision 73 (RSienaTest only)

	* R/print01Report.r: change to text about missing values
	* doc/s_man400.tex: updated manual source
	* doc/RSienaDeveloper.tex: updated documentation
	* inst/doc/s_man400.pdf: updated manual

2010-03-30 R-forge revision 72 (RSienaTest only)

	* doc/RSiena.bib: added bibliography file

2010-03-27 R-forge revision 71 (RSienaTest only) (cf revision 68, 69, 70 for RSiena)

	* data/allEffects.csv, src/model/effects/EffectFactory.cpp:
	renamed 4-cycle shortname to cycle4. Needs to be a permissible R
	name.
	* DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.12
	* NAMESPACE: removed addAttributes.default as does not exist
	* R/maxlike.r, phase2.r: altered comments
	* R/phase1.r (FiniteDifferences) ensure z$npos update is always a
	vector (a dimension could be lost).
	* R/simstatsc.r, R/phase3.r: move definition of ntim to phase3
	* R/print01Report.r: some percentages had not been multiplied by 100.
	* R/printInitialDescription.r: another fix re crashing with one mode and
	bipartite networks together.
	* R/siena01.r: fix to carrying forward theta if abnormal termination
	* R/siena07.r: remove tk variables from return object
	* R/sienaDataCreateFromSession.r: fix to allow more than one
	value indicating missing for covariates etc.
	* R/sienaDataCreateFromSession.r: allow periods to be numbered
	other than from 1 in siena net input.
	* R/simstatsc.r: sped up carry forward for NA arcs in sparse
	input. Also new function to initialise. Some changes relevant for ML.
	* R/simstatsc.r (unpackBehavior) carry forward and back or use
	mode for missings
	* src/many changes for ML

2010-03-27 R-forge revision 70 (RSiena only)

	* R/simstatsc.r, R/phase3.r: move definition of ntim to phase3
	* R/simstatsc.r (unpackBehavior) carry forward and back or use
	mode for missings
	* R/siena07.r: remove tk variables from return object
	* R/phase1.r (FiniteDifferences) ensure z$npos update is always a
	vector (a dimension could be lost).

2010-03-24 R-forge revision 69 (RSiena only) (cf revision 63, 67 for RSienaTest)

	* src/many: mostly incomplete, changes for ML.
	* R/simstatsc.r: sped up carry forward for NA arcs in sparse
	input. Also new function to initialise. Some changes relevant for ML.
	* R/print01Report.r: some percentages had not been multiplied by 100.
	* R/sienaDataCreateFromSession.r: fix to allow more than one
	value indicating missing for covariates etc.
	* data/allEffects.csv, src/model/effects/EffectFactory.cpp:
	renamed 4-cycle shortname to cycle4. Needs to be a permissible R
	name.
	* inst/examples/baerveldt3.csv, baerveldt4.csv: changed the
	changing covariates to constant as only 2 periods.
	* R/siena08.r, R/iwlsm.r, man/siena08.Rd, man/print.sienameta.Rd,
	man/iwlsm.Rd, summary.iwlsm.Rd: siena08 Meta analysis
	* R/robmon.r, R/sienaModelCreate.r, man/sienaModelCreate.Rd:
	remove the function from the model object. Use name instead so no
	need to load package on R startup with model object in .RData.
	* R/siena01.r: now uses sienaModelCreate rather than creating object
	itself.
	* R/siena07.r, R/phase1.r, R/phase2.r, R/phase3.r, R/robmon.r,
	R/simstatsc.r, R.sienaDataCreate.r, src/siena07.cpp,
	man/siena07.Rd:
	fixed rlecuyer random numbers and added facility to use multiple
	processors by wave.
	* R/globals.r, R/print01Report.r, R/siena07.r: Report function can
	now be used with optional output file
	* R/print01Report.r, R/sienaDataCreate.r, src/siena07.cpp: missing
	values in dyadic covariates (incomplete!)
	* R/siena01.r: fix to creation of model for unconditional
	estimation, fix to carrying forward theta if abnormal termination
	* R/phase3.r: fix to timing of progress reports for multiple processors
	* R/printInitialDescription.r: fix, was crashing with one mode and
	bipartite networks together.

2010-03-21 R-forge revision 68 (RSiena only) new version number 1.0.11 for RSiena

	* R/sienaDataCreateFromSession.r: allow periods to be numbered
	other than from 1 in siena net input.

2010-03-17 R-forge revision 67 (RSienaTest only)

	* R/siena01.r: fix to creation of model for unconditional estimation
	* R/phase3.r: fix to timing of progress reports for multiple processors
	* R/printInitialDescription.r: fix, was crashing with one mode and
	bipartite networks together

2010-03-17 R-forge revision 66

	* R/simstatsc.r: bug fix: user interaction effects did not work
	with multiple processors.

2010-03-17 R-forge revision 65 (RSienaTest only)

	* src/model/ml/MLsimulation.cpp, src/model/ml/MLsimulation.ch:
	forgotten files

2010-03-16 R-forge revision 64

	* data/allEffects.csv: covarBipartite egoX should have been an ego
	effect not dyadic.

2010-03-15 R-forge revision 63 (RSienaTest only)

	* R/siena08.r, R/iwlsm.r, man/siena08.Rd, man/print.sienameta.Rd,
	man/iwlsm.Rd, summary.iwlsm.Rd: siena08 Meta analysis
	* R/robmon.r, R/sienaModelCreate.r, man/sienaModelCreate.Rd:
	remove the function from the model object. Use name instead so no
	need to load package on R startup with model object in .RData.
	* R/siena01.r: now uses sienaModelCreate rather than creating object
	itself.
	* R/siena07.r, R/phase1.r, R/phase2.r, R/phase3.r, R/robmon.r,
	R/simstatsc.r, R.sienaDataCreate.r, src/siena07.cpp,
	man/siena07.Rd:
	fixed rlecuyer random numbers and added facility to use multiple
	processors by wave.
	* R/globals.r, R/print01Report.r, R/siena07.r: Report function can
	now be used with optional output file
	* R/print01Report.r, R/sienaDataCreate.r, src/siena07.cpp: missing
	values in dyadic covariates (incomplete!)

2010-03-15 R-forge revision 62 (RSienaTest only)

	* doc/RSienaDeveloper.tex, doc/Siena_algorithms2.tex
	* inst/examples/baerveldt3.csv, inst/examples/baerveldt4.csv:
	altered changing covariate text to constant covariate as only 2
	waves.
	* src/data/BehaviorLongitudinalData.cpp, .h: C++ support for
	structural variables. (Not yet in R)
	* src/model/many: more code for ML routine.
	* src/utils/Random.cpp: changes to commments

2010-02-27 R-forge revision 61 (Riena only)

	* R/robmon.r: generate rlecuyer random numbers from the siena01
	seed.
	* R/phase3.r: bug in displaying information with few iterations.

2010-02-16 R-forge revision 60 (RSienaTest only)

	* R/printInitialDescription.r, R/sienaDataCreate.r,
	src/data/NetworkLongitudinalData.h,
	src/data/NetworkLongitudinalData.cpp, src/siena07.cpp: average
	indegrees and outdegrees added to data objects, reports and passed
	into to C++

	* R/print01Report.r: report on constraints, reformat list of
	inactive actors.

	* R/simstatsc.r, R/phase2.r, R/maxlike.r: fixes for maxlike
	routine.

2010-02-12 R-forge revision 59 (RSienaTest only except for manual)

	* DESCRIPTION, man/RSiena-package.Rd: new version: 1.0.11
	* R/siena07.r, R/zzz.R, R/siena01.r, R/sienaRDocumentation.r,
	R/robmon.r, R/print01Report.r, R/getTargets.r, R/simstatsc.r:
	bug fix: replace string "RSiena" or "RSienaTest" by variable containing
	package name
	* R/makelike.r, R/maxlikecalc.r, man/maxlikefn.Rd,
	man/sienaModelCreate.rd, R/phase2.r, R/phase3.r,
	R/sienaModelCreate.r, R/sienaprint.r, NAMESPACE: simple MCMC
	routine intended for algorithm testing only.

2010-02-11 R-forge revision 58 (RSiena only)

	* man/, src/: some files from revision 56 which got missed.

2010-02-11 R-forge revision 57

	* R/siena01.r: fix bug which stopped Siena update of effects
	initial values after conditional estimation.

2010-02-11 R-forge revision 56 (RSiena only, cf revision 47)

	* DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.10
	* src/model/effects/generic/*, src/model/effects/effectfactory.cpp:
	multiple networks
	* src/model/filters, src/model/EpochSimulation.cpp,
	src/model/variables/*,
	src/data/Data.cpp, R/sienaDataCreate.r, R/sienautils.r,
	R/simstatsc.r, NAMESPACE: constraints between pairs of networks.
	* src/Makefile, Makefile.win: add new directories
	* R/sienaDataCreate.r, R/print01Report.r: separate balance means
	etc. for groups
	* src/model/ml/*: functions for ML, work in progress.

2010-02-11 R-forge revision 55 (RSienaTest only, (cf revision 52)

	* R/globals.r, R/siena07.r, man/siena07.Rd:
	new silent option with no output.
	* tests/parallel.R, tests/parallel.Rout.save: suppress progress
	message output and include prints of results.

2010-02-11 R-forge revision 54 (RSienaTest only)

	* R/print07Report.r: source formatting
	* data/allEffects.csv: bug in covariate behavior effects
	* configure.win, src/Makefile.win, src/win32/Makefile:
	changes for Win64

2010-02-11 R-forge revision 53

	* R/siena01.r: fixed bug in editing all effects

2010-02-07 R-forge revision 52 RSiena

	* R/globals.r, R/siena07.r, man/siena07.Rd:
	new silent option with no output.
	* tests/parallel.R, tests/parallel.Rout.save: suppress progress
	message output and include prints of results.

2010-02-04 R-forge revision 51 RSiena

	* data/allEffects/csv: Bug in covariate behavior effects
	* configure.win, src/Makefile.win, src/Makevars, src/win32/Makefile:
	changes for Win64
	* r/effects.r: minor fixes to getEffects function (default effects
	for multiple dependent networks.)

2010-02-01 R-forge Revision 50

	* doc/s_man400.tex

2010-02-01 R-forge Revision 49 RSienatest

	* R/simstatsc.r, src/siena07.cpp: fixes to constraint
	* src/model/effects/EffectFactory.cpp,
	src/model/effects/generic/ConstantFunction.cpp: fixes to multiple
	network effects

2010-01-28 R-forge revision 48

	* R/simstatsc.r: fixed bug in sort order of effects

2010-01-26 R-forge revision 47 RSienaTest

	* DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.10
	* src/model/effects/generic/*, src/model/effects/effectfactory.cpp:
	multiple networks
	* src/model/filters, src/model/EpochSimulation.cpp,
	src/model/variables/*,
	src/data/Data.cpp, R/sienaDataCreate.r, R/sienautils.r,
	R/simstatsc.r, NAMESPACE: constraints between pairs of networks.
	* src/Makefile, Makefile.win: add new directories
	* R/sienaDataCreate.r, R/print01Report.r: separate balance means
	etc. for groups
	* src/model/ml/*: functions for ML, work in progress.
	* doc/Siena_algorithms.tex, doc/Siena_ChainStructures.tex: added

2010-01-19 R-forge revision 46 RSienaTest

	* R/effectsDocumentation.r, man/effectsDocumentation.Rd,
	inst/doc/effects.pdf: effects documentation system.

2010-01-19 R-forge revision 45 RSiena

	* NAMESPACE, R/effectsDocumentation.r,
	man/effectsDocumentation.Rd: new documentation function
	* inst/doc/effects.pdf: output from the documentation function/

2010-01-18 R-forge revision 44 RSiena

	* src/model/effects/various.cpp, .h: removed superfluous files

2010-01-18 R-forge revision 43 Siena

	* DESCRIPTION: new version 1.0.9
	* NAMESPACE: new utility functions
	* data/alleffects.csv : new behavior effects, user-specified
	interactions.
	* R/sienaeffects.r, man/includeEffects.Rd,
	man/includeInteractions.Rd, man/setEffect.Rd: utilities to update
	effects object.
	* R/effects.r, man/getEffects.Rd: new parameter for number of
	behavior interaction effects.
	* src/model/effects/many: new behavior effects, user-specified
	interactions.

2010-01-15 R-forge revision 42 RSienaTest

	* inst/doc/s_man400.pdf: new manual

2010-01-15 R-forge revision 41 RSienaTest

	* doc/*, .Rbuildignore, src/sienaProfile.cpp: added developer
	documentation
	* data/allEffects.csv: new effect, altered effect1-3 to integers
	to remove bug in fix(myeff)
	* inst/*.out, *.Rdata: removed stray files from examples directory
	* R/sienaeffects.r, NAMESPACE, man/includeEffects.Rd,
	man/includeInteraction.Rd, man/setEffect.Rd: utility functions to
	update effects object
	* R/siena01.r, R/simstatsc.r, R/printDataReport.r, R/print07Report.r,
	R/Sienatest.r: no longer necessary to include underlying effects
	for interactions.
	* R/effects.r, man/getEffects.Rd: user parameter for number of
	unspecified behavior interactions
	* R/print07report.r, R/sienaprint.r: remove extra sqrt roots in
	standard error of rates for conditional estimation (see revision
	31)
	* R/zzz.r: minor typo
	* src/Makefile.win, src/win32/Makefile: Changes to makefile for 64 bit
	windows
	* src/model/effects/AllEffects.h, src/model/effects/EffectFactory.cpp,
	src/model/effects/PopularityAlterEffect.cpp: New effect
	* src/model/variables/BehaviorVariable.h,
	src/model/effects/BehaviorVariable.cpp: new method
	* tests/parallel.R, tests/parallel.R.save: reduce tests to
	save time in Check.
	* man/RSiena-package.Rd, man/siena07.Rd, man/simstats0c.Rd,
	man/sienaFit.Rd: made examples faster.

2010-01-15 R-forge revision 40 RSiena

	* R/print01report.r, R/sienaprint.r: remove extra sqrt roots in
	standard error of rates for conditional estimation (see revision 32)
	* src/Makefile.win, src/win32/Makefile: Changes to makefile for 64 bit
	windows
	* tests/parallel.R, tests/parallel.R.save: remove timers from
	tests to reduce differences with output.

2010-01-12 R-forge revision 39 RSiena

	* tests/parallel.r: fix bug: use library RSiena not RSienaTest

2010-01-12 R-forge revision 38 RSiena

	* man/RSiena-package.Rd, man/siena07.Rd, man/sienaFit.Rd,
	man/simstats0c.Rd: reduce time for examples
	* tests/parallel.r, tests/parallel.Rout.save: reduce time for tests

2010-01-12 R-forge revision 37: RSienaTest

	* inst/sienascript: reverted to LF eol-style

2010-01-12 R-forge revision 36: RSienaTest

	* all source files: eol-style: native

2010-01-11 R-forge revision 35 RSienaTest

	* inst: added manual and examples to RSienaTest

2010-01-02 R-forge revision 34 RSiena and RSienaTest

	* R/sienaprint.r: corrected layout of sienaFitThetaTable for
	models with both behavior and network variables

2010-01-01 R-forge revision 33 RSiena and RSienaTest

	* inst/doc: updated changes in manual
	* CHANGELOG: updated

2010-01-01 R-forge revision 32 (RSiena: copy of relevant changes from revisions 29-31 to
	RSienaTest)

	* R/simstatsc.r: bug fixes to interactions (not yet functional)
	and name in header block

	* R/print07report.r: took square root of standard errors of rate
	estimates for conditional estimation.

2009-31-12 R-forge revision 31

	* R/simstatsc.r: name in header

	* R/effects.r: made covariate from effects all use the same short
	name.

	* R/print07report.r: standard errors for rate estimate for
	conditional estimation needed square roots.

	* src/*.cpp, src/*.h: many changes, additions and deletions for
	(new) behavior 	effects.

	* data/allEffects.csv: turned off endowment effects where not
	implemented.

2009-12-17 R-forge revision 30

	* R/simstatsc.r: fixed typo in dyadic interactions

2009-12-17 R-forge revision 29

	* R/simstatsc.r: fixed typo in 3-way interations

2009-12-14 R-forge revision 27

	* R/simstatsc.r: fixed problem with multiple processors.

2009-12-01 R-forge revision 26 added RSienaTest version 1.0.9

	* Added many files for user-specified interactions.

	* DESCRIPTION, NAMESPACE, R/simstatsc.r, tests/parallel.r,
	src/Makefile.win: changes necessary for the new package

2009-11-20 R-forge revision 25 new version 1.0.8

	* R/simstatsc.r, R/siena01.r:  default method for estimation is
	conditional if there is only one dependent variable.
	* R/simstatsc.r: fixed bug if only one missing value: missing
	drop=FALSE.
	* R/simstatsc.r: fixed bug in naming of returned simulations
	* inst/sienascript: set to LF only eol style.
	* R/effects.r: uponly, downonly: remove	density effect and linear
	shape effect
	* R/sienaDataCreate.r: set the uponly, downonly flags correctly
	for behavior variables.
	* R/effects.r: corrected bug in creation of effects data
	frame for changing dyadic covariates.
	* R/effects.r: amend some matches for nodesets for bipartite nets
	* R/effects.r, R/printInitialDescription.r: remove structValid
	argument from getNetworkStartingVals as unused
	* R/effects.r: Named the rows and columns of matrix of changes in
	getNetworkStartingVals and getBipartiteStartingVals
	* R/phase3.r, R/sienaprint.r: added t-stat to print method for
	sienaFit objects, improved xtable method
	* R/print01Report.r: added warning about non-integer behavior
	variables
	* R/siena01.r: fixed a bug in deleting rows from table: format and
	object type were out of sync
	* R/sienaDataCreate.r: new methods for adding attributes to
	covariate objects
	* R/Sienatest.r: fix bug: change sign of one-sided tests
	* R/simstatsc.r: change to returndeps flag to avoid it in phase 2.
	* R/simstatsc.r: Create names for interaction effects in
	fixUpEffectNames
	* src/model/EpochSimulation.h,
	src/model/variables/BehaviorVariables.cpp,
	src/model/variables/NetworkVariable.h: removed outdated comments
	and unused variables.
	* R/siena01.r: fixed bug in editing all effects rather than a
	subset.
	* R/print01Report.r: added or corrected report of uponly and downonly
	processing.

2009-11-08 R-forge revision 24

	* DESCRIPTION, man/RSiena.RD: version Number 1.0.7

2009-11-08 R-forge revision 23

	* R/phase1.3, R/phase3.r: Created subroutine to calculate
	derivative matrix
	* R/effects.r: corrected possible bug in creation of effects data
	frame for multigroup projects.
	* R/effects.r: corrected bug in creation of effects data
	frame for changing covariates.
        * R/siena07.r: added effect numbers to the Estimation screen and
	rationalised the display routines.
        * R/sienaTest.r: altered function interface so can call the
	scoreTest function from outside siena07 context. Corrected a
	missing change of sign for onesided test values.
	* R/sienaPrint.r: print methods now return their argument
	invisibly
	* src/siena07.cpp: altered flag for return of simulated dependent
	variables.

2009-11-08 R-forge revision 22

	* R/siena01.r new option to edit effects split by dependent
	variable. Only partially functioning...

2009-11-08 R-forge revision 21

	* src/model/variables/BehaviorVariable.cpp,
	src/model/variables/BehaviorVariable.h: Uninitialised data in scores
	causing NaN's in derivative.

2009-11-05 R-forge revision 20

	* man/siena07.Rd: added detail to return value description
	* src/siena07.cpp: added functionalilty for user-specified
	interactions

2009-11-04 R-forge revision 19

	* R/phase1.r, R/phase2.r, R/phase3.r, R/simstatsc.r; corrected
	finDiff.method flag

2009-10-31 R-forge revision 18

	* src/model/tables/NetWorkCache.cpp, etc: New files added

2009-10-31 R-forge revision 17 many minor bug-fix changes also

	* DESCRIPTION, man/RSiena.RD: version Number 1.0.6
	* NAMESPACE, DESCRIPTION, R/sienaPrint.r : xtable method
	* R/phase1.r, R/phase2.r, R/phase3.r: stopped using ... in call to
	FRAN, which restored speed gain of multiple processors.
	* data/allEffects.R, data/alleffects.csv, R/effects.r: new R effects
	system
	* tests: directory added
	* R/sienaDataCreate.r, R/effects.r, R/printDataReport.r,
	R/simstatsc.r, R/sienaDataCreateFromSession.r, R/print01Report.r,
	R/printInitialDescription: bipartite nets
	* src/data, src/model, src/network, src/utils, src/siena07.cpp:
	new C++ effects system
	* src/model/statisticCalculator.cpp: structural zeros code
	corrected
	* src/model/EpochSimulation.cpp: revert to proper random number
	generator unless parallel running.

2009-10-31 R-forge revision 16 added eol-style properties to text files
