2013-06-18 R-forge revision 232
Changes in RSiena:
   * Drop the possibility to use obsolete package snow and rlecuyer
     if Rversion < 2.14.0; functionality replaced by
     package parallel (siena07.r).
   * Correct DESCRIPTION file to satisfy CRAN requirements.
   * Correct lines in various help pages that were too long
     in the pdf version.

2013-06-15 R-forge revision 231
Changes in RSiena as well as RSienaTest:
   * Make the "cumulative" option operational in BehaviorDistribution()
     (sienaGOF.r).
   * Correct bug in treatment of missing values in sparseMatrixExtraction()
     (sienaGOF.r).
   * Allow sparse observed data matrices, and structural zeros and ones, in
     sparseMatrixExtraction() and networkExtraction(),
     and bipartite networks in networkExtraction() (sienaGOF.r).
   * In case prevAns exists, recalculate z$dinvv instead of taking it
     from prevAns (initializeFRAN.r) (parameter diag may have changed)
   * Report correct centering (by overall means) of individual
     covariates for multi-group objects (print01Report.r).
   * in sienaTimeTest: string in toTest$effectName set to "chisq="
     instead of "p=" (sienaTimeTest.r)
   * In print method for sienaAlgorithm, report of conditional corrected
     in case !x$cconditional (sienaprint.r)
   * If there is a composition change object, MoM estimation is forced
     to be non-conditional (initializeFRAN.r). This is reported in the help file
     (sienaCompositionChange.Rd).     
   * Small changes in help files sienaAlgorithm.Rd, plot.sienaTimeTest.Rd,


2013-05-10 R-forge revision 230
Changes in RSiena as well as RSienaTest:
	* Add attribute maxObsOutDegree to <object of class siena>$depvars[[.]]
     (sienaDataCreate.r).
   * Check whether this maximum observed degree is not higher than maxDegree
	  (printDataReport.r).
	* Fix bug in implementation of maxDegree (initializeFRAN.r)
	* Fix bug in print.siena and extend print.siena (sienaprint.r).
	* Make print method for sienaDependent (sienaprint.r).
Changes only in RSienaTest:
	* File
	  \pkg\RSienaTest\inst\doc\effects.pdf
	  was updated.

2013-05-10 R-forge revision 229
Changes only in RSiena:
   * Korean translation of R messages is updated: changed file
     \pkg\RSiena\po\R-RSiena.pot

2013-04-20 R-forge revision 228
Changes only in RSiena:
	* Files
	  \pkg\RSiena\src\model\variables\DiffusionEffectValueTable.cpp
	  \pkg\RSiena\src\model\variables\DiffusionEffectValueTable.h
	  \pkg\RSiena\man\sienaGOF-auxiliary.Rd
	  \pkg\RSiena\man\sienaGOF.Rd
	  were erroneously not committed in revision 227.
	  Therefore this was done now. 
	* Also, file
	  \pkg\RSiena\inst\doc\effects.pdf
	  was updated.

2013-04-19 R-forge revision 227
Changes in RSiena as well as RSienaTest;
both now are very similar; sienaBayes, algorithms, and profileLikelihoods
are the only functions in RSienaTest not in RSiena.
Available effects now are the same.

I hope the list of changes indicated here is complete.

For Siena only:
	* function bayes() was removed (still under development in RSienaTest).
	* Attributes "allowOnly" and "simOnly" ported from RSienaTest.
	* Improved error messages in  includeEffects ported from RSienaTest.
	* sienaGOF ported from RSienaTest.
	* siena.table() ported from RSienaTest, in file sienatable.r.
	* Changes of revision 226 ported from RSienaTest.

For RSienaTest only:
	* bayes() renamed to sienaBayes() and considerably changed.
	* Added function print.sienaBayesFit to sienaprint.r, with
		new documentation file printsienaBayesFit.Rd.
	* Some invisible developments for settings model.

For RSiena and RSienaTest:
	* Changes to sienaGOF: new use structure with auxiliary functions
		sparseMatrixExtraction, networkExtraction, behaviorExtraction,
		allowing to test any dependent variable;
		commented out some superfluous lines.
	* The function sienaModelCreate() is now called sienaAlgorithmCreate(),
		but the earlier name is still retained as an alias;
		the class name of the object created by this function is now called
		sienaAlgorithm.
	* The function sienaNet() is now called sienaDependent(),
		but the earlier name is still retained as an alias;
		the class name of the object created by this function is now
		sienaDependent.
	* The function effectsDocumentation() now has an extra argument "effects";
		if this points to an effects object, all available effects
		in this effects object are listed with shortName,
		with a variety of other often used characteristics.
	* Effect type "covarBehaviorOneModeRate" was added.
	* Added effects (some existed already in RSienaTest):
		average exposure effect on rate xxxxxx, avExposure
		susceptibility to av. exp. by indegree effect on rate xxxxxx,
			susceptAvIn
		total exposure effect on rate xxxxxx, totExposure,
		infection by indegree effect on rate xxxxxx, infectIn,
		infection by outdegree effect on rate xxxxxx,  infectOut,
		susceptibility to av. exp. by zzzzzz effect on rate xxxxxx,
			susceptAvCovar
		infection by zzzzzz effect on rate xxxxxx, infectCovar,
		WW=>X cyclic closure of xxxxxx, cyWWX
		WW=>X shared incoming xxxxxx, InWWX
		WW=>X shared outgoing xxxxxx, OutWWX
		xxxxxx alter at distance 2 (#), altDist2
		xxxxxx similarity at distance 2, simDist2
		transitive triplets xxxxxx similarity, simXTransTrip
		transitive triplets same xxxxxx, sameXTransTrip
		transitive triplets jumping xxxxxx, jumpXTransTrip
		transitive reciprocated triplets, transRecTrip
		GWESP I -> K -> J (#), gwespFF
		GWESP I <- K <- J (#), gwespBB
		GWESP I <- K -> J (#), gwespFB
		GWESP I -> K <- J (#), gwespBF
		GWESP I <> K <> J (#), gwespRR
		isolate - popularity, isolatePop
		in-isolate Outdegree, inIsDegree
		network-isolate, isolateNet
		outdegree^(1/#) xxxxxx popularity, outPopIntn xxxxxx
		closure jumping yyyyyy, jumpWWClosure
		mixed xxxxxx closure jumping yyyyyy, jumpWXClosure
		cyclic closure of xxxxxx, cyClosure
		shared incoming xxxxxx, sharedIn
	* Outdegree-popularity effect: multiplication by n dropped.
	* GWESP effects: default parameter changed from 25 to 69
		(corresponding to alpha = log(2).) See the manual.
	* Added to siena07:
		option "Dolby" for variance reduction.
		Correlations between scores and statistics are reported in output file;
		this is a measure for the amount of variance reduction.
	* Added to siena07:
		option "diagonalize" for having more possibilities for
		tuning the algorithm
		(extent of diagonalization of matrix D in Robbins-Monro update).
	* sienaTimeTest() updated; now also contains effect-wise tests,
		groupwise tests (for group objects), automatic exclusion of
		collinear effects, and has prettier output and improved	summary.
	* Truncation of update steps in phase2.r modified.
	* Overall maximum convergence ratio, x$tconv.max
		(maximum value of t-ratio for convergence, for any linear combination)
		added to result of siena07.
	* The print method for objects of class siena (created by sienaDataCreate)
		has been extended with printing "uponly" and "downly" attributes,
		if these are TRUE.
	* A bug in the starting values for two-mode networks was corrected.
	* Small bug fixed in print01Report() for reporting of uponly and downonly,
		in the case where this does not affect all periods.
	* Changed almost all .Rd documentation files: sometimes to make them
		better understandable or complete, sometimes to make more appropriate 
		examples, sometimes only minor prettifications.
	* Updated:
		pkg\RSiena(Test)\inst\scripts\Rscript01DataFormat.R, 
	 	pkg\RSiena(Test)\inst\scripts\Rscript02VariableFormat.R,
 	 	pkg\RSiena(Test)\inst\scripts\Rscript03SienaRunModel.R,
 	 	pkg\RSiena(Test)\inst\scripts\Rscript04SienaBehaviour.R.
		(of pkg\RSiena(Test)\inst\scripts\RSienaDescriptives
		 only the date was changed.)
 	* Updated tests\scriptfile.Rout.win to current version
		(scriptfile.Rout.save).
	* Manual and siena.bib updated.

2013-04-17 R-forge revision 226 RSienaTest only

	* changed:
		pkg/RSienaTest/src/model/effects/generic/AlterPredicate.h
		pkg/RSienaTest/src/model/effects/generic/CovariatePredicate.h
		pkg/RSienaTest/src/model/filters/PermittedChangeFilter.
		Note: changes:
        base classes have always a virtual destructor
        reduced visibility of abstract class constructors

2013-03-12 R-forge revision 225

	* Removed files and directories that were put in, at the highest directory
		level, by mistake at revision 220.

2013-02-14 R-forge revision 224 RSiena only

	* Added pkg//RSiena/po/R-ko.mo and pkg//RSiena/po/R-ko.po

2013-01-01 R-forge revision 223

	* R/sienaDataCreateFromSession.R: change assignments to frame of
	function rather than using global environment.

2012-12-24 R-forge revision 222 mostly RSienaTest only

	* tests/slowtest.R (added), R/document.R, .Rbuildignore: Created function
	to concatenate all examples and run them, including the dontrun ones.
	* R/bayes, R/algorithms.r, man/sienaGOF.Rd,
	man/sienaNet.Rd (also RSiena): minor changes to make the new test
	run sensibly.
	* tests/effectsTest.R: edited comments

2012-12-23 R-forge revision 221 RSiena and RSienaTest

	* R/robmon.r, siena07.r, simstatsc.r: corrected check for R version
	so will work with R version 3.0.0.

2012-09-10 R-forge revision 220

	* Unintended changes in highest directory (i.e., without effect on packages);
     undone in revision 225.

2012-07-06 R-forge revision 219
	For RSiena and RSienaTest:
	* Added matrices N3401, N3403, N3404, N3406, and HN3401, HN3403, HN3404,
		HN3406 to RSiena.Rda, with associated documentation files
		N3401.Rd and HN3401.Rd.
	* Updates to manual and RSiena.bib.
   For RSienaTest only:
	* Further serious changes in bayes.r and documentation bayes.tex.
	* Added function print.sienaBayesFit to sienaprint.r, with
		new documentation file printsienaBayesFit.Rd
	* Small changes to sienaGOF: commented out some superfluous lines.
	* Made all siena07 calls in tests and examples to batch=TRUE:
		this affected tests\effectsTest.R, man\plot.sienaTimeTest.Rd,
		man\sienaTimetest.Rd.
	* Changed documentation files bayes.Rd, sienaGroupCreate.Rd,
		siena08.Rd, siena07.Rd, sienaDataCreate.Rd, sienaModelCreate.Rd.
	* Updated tests\scriptfile.Rout.win to current version (scriptfile.Rout.save
		still needs to be done!)
	* New and changed effects: changes to
		\src\AllEffects.h, \data\allEffects.csv,
		in \src\model\effects : \EffectFactory.cpp, AllEffects.h,
			SameCovariateTransitiveTripletsEffect.cpp,
			new files JumpCovariateTransitiveTripletsEffect.cpp and .h
		in \src\model\effects\generic : MixedNetworkAlterFunction.cpp and .h,
			SameCovariateMixedTwoPathFunction.cpp and .h,
			SameCovariateTwoPathFunction.cpp and .h,
			CovariateMixedNetworkAlterFunction.cpp and .h.
   * Removed some extra documentation producing a warning in R CMD check.

2012-06-07 R-forge revision 216

   All for RSienaTest only.
	* R/bayes.r: considerable update (no known errors now,
		except multigroup does not work for dyadic covariates.)
	* R/print07report.r: small cosmetic change
   * data/allEffects.csv,
	  src/model/effects/AllEffects.h, src/model/effects/effectFactory.cpp,
	  src/model/effects/InIsolateDegreeEffect.h,
	  src/model/effects/InIsolateDegreeEffect.cpp,
	  src/model/effects/IsolateNetEffect.h,
	  src/model/effects/IsolateNetEffect.cpp,
	  src/model/effects/IsolatePopEffect.h,
	  src/model/effects/IsolatePopEffect.cpp,
	  src/model/effects/WWXClosureEffect.h,
	  src/model/effects/WWXClosureEffect.cpp,
	  src/model/effects/generic/OutStarFunction.h,
	  src/model/effects/generic/OutStarFunction.cpp,
	  src/model/effects/generic/ReverseTwoPathFunction.h,
	  src/model/effects/generic/ReverseTwoPathFunction.cpp:
	  new effects.
	* R/printInitialDescription.r: minor rewriting.
	* Manual correspondingly updated.

2012-05-18 R-forge revision 213

   All for RSienaTest only.
	* R/effects.r and R/printInitialDescription.r:
	  protect against situations where matrix matchange has zero rows or columns
	  (i.e., prevent runtime error)
	* R/sienaprint.r, R/print07Report.r, R/phase3.r, R/terminateFRAN.r,
	  R/robmon.r, R/sienaModelcreate.r, man/siena07.Rd, man/sienaModelCreate.r:
	  incorporate argument simOnly in sienaModelCreate() to facilitate
	  simulation without estimation.
   * R/initializeFRAN.r, R/sienaDataCreate.r, R/sienautils.r, man/sienaNet.Rd:
     incorporate argument allowOnly in sienaNet() to permit
	  ignoring monotonicity in data and its consequences for upOnly and downOnly.
   * data/allEffects.csv,
	  src/model/effects/AllEffects.h, src/model/effects/effectFactory.cpp,
     src/model/effects/SameCovariateTransitiveTripletsEffect.cpp,
     src/model/effects/SameCovariateTransitiveTripletsEffect.h,
     src/model/effects/TransitiveReciprocatedTripletsEffect.h,
     src/model/effects/TransitiveReciprocatedTripletsEffect.cpp,
     src/model/effects/SimilarityTransitiveTripletsEffect.h,
     src/model/effects/SimilarityTransitiveTripletsEffect.cpp:
     new effects

2012-03-29 R-forge revision 212

   * update of RSiena_Manual.tex, RSiena.bib (both packages)

2012-03-29 R-forge revision 211

	* doc/RSiena_Manual.tex, doc/siena1.png, doc/siena2.png,
	doc/siena3.png, doc/ilcampo.jpg, doc/RSiena.bib moved to inst/doc/
	and copied to RSiena to comply with GPL. Both packages now include
	these files in the tarball but not the binary.
	* .Rinstignore: added
	* .Rbuildignore: added to RSiena and updated in RSienaTest to
	exclude temporary latex files from the tar ball.
	* R/effectsDocumentation.r: bug fix for newly added groups.
	* inst/doc/effects.pdf: updated

2012-03-29 R-forge revision 210 NB new version number sequence. 1.1.210

	* src.siena07utilities.cpp, siena07setup.cpp: changes to R/C++
	interface code. Moved a call to PutRNGstate to _before_ the
	UNPROTECT to fix an intermittent error.
	* tests/effectsTest.R: changes to comments only
	* doc/RSienaDeveloper.tex, tests/scripts.Rout.save: updated output
	file, minor additions to documentation.
	* tests/testrefs/M44compare.out, tests/testrefs/M45compare.out:
	updated test outputs. (RSienaTest only)
	* tests/testrefs/*compare.out: some files got missed last time

2012-03-28 R-forge revision 209 (RSienaTest only)

	* src/model/effects/DiffusionRateEffect.cpp: bug fix

2012-03-25 R-forge revision 208

	* src/data/BehaviorLongitudinalData.cpp: fix memory leak
	* src/model/effects/generic/CovariateDistance2NetworkFunction.cpp:
	fix memory leak
	* src/model/variables/NetworkVariable.cpp: fix bug in endowment
	and creation effect scores for no change.
	* data/allEffects.csv, R/effects.r, R/effectsDocumentation.r:
	split behavior network effects between symmetric and other networks.
	* src/model/model.cpp (RSiena only),
	src/model/variables/DependentVariable.cpp,
	src/model/variables/EffectValueTable.h (RSiena only): added
	comments, formatting
	* src/model/effects/DiffusionRateEffect.cpp: bug fix (RSienaTest
	only)
	* doc/RSienaDeveloper.tex: updated doc (RSienaTest only)
	* doc/MCMCandRM.pdf: added
	* tests/effectsTest.R, tests/sampson.r, testrefs/*,
	.Rbuildignore: new testing files added, not to be included in tar
	ball. (RSienaTest only)
	* inst/examples/Sampson_t2.txt, inst/examples/Sampson_t3.txt,
	inst/examples/Sampson_t4.txt, inst/examples/vtextexoreal.dat:
	added.
	* src/effects.r: correct bug causing crash with sparse matrices
	with changes all in one direction.
	* src/model/EpochSimulation.cpp: added comments
	* src/model/ml/MLSimulation.cpp: correct test when storing
	rejection numbers.
	* src/model/StatisticCalculator.h: formatting (RSienaTest only)
	* src/model/ml/chain.cpp: initialize finalReciprocalRate explicitly.

2012-03-21 R-forge revision 207 (RSienaTest only)
	* siena07internals.cpp, DependentVariable.h,
	DependentVariable.cpp: changed calculation of scores for diffusion
	rate effects
	* StatisticCalculator.h, StatisticCalculator.cpp, DependentVariable.h,
	DependentVariable.cpp, DiffusionRateEffect.h,
	DiffusionRateEffect.cpp: added a function to calculate value of
	a type of diffusion rate effect

2012-03-16 R-forge revision 206 (RSienaTest only)

	* R/effects.R, R/effectsDocumentation.R: added a new behavior rate
	effectGroup covarBehaviorOneModeRate
	* data/allEffects.csv, siena07internals.cpp,
	StatisticCalculator.cpp, DependentVariable.cpp,
	DependentVariable.h, DiffusionRateEffect.cpp,
	DiffusionRateEffect.h: added new diffusion behavior rate effects
	susceptAvIn, susceptAvCovar, infectIn, infectOut, infectCovar,
	totExposure

2012-03-07 R-forge revision 205

	* 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: removed as
	no longer used
	* src/model/effects/allEffects.h: remove the .h's from previous
	entry
	* src/model/effects/CovariateAndNetworkBehaviorEffect.cpp: correct
	memory leak.
	* src/model/effects/generic/CovariateDistance2NetworkFunction.cpp:
	adjust preprocessEgo method.
	* src/model/effects/InteractionCovariateEffect.cpp: amend test for
	missing as in revision 197.
	* src/model/variables/NetworkVariable.cpp: correct calculation of
	this->lalterProbability.

2012-02-29 R-forge revision 204

	* src/model/effects/SimilarityEffect.cpp: fixed bugs in
	endowment/creation statistics.
	* src/model/ml/Chain.cpp: fixed bug causing failure in connect
	with constraints
	* src/model/EpochSimulation.cpp: allow for underflow of sigma2
	when taking square root.
	* src/model/variables/NetworkVariable.cpp: fix bug in creation and
	endowment effect scores for pairwise symmetric network models.
	* R/simstatsc.r: fix bug which stopped chains being returned
	* R/sienaprint.r: amend model print
	* R/sienaDataCreate.r: amend error message for incorrect dyadic
	covariate.
	* R/siena08.r: suppress printed NULLS at end of summary.
	* R/robmon.r: remove cluster.out before using it again.
	* R/phase3.r: change format of report of autocorrelations in phase
	3.
	* R/initializeFRAN.r: forbid maximum likelihood estimation with
	composition change, round calculation of number of MH steps.
	* R/bayes.r: fix incorrect condition, allow to work with non
	constant rates if a dfra is provided, minor reformatting.
	* doc/missingEtc.tex: minor update.
	* po/R-RSiena.pot, po/R-RSienaTest.pot: updated error message
	files

2012-02-19 R-forge revision 203

	* src/siena07setup.cpp: initialize permutation length correctly in
	setup phase of ML.
	* R/robmon.r, R/zzz.r: add check for same package if using
	multiple processes.
	* doc/RSiena_manual.tex: 1) removed details about snow and rlecuyer
	packages 2) amended code to make sparse matrices. (RSienaTest only)
	* tests/scripts.Rout.save: update for reduced diffs.

2012-02-10 R-forge revision 202 (RSienaTest only)

	* doc/RSienaDeveloper.tex: updated various details. Reformatted pages

2012-02-08 R-forge revision 201 (RSienaTest only)

	* R/sienatable.r: added property eol-style=native.
	* src/model/StatisticCalculator.cpp,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/NetworkVariable.cpp: fix some memory leaks in
	settings model.

2012-02-07 R-forge revision 200

	* src/model/variables/DependentVariable.cpp: removing
	networkVariable conditions so score sum terms are calculated for
	behaviour rate effects. (As RSienaTest Revision 199)
	* src/model/EpochSimulation.cpp: remove automatic cast in call to
	log.
	* tests/scripts.R: alter order of testing so less output produced
	when scripts are not tested.
	* src/siena07setup.cpp, src/siena07internals.cpp,
	src/siena07internals.h, src/network/NetworkUtils.cpp,
	src/network/NetworkUtils.h, src/model/Model/cpp,
	src/model/Model.h, src/model/StatisticCalculator.cpp,
	src/model/StatisticCalculator.h,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h,
	src/data/ChangingDyadicCovariate.cpp,
	src/data/ChangingCovariate.h,
	src/data/NetworkLongitudinalData.cpp,
	src/data/NetworkLongitudinalModel.h,
	R/initializeFRAN.r: settings Model. RSienaTest only
	* R/phase3.r: formatting, suppress error problems
	* R/phase1.r: stop if cannot get a derivative matrix in phase 1.
	* R/initializeFRAN.r, src/siena07utilities.cpp, src/siena07utilities.h,
	src/siena07setup.cpp, src/siena07setup.h, src/siena07models.cpp,
	src/siena07sinternals.cpp, src/siena07internals.h: remove
	redundant parameters
	* doc/RSienaDeveloper.tex: fix typo (RSienaTest only)

2012-02-07 R-forge revision 199 (RSienaTest only)

	* src/model/variables/DependentVariable.cpp,
	src/model/variables/EffectValueTable.h,
	src/model/variables/DiffusionEffectValueTable.h: removing
	backslashes from within comments.
	* src/model/variables/DependentVariable.cpp: removing
	networkVariable conditions so score sum terms are calculated for
	behaviour rate effects.
	* src/model/variables/DependentVariable.cpp,
	src/model/variables/DiffusionEffectValueTable.cpp: correction
	calculation of average exposure diffusion rate effect.
	* R/sienatable.r: removal of superfluous variables.

2012-01-29 R-forge revision 198

	* src/siena07internals.cpp: fix a bug causing initialisation of ML
	to be done using the wrong rate parameter. Will change results
	slightly if there was a behavior variable or a bipartite variable.

2012-01-29 R-forge revision 197

	* src/model/effects/CovariateDependentBehaviorEffect.cpp,
	src/model/effects/CovariateDependentBehaviorEffect.h,
	src/model/effects/MainCovariateEffect.cpp: fix bug in changing
	covariate in MainCovariate effect
	* src/model/variables/BehaviorVariable.cpp: fix bug in derivatives
	for maximum likelihood creation effects.

2012-01-28 R-forge revision 196 (RSienaTest only)

	* doc/Debugging.pdf, doc/RSiena_R20104up.pdf: added
	* doc/Siena_algorithms4.tex: amended maximum likelihood spec

2012-01-20 R-forge revision 195

	* inst/scripts/Rscript01DataFormat.R,
	inst/scripts/Rscript02SienaVariableFormat.R,
	inst/scripts/Rscript03SienaRunModel.R,
	inst/scripts/Rscript04SienaBehavior.R: new versions now in RSiena
	too. Also one or two typos corrected.
	* tests/scriptfile.Rout.save, tests/scriptfile.Rout.win,
	tests/scripts.Rout.save, tests/parallel.Rout.save: updated targets for
	checks.
	* tests/scripts.R: Run sub process with --vanilla. Also some
	debugging code added.
	* src/sienaInternals.cpp: treat NaN in covariates the same as NA,
	as is done in the R part of RSiena.
	* src/siena07Models.cpp, src/siena07Utilities.cpp,
	src/model/EpochSimulation.cpp, src/model/Model.cpp,
	src/model/StatisticCalculator.cpp,
	src/ml/MLSimulation.cpp, src/ml/Chain.cpp: minor changes to
	remove compiler warnings.
	* doc/RSienaDeveloper.tex: revisions, additions
	* inst/examples/arclistdata.dat: added file
	* man/algorithms.Rd: corrected spelling
	* man/RSiena-package.Rd: new maintainer email address
	* R/sienaprint.r: leave fixed values of theta in the print

2012-01-17 R-forge revision 194

	* doc/RSIENAspec.tex, man/coDyadCovar.Rd, man/varDyadCovar.Rd,
	R/effects.r, R/initializeFRAN.r, R/sienaDataCreate.r,
	R/sienautils.r, src/data/Data.cpp,
	src/data/NetworkLongitudinalData.cpp,
	src/data/NetworkLongitudinalData.h,
 	src/data/OneModeNetworkLongitudinalData.cpp,
	src/model/filters/LowerFilter.cpp,
	src/model/ml/NetworkChange.cpp,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h,
	src/model/network/Network.h: make treatment of bipartite networks and
	dyadic covariates consistent.
	* R/globals.r: make PrtOutMat cope with null matrices
	* R/initializeFRAN.r: fix to calculation of number of ML steps,
	relax restrictions on behavior interactions.

2012-01-17 R-forge revision 193. RSienaTest only.

	* R/sienatable.r: file added with siena.table function.
	* NAMESPACE: siena.table function added.

2012-01-17 R-forge revision 192.

	* minor but extensive changes to manual
	* inst/scripts/Rscript01DataFormat.R,
	inst/scripts/Rscript02SienaVariableFormat.R,
	inst/scripts/Rscript03SienaRunModel.R,
	inst/scripts/Rscript04SienaBehavior.R: minor changes to scripts
	(RSienaTest only)

2011-12-15 R-forge revision 191.

	* src/model/variables/BehaviorVariable.cpp,
	src/model/variables/NetworkVariable.cpp: altered calculations of
	probabilities to avoid overflow.
	* R/bayes.r: fix bug in accumulation of MII
	* src/model/filters/lowerfilter.cpp: fix bug which made no change
	not permitted
	* data/allEffects.csv: removed endowment effect for indTies for
	symmetric networks
	* R/algorithms.r, R/maxlikec.r, R/phase1.r, R/simstatsc.r,
	src/siena07utilities.cpp, src/siena07models.cpp,
	src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h:
	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/NetworkVariable.cpp,
	src/model/variables/BehaviorVariable.h,
	src/model/variables/NetworkVariable.h,
	src/model/variables/DependentVariable.h:
	removed option (non-functioning) to store change contributions on
	ministeps
	* src/model/EpochSimulation.cpp, src/model/EpochSimulation.h,
	src/siena07Models.cpp, src/siena07models.h:
	remove some non-functioning options to do calculations for chains.
	* R/siena07.r: more attempts to reset the random number kind
	* tests/scripts.R: copied more data files to use for further
	scripts

2011-12-14 R-forge revision 190.

	* R/bayes.r: fix bugs from previous changes

2011-12-14 R-forge revision 189.

	* po/R-RSiena.pot, po/RSienaTest.pot added files for translators.
	* doc/RSienaDeveloper.tex: updated to reflect changes in
	algorithms and other minor details.
	* data/allEffects.csv: fixed typo in shortName for symmetric
	networks
	* man/sienaModelCreate.Rd: updated details
	* R/initializeFRAN.r, R/simstatsc.r, R/maxlikec.r, R/bayes.r,
	R/phase1.r, R/phase2.r, R/robmon.r,
	R/algorithms.r (RSienaTest only): rationalized and tidied code.
	* man/maxlikec.Rd: removed file, details now in man/simstatsc.Rd.
	* max/simstatsc.Rd: expanded to include maxlikec, initializeFRAN
	and terminateFRAN.
	* R/print01Report.r, R/printDataReport.r, R/sienaPrint.r, : minor
	changes to reports.
	* R/sienaeffects.r: fixed bug in error messages
	* src/model/ml/MLSimulation.cpp, src/model/Model.cpp,
	src/siena07Models.cpp: formatting source only.

2011-12-07 R-forge revision 188.

	* added directories po ready for translation files.

2011-12-06 R-forge revision 187.

	* src/siena07setup.cpp: correct change to name of included file in
	previous version: did not compile on case-sensitive systems.
	* doc/RSienaDeveloper.tex: fixed a latex error. (RSienaTest only)

2011-12-04 R-forge revision 186.

	* R/bayes.r, R/initializeFRAN.r, R/maxlikec.r, R/phase1.r,
	R/phase2.r, R/phase3.r, R/robmon.r, R/simstatsc.r,
	src/siena07models.cpp, src/siena07models.h, src/siena07setup.cpp,
	src/siena07utilities.cpp, src/model/EpochSimulation.cpp,
	src/model/EpochSimulation.h, src.model/Chain.cpp,
	src/model/Model.cpp, src/model/Model.h, src/model/State.cpp,
	src/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h: added
	facility to return log likelihood after simulation, stopped
	returning of chains every iteration. Bug fixes for ML.
	* R/algorithms.r: added to RSienaTest (from examples directory).
	* man/profileLikelihoods.Rd, man/algorithms.Rd: (RSien aTest only)
	help files for functions in algorithms.r.

2011-11-27 R-forge revision 185.

	* R/robmon.r, inst/examples/algorithms.r, inst/examples/runalg.r:
	minor changes to paths. Added parallel package to algorithm code
	(RSienaTest only for the algorithm code)
	* R/bayes.r: made functions internal to reduce copying. Replaced snow
	and Rlecuyer by parallel (non optionally)
	* src/model/ml/Chain.cpp, src/model/ml/MLSimulation.cpp,
	src/model/model.cpp: remove memory leaks.
	* src/siena07models.cpp: Ensure end state is on stored chain. Fix
	protection imbalance.
	* src/siena07utilities.cpp: correct copy of initial state to sub
	processes.
	* src/siena07setup.cpp: remove print of probabilities at start.
	* src/model/ml/Chain.h, src/model/MLSimulation.h,
	src/model/Model.h, src/model/tables/Cache.cpp,
	src/model/tables/Cache.h: altered comments only

2011-11-14 R-forge revision 184.

	* src/model/StatisticCalculator.cpp: fix memory leaks in network and
	behavior rate statistics. (Latter is long standing, former
	introduced in revision 181.

2011-11-11 R-forge revision 183.

	* R/initializeFRAN.r, R/phase1.r, R/phase3.r: fix minor
	bugs. Could not interrupt phase 1 or 3 of siena07, could use dfra
	from MOL with ML and vice versa.

2011-11-11 R-forge revision 182.

	* R/bayes.r, src/siena07models.cpp:correct return of acceptances
	etc. and new format of dff
	* R/sienaTimeTest.r: fix bug with multi groups and differing actor
	set sizes.

2011-11-04 R-forge revision 181.

	* src/data/BehaviorLongitudinalData.cpp,
	src/data/BehaviorLongitudinalData.h,
	src/data/NetworkLongitudinalData.cpp, src/siena07Setup.cpp,
	src/data/NetworkLongitudinalData.h, src/siena07Internals.cpp,
	src/model/StatisticCalculator.cpp, src/network/NetworkUtils.h,
	src/model/StatisticCalculator.h, src/network/NetworkUtils.cpp,
	R/initializeFRAN.r: Reorganised calculation of dependent variables
	with missing data removed. Hopefully speedier.
	* src.network/Network.cpp: added a doxygen commment for clone
	* R/siena07.r, R/robmon.r: reset the random number generator to
	* src/model/effects/behaviorInteractionEffect.h: correct
	properties to be eol-style not executable
	normal type after using parallel package. (RSiena only)

2011-11-04 R-forge revision 180.

	* R/phase1.r, R/phase3.r: revision to avoid time consuming copies
	* src/model/StatisticalCalculator.cpp: stop setting up of extra networks
	if no endowment or creation effects. (Diffusion rate effects were
	included in RSiena inadvertently: code removed in revision 181)..
	* src/model/effects/behaviorInteractionEffect.cpp: correct
	properties to be eol-style not executable (RSiena only)

2011-10-28 R-forge revision 179.

	* R/robmon.r: fix problem with forking clusters.
	* tests/scriptfile.Rout.save: updated version of script test output.

2011-10-27 R-forge revision 178. Fixes from rev 175 and rev 177 copied to RSiena.

	* R/phase3.r: correct covariance matrix for effects that have been
	fixed. Second attempt for RSienaTest
	* R/sienaGOF.r: RSienaTest only: back out change in rev 177.
	* R/effects.r: Rsiena only: remove out-of-date comments
	* R/sienaDataCreate.r: RSiena only. Remove inter-network
	constraints which relate a symmetric network to a non-symmetric
	network.
	* R/effectsMethods.r: RSiena only. make fix(myeff) return quietly
	with no change if session is not interactive.
	* man/bayes.Rd, man/maxlikec.Rd, R/bayes.r, NAMESPACE: bayes now
	exported in RSiena too (see rev 168)
	* man/updateTheta.Rd, R/initializeFRAN.r, NAMESPACE: new function:
	updateTheta (See rev 168/9)
	* inst/examples/s50e.dat, inst/scripts/*, tests/scripts.R,
	tests/scriptfile.Rout.save, tests/scripts.Rout.save,
	tests/scriptfile.Rout.win: added scripts, data file
	to use in script checking (see rev 175/6)
	* R/simstatsc.r, R/siena07.R, R/robmon.R, man.siena07.Rd:
	snow/rlecuyer or parallel used depending on R version. New
	argument for siena07 to allow option FORK as well as PSOCK.
	* man/sienaModelCreate.Rd, R/sienaModelCreate.r: altered
	multiplication factor from 4 to 5.
	* man/sienaTimeTest.Rd,R/sienaTimeTest.r: added tests for models
	fitted by finite differences or maximum likelihood.
	* R/simstatsc.r, R/maxlikec.r, R/phase1.r, R/phase3.r: simplified
	code, added new utility functions, changed format of stored
	derivative matrices and made the by wave set optional to save
	memory. Matrix objects are used for maxlike (as symmetric and this
	will save space) with minimal compatible changes to finite
	differences. Revert to normal matrix for dfra. (see rev 168)
	* R/sienaprint.r, NAMESPACE, man/xtable.Rd: added dummy xtable command
	to call real one.
	* src/model/ml/Chain.cpp, src/model/ml/MiniStep.cpp,
	src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h,
	src/siena07models.cpp, src/siena07setup.cpp, src/siena07models.h:
	maximum likelihood updates
	* src/model/variables/DependentVariable.cpp,
	src/model/variables/NetworkVariable.cpp: fix bug causing crashes with
	symmetric networks alongside either behavior variable or non-symmetric
	network. (see rev 175)
	* tests/parallel.Rout.save: updating the comparison file.
	* doc/_emacs, doc/.emacs: sample emacs initialization files

2011-10-27 R-forge revision 177 RSienaTest only (committed prematurely!)

	* inst/scripts/Rscript01DataFormat.R, inst/examples/s50e.dat,
	tests/scripts.R, tests/scriptfile.Rout.save,
	tests/parallel.Rout.save: added data file for testing scripts. Minor
	textual changes. Removed library commands for snow and rlecuyer as
	will not be necessary in 2.14.0.
	* src/model/variables/DependentVariable.cpp, R/sienaDataCreate.r:
	formatting changes
	* R/simstatsc.r, R/siena07.R, R/robmon.R, man.siena07.Rd:
	snow/rlecuyer or parallel used depending on R version. New
	argument for siena07 to allow option FORK as well as PSOCK.
	* R/phase3.r: correct covariance matrix for effects that have been
	fixed.
	* R/sienaTimeTest.r: fix bug since replaced arrays for derivatives
	by wave by lists of sparse matrices: the error trap failed.
	* doc/RSienaDeveloper.tex: added comments about emacs, debugging
	R, new parallel package, etc.
	* R/sienaGOF.r: local change committed in error: backed our in
	r178.

2011-10-14 R-forge revision 176 RSienaTest only

	* inst/scripts/RScriptDataFormat.R,
	inst/scripts/RScriptSienaVariable.R,
	inst/scripts/RScriptSienaRunModel.R,
	inst/scripts/RScriptSienaBehaviour.R,
	inst/scripts/RSienaSNADescriptives.R: removed sna and network code to
	separate file which is excluded from testing by containing 'SNA' in the
	name
	* R/siena07.r, tests/scripts.R, tests/scriptfile.Rout.save,
	tests/scripts.Rout.save, tests/scriptfile.Rout.win:
	amended to work better multi-platform, although linux not yet tested.
	* R/document.r, doc/auto.tex, RSienaDeveloper.tex: new function to
	automate construction of the function table in the manual.
	* src/model/variables/DependentVariable.cpp: fix bug in diffusion
	effects.

2011-10-06 R-forge revision 175 RSienaTest only

	* doc/RScriptDataFormat.R, doc/RScriptSienaVariable.R,
	doc/RScriptSienaRunModel.R, doc/RScriptSienaBehaviour.R: moved to
	inst/scripts. Renamed to have a numbering sequence so can concatenate in
	correct order for testing. Minimal changes to make the tests work within
	R CMD check sequence.
	* R/siena07.r: check for availability of X11 device on non-Windows and
	force batch=TRUE if necessary. Only set random seed if not testing
	scripts.
	* R/effectsMethods.r: make fix command for a sienaEffects object
	terminate return the object unchanged if called non-interactively.
	* R/sienaprint.r, NAMESPACE, man/xtable.Rd: added dummy xtable command
	to call real one.
	* tests/scripts.R, tests/scripts.Rout.save, tests/scriptfile.Rout.save:
	added file to test scripts, controlled by an environment variable.
	* doc/RSiena_Manual.tex: altered path to scripts and file names.
	* R/sienaDataCreate.r: remove inter-network constraints which relate a
	symmetric network to a non-symmetric network
	* src/model/variables/DependentVariable.cpp,
	src/model/variables/NetworkVariable.cpp, doc/simstats0c.tex,
	doc/RSienaSpec.tex: fix bug causing crashes with
	symmetric networks alongside either behavior variable or non-symmetric
	network.
	* src/model/effects/DiffusionRateEffect.cpp,
	src/model/StatisticCalculator.cpp,
	src/model/variables/DiffusionEffectValueTable.cpp: minor formatting

2011-10-04 R-forge revision 174

	* doc/RSiena_Manual.tex, doc/Siena_algorithms4.tex: added meta-analysis,
	minor changes to manual.

2011-09-29 R-forge revision 173

	* doc/RSiena_Manual.tex: some changes, explanation mainly
	* doc/RSiena.bib: very small updates.

2011-09-19 R-forge revision 172 RSienaTest only (NB version number did not match)

	* src/model/effects/DiffusionRateEffect.cpp,
	src/model/effects/DiffusionRateEffect.h,
	src/model/variables/DiffusionEffectValueTable.cpp,
	src/model/variable/DiffusionEffectValueTable.h: files created to
	implement diffusion rate effects.
	* data/allEffects.csv, src/siena07internals.cpp,
	src/model/StatisticCalculator.cpp,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h: diffusion rate effect
	averageExposure added.

2011-09-07 R-forge revision 171

	* R/globals.r, R/siena08.r, man/siena08.Rd: fix bugs in siena08 which was
	using out of date effects object which included unselected underlying
	effects from interactions, and report would not print if it had
	previously been displayed. New parameter to control maximum numnber of
	iterations.
	* R/printInitialDescription.r: fix bug in description of more than two
	groups.
	* R/initializeFRAN.r: (RSienaTest only) add some validation to
	updateTheta.
	* R/globals.r: (To Rsiena also now) allow format of printed matrices to
	be controlled by an environment variable. Designed for use in testing as
	there are rounding incompatibilities between platforms.
	* man/simstats0c.Rd: (RSiena only) updated page.
	* R/sienaprint.r, R/printDataReport.r, R/print07report.r, R/robmon.r,
	R/siena07Gui.r: (RSiena only) as for revision 168 in RSienatest.

2011-08-22 R-forge revision 170

	* doc/RSiena_Manual.tex: changes mainly for non-directed models
	* doc/RSiena.bib: small updates.

2011-08-09 R-forge revision 169 RSienaTest only

	* R/initializeFRAN.r: bug fix to order of sienaTimeFix and prevans etc.

2011-08-08 R-forge revision 168 RSienaTest only.

	* R/sienaprint.r: altered headings from 't-statistics for convergence'
	to 'convergence t-ratios'
	* doc/bayes.tex, doc/maxlikec.tex, doc/RSiena_Manual.tex,
	doc/RSienaDeveloper.tex, doc/RSIENAspec.tex, doc/simstats0c.tex:
	updates to the documentation.
	* R/bayes.r, R/maxlikec.r, R/initializeFRAN.r, R/printDataReport.r,
	R/print07Report.r, R/robmon.r, R/siena07Gui.r, R/sienaModelCreate.r,
	R/simstatsc.r, man/bayes.Rd, man/maxlikec.Rd, man/sienaModelCreate.Rd,
	man/simstats0c.Rd, NAMESPACE, src/siena07Models.cpp,
	src/siena07Models.h, src/siena07utilities.cpp, src/siena07setup.cpp,
	src/model/ml/MiniStep.cpp, src/model/ml/MLSimulation.cpp,
	src/model/ml/MLSimulation.h, src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h: exported bayes, added help
	pages for maximum likelihood and bayes.  Various changes to maximum
	likelihood: still in progress.
	* man/updateTheta.Rd, R/initializeFRAN.r: new function to update theta
	initial values from a sienaFit. Reordered adding time dummies to happen
	before prevAns processing in siena07.
	* R/effects.r, src/model/ml/chain.cpp: tidy up code.
	* R/globals.r: allow format of printed matrices to be controlled by an
	environment variable. Designed for use in testing as there were rounding
	incompatibilities between platforms.
	* R/maxlikec.r, R/phase1.r, R/phase3.r, R/sienaTimeTest.r,
	man/sienaTimeTest.Rd: simplified code, added new utility functions,
	changed format of stored derivative matricesand made the by wave set
	optional to save memory. Matrix objects are used for maxlike
	(as symmetric and this will save space) with minimal compatible changes
	to finite differences. Revert to normal matrix for dfra.
	* src/data/ConstantDyadicCovariate.cpp,
	src/data/ConstantDyadicCovariate.h,
	src/model/variable/NetworkVariable.cpp,
	src/model/variable/NetworkVariable.h: Added access method to map of row
	values. Also some commented out code eg to select alter from a smaller
	set.
	* tests/parallel.Rout.save: updated output from tests

2011-08-03 R-forge revision 167

	* doc/RSiena_Manual.tex: minor changes
	* data/allEffects.csv, src.effects/effectFactory.cpp: renamed avSimX,
	totSimX, avAltX to avSimEgoX etc in preparation for avSimAlterX etc
	to appear soon!
	* R/effects.r: added network names to behavior effects if there is more
	than one network.
	* R/initializeFRAN.r: removed duplicate variable names from network
	interaction effects.
	* R/siena01.r, doc/RscriptDataFormat.R: change name of manual in model
	help function and script.
	* R/sienaDataCreate.r: trap missing Actors node set if node sets are
	supplied. (was crashing!)
	* DESCRIPTION: added BuildResaveData:no to stop allEffects.r being
	compressed in the build.

2011-08-02 R-forge revision 166

	* doc/RSiena_Manual.tex: corrections
	* doc/RSiena.bib: small format corrections

2011-07-28 R-forge revision 165

	* doc/RSiena_Manual.tex: corrections
	* doc/RSiena.bib: a few additions

2011-07-27 R-forge revision 164

	* R/effects.r: change default behavior effects to include quadratic
	shape unless range is less than 2 (from less than or equal to 2).
	* R/siena01.r: change name of manual.
	* R/initializeFRAN.r: remove duplicate variable names from behavior
	interaction effects.
	* man/siena07.Rd: correct description of prevAns.

2011-07-23 R-forge revision 163

	* R/effectsDocumentation.r: fix bug caused by changes to effects
	* R/phase1.r: avoid allocation of unnecessary storage for derivatives

2011-07-10 R-forge revision 162

	* src/model/effects/OutTruncEffect.cpp,
	src/model/effects/OutTruncEffect.h, src/model/effects/allEffects.h,
	src/model/effects/EffectFactory.cpp: renamed effect to TruncatedOutDegree
	to comply with standards.
	* src/model/effects/BehaviorInteractionEffect.cpp: remove extraneous
	variable definitions to remove compiler warnings.

2011-07-02 R-forge revision 161

	* man.siena08.Rd: add note that names of effects must match
	* man/siena07.Rd, man/simstats0c.Rd: minor edits.
	* R/effects.r, R/sienaDataCreate.r: minor edits of comments
	* R/bayes.r, R/maxlikec.r, inst/examples/algorithms.r: Bayesian routine
	was failing for single data objects.
	* R/RSienaRDocumentation.r: fix for internal functions of internal
	functions. Clumsy at present.
	* man/RscriptSienaRunModel.R: minor correction to text, many trailing
	spaces removed.

2011-06-24 R-forge revision 160

	* src/model/effects/BehaviorInteractionEffect.cpp,
	src/model/effects/AltersCovariateAverageEffect.cpp,
	src/model/effects/LinearShapeEffect.cpp,
	src/model/effects/MainCovariateEffect.cpp,
	src/model/effects/IndegreeEffect.cpp,
	src/model/effects/OutdegreeEffect.cpp,
	src/model/effects/SimilarityEffect.cpp (this one was changed in the
	previous revision): make endowment and creation
	effects consistently subtract the previous value. Interactions now
	divide by minus the difference rather than the current value.

2011-06-23 R-forge revision 159

	* src/model/effects/BehaviorInteractionEffect.cpp,
	src/model/effects/BehaviorInteractionEffect.h: forgotten in previous
	revision.

2011-06-22 R-forge revision 158

	* data/allEffects.csv, R/effects.r,
	src/model/effects/InteractionCovariateEffect.cpp,
	src/model/effects/InteractionCovariateEffect.h,
	src/model/effects/SimilarityEffect.cpp,
	src/model/effects/SimilarityEffect.h: fix replication bug in unspecified
	interactions, remove influence 1-sided effects, replace influence
	interaction effects by 3 options. Tidy up covarBehaviorObjective group.
	* data/allEffects.csv, R/effectsMethods.r, R/initializeFRAN.r,
	src/model/effects/allEffects.h,
	src/model/effects/AltersCovariateAverageEffect.cpp,
	src/model/effects/AltersCovariateAverageEffect.h,
	src/model/effects/AverageAlterEffect.cpp,
	src/model/effects/AverageAlterEffect.h,
	src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h,
	src/model/EffectFactory.cpp,
	src/model/effects/IndegreeEffect.cpp, src/model/effects/indegreeEffect.h,
	src/model/effects/LinearShapeEffect.cpp,
	src/model/effects/LinearShapeEffect.h,
	src/model/effects/MainCovariateEffect.cpp,
	src/model/effects/MainCovariateEffect.h,
	src/model/effects/OutdegreeEffect.cpp,
	src/model/effects/OutdegreeEffect.h,
	src/model/variables/BehaviorVariable.cpp: behavior interactions
	* R/initializeFRAN.r: fix bug: underlying effects of interactions with
	include = FALSE were being included.
	* R/sienaTimeTest.r, doc/sienaTimeFix.doc (RSienaTest only): implement
	time dummies for behavior effects.

2011-06-18 R-forge revision 157

	* R/phase2.r: corrected definition of standard deviation used to control
	maximum jump. Was incorrect if using prevAns as it had the deviations
	from phase 3 rather than phase 1.
	* R/phase1.r, R/maxlikec.r, R/siena08.r: reformatting, using complete
	object names
	* R/bayes.r: remove unused variables to avoid warnings
	* man/sienaFit.Rd, R/effectsDocumentation.r, R/RSienaRDocumentation.r,
	R/sienaprint.r, DESCRIPTION, NAMESPACE: alter interface to xtable to
	allow loading package without it.

2011-06-13 R-forge revision 156

	* R/bayes.r, R/maxlikec.r, R/initializeFRAN.r, R/phase1.r,
	src/model/ml/chain.cpp, src/model/ml/chain.h,
	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/siena07internals.cpp, src/siena07internals.h,
	src/siena07models.cpp, src/siena07models.h, src/siena07setup.cpp,
	src/siena07/utilities.cpp, src/siena07utilities.h: Bayesian
	routine now in R, calling normal maxlike routine. Also end state vector
	for chains.
	* R/effects.r: minor bug if up or down only for some waves only and
	bipartite. Density effect was removed.
	* R/sienaprint.r: new method to print initial and end states of chains:
	chains.data.frame.

2011-06-12 R-forge revision 155

	* R/initializeFRAN.r: fix bug re behavior variables with values 10 or 11
	* data/allEffects.csv: alter short name for egoXaltX for symmetric
	networks to match that for non-symmetric ones.

2011-06-05 R-forge revision 154 RSienaTest only

	* doc/missingsEtc.tex, doc/bayes.tex, doc.maxlikec.tex: added
	* doc/RSienaSpec.tex, doc/simstats0c.tex: updated
	* R/bayes.r, R/maxlikec.r, R/initializeFRAN.r: new Bayes routine

2011-06-04 R-forge revision 153

	* R/effects.r, R/initializeFRAN.r, R/print07Report.r, R/sienaprint.r,
	src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h,
	src/model/effects/NetworkEffect.cpp, src/model/effects/NetworkEffect.h,
	src/model/EpochSimulation.cpp,
	src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h,
	src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h,
	src/model/model.cpp, src/model/model.h,
	src/model/StatisticCalculator.cpp, src/model/StatisticCalculator.h,
	src/model/variables/BehaviorVariable.cpp,
	src/model/variables/BehaviorVariable.h,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h,
	src/siena07internals.cpp: creation effects (incomplete)
	* src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h:
	Minor changes to algorithm for model type B.
	* R/initializeFRAN.r, R/maxlikec.r, R/phase3.r, R/simstats0c.r
	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/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h
	src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h,
	src/siena07models.cpp, src/siena07setup.cpp, src/siena07setup.h,
	src/siena07utilities.cpp, src/siena07utilities.h: ML work in progress.
	Includes corrections for bipartites, new parameter to return the chains,
	construction of initial chain corrected with constraints between
	networks, variable permutation lengths
	* R/bayes.r, src/model/effects/StructuralRateEffect.cpp,
	src/model/effects/StructuralRateEffect.h,
	src/model/EpochSimulation.cpp, src/model/EpochSimulation.h,
	src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h, src/siena07internals.cpp,
	src/siena07models.cpp, inst/examples/algorithms.r, int/examples/runalg.r:
	Bayes, algorithms (still incomplete)
	* R/effectsMethods: fix bug which prevented time dummies showing
	on a print of the effects object.
	* R/phase3.r: minor change to code controlling iterations for
	multiple processors. Stop allocating unnecessary arrays.
	* R/siena07.r, R/siena01.r, R/sienatest.r,
	src/model/effects/OutTruncEffect.cpp: reformatting only
	* (RSienaTest only)
	src/model/effects/EffectFactory.cpp, src/model/effects/AllEffects.h,
	src/model/effects/generic/GwespFunction.cpp,
	src/model/effects/generic/GwespFunction.h: replaced GwespEffects by a
	generic one using a GwespFunction.
	* doc/RSiena_Manual.tex rename from doc/s_man400.tex
	*doc/RSienaDeveloper.tex: added C++ standards, notes about environment
	variables for use when checking packages.

2011-05-29 R-forge revision 152 RSienaTest only

	* R/sienaGOF.r: Fixed a few bugs,  doc/s_400.tex: updated the script

2011-05-27 R-forge revision 151

	* R/observationErrors.r: added various traps for vectors of length
	1, removed spaces from function comments (RSienaTest was missed in
	revision 150).
	* R/effects.r: remove final few unused variables.

2011-05-27 R-forge revision 150

	* cleanup.win, cleanup, src/Makevars, src/Makevars.win: changes
	for building and cleaning directories.
	* src/siena07utilities.cpp, src/sienaModels.cpp,
	src/models/ml/chain.cpp: remove compiler warning about set but
	unused variables
	* R/phase3.r, R/print01Report, R/siena08.r, R/sienaDataCreate.r,
	R/sienaDataCreateFromSession.r: remove partial argument matches
	* R/bayes.r, R/effects.r, R/initializeFRAN.r, R/maxlike.r,
	R/maxlikecalc.r, R/observationErrors.r, R/phase1.r, R/phase2.r,
	R/print01Report.r, R/printDataReport.r,
	R/printInitialDescription.r, R/robmon.r, R/RSienaRDocumentation.r,
	R/siena01.r, R/siena07.r, R/sienaDataCreate.r,
	R/sienaDataCrateFromSession.r, R/Sienatest.r, R/simstatsc.r:
	remove codetools warnings about variables set but unused
	* R/observationErrors.r: added various traps for vectors of length
	1, removed spaces from function comments.

2011-05-26 R-forge revision 149 RSienaTest only

	* R/sienaGOF.R, NAMESPACE, doc/RSiena.bib, doc/s_man400.tex:
	Minor debugs for multi-wave
	data in sienaGOF, added summary.sienaGOF functionality,
	added a model selection script to the manual.

2011-05-25 R-forge revision 148 RSienaTest only

	* man/sienaGOF.Rd, man/sienaGOFsupplement.Rd,
	R/sienaGOF.R, NAMESPACE,
	src/initializeFRAN.r: overhaul of sienaGOF.

2011-05-19 R-forge revision 147 RSienaTest only

	* doc/s_man400.tex, doc/Siena_algorithms4.tex: updated
	documentation

2011-05-16 R-forge revision 146

	* src/Makevars.win: alter linking to reduce command line length
	* doc/s_man400.tex: add tex code to reduce size of pdf, many
	updates
	* doc/RSiena.bib, doc/simstatsc.tex, doc/RSienaDeveloper.tex:
	updated documentation for symmetric networks and other minor changes.
	* R/siena08.r: formatting changes only
	* R/sienaDataCreate.r: set diagonals to NA for sparse matrices
	when calculating degree and setting attributes
	* R/sienaDataCreateFromSession.r: if using read.pajek to read a
	non-directed network duplicate the ties in the edgelist.

2011-04-20 R-forge revision 145

	* src/model/effects/outTruncEffect.cpp: reformating

2011-04-19 R-forge revision 144

	* data/allEffects.csv, src/model/effects/AllEffects.h,
	src/model/effects/EffectFactory.cpp,
	src/model/effects/OutTruncEffect.h,
	src/model/effects/OutTruncEffect.spp: new effect OutTruncEffect

	* R/siena08.r, R/observationsErrors.r,
	man/print.sienaMeta.Rd, man/siena08.Rd: added ML
	method to siena08, enhanced plots.

	* doc/RSiena.bib, doc/Siena_algorithms4.tex,
	doc/s_man400.tex, doc/RscriptDataFormat.R,
	doc/RscriptSienaBehaviour.R, doc/RscriptSienaRunModel.R,
	doc/RscripSienaVariableFormat.R: major edits, scripts now included
	in latex.

	* man/includeEffects.Rd: added another example

	* man/s50.Rd, man/s501.Rd, man/s502.Rd, man/s503.Rd, man/s50a.Rd:
	more helpful information.

	* R/initializeFRAN.r, R/maxlikec.r, man/summary.iwlsm.Rd:
	added eolstyle property.

2011-03-13 R-forge revision 143 RSienaTest only

	* data/allEffects.csv: Modified default parm for Gwesp effects
	* src/model/effects/GwespEffect.h added as superclass to all Gwesp effects
	* src/model/effects/GwespEffect.cpp Now implements GwespAbstract class
	* src/model/effects/GwespBFEffect.h Now implements GwespAbstract class
	* src/model/effects/GwespFBEffect.h Now implements GwespAbstract class
	* src/model/effects/GwespBBEffect.h Now implements GwespAbstract class
	* src/model/effects/GwespFFEffect.h Now implements GwespAbstract class
	* src/model/effects/GwespRREffect.h Now implements GwespAbstract class
	* src/model/effects/GwespBFEffect.cpp Now implements GwespAbstract class
	* src/model/effects/GwespFBEffect.cpp Now implements GwespAbstract class
	* src/model/effects/GwespBBEffect.cpp Now implements GwespAbstract class
	* src/model/effects/GwespFFEffect.cpp Now implements GwespAbstract class
	* src/model/effects/GwespRREffect.cpp Now implements GwespAbstract class
	* man/sienaGOF.Rd: Added primitive snow cluster support,
	option for robust covariance estimation
	* R/sienaGOF.r: Added primitive snow cluster support,
	option for robust covariance estimation

2011-03-06 R-forge revision 142 RSienaTest only

	* R/sienaGOF: fixed a plotting issue with missing data
	*  src/model/effects/EffectFactory.cpp: added GWESP terms
	* src/model/effects/AllEffects.h: added GWESP terms
	* src/model/effects/EffectFactory.cpp: added GWESP terms
	* data/allEffects.csv: added GWESP terms
	* man/sienaGOF.Rd: Incorporated GWESP into the model
	* src/model/effects/GwespBFEffect.h added
	* src/model/effects/GwespFBEffect.h added
	* src/model/effects/GwespBBEffect.h added
	* src/model/effects/GwespFFEffect.h added
	* src/model/effects/GwespRREffect.h added
	* src/model/effects/GwespBFEffect.cpp added
	* src/model/effects/GwespFBEffect.cpp added
	* src/model/effects/GwespBBEffect.cpp added
	* src/model/effects/GwespFFEffect.cpp added
	* src/model/effects/GwespRREffect.cpp added
	* NOTE: the 'parm' column needs an integer, and I got
	around this by using it as a "hundredths" interpretation
	so that I x 100 when it reaches the effect object's
	constructor. It would be nice to have it imported in
	"createEffect" as a double.

2011-02-26 R-forge revision 141

	* man/RSiena-package.Rd, DESCRIPTION: fix typos, one making check fail!

2011-02-24 R-forge revision 140

	* R/sienaGOF.r: Added cumulative tests, simulated image
	  function imageGOF, and cleaned up the code to reflect
	  RSiena coding standards. Added image plot to plot.sienaGOF.
	* man/sienaGOF.Rd: Changes to reflect the above

2011-02-23 R-forge revision 139

	* src/model/ml/MLsimulation.cpp,
	src/model/variables/NetworkVariable.cpp: ML for bipartite
	networks.

2011-02-22 R-forge revision 138

	Change version number on RSiena to 137

2011-02-22 R-forge revision 137

	* Changes to RSienaTest Only
	* DESCRIPTION: removed dependency on snopgof (for now!) and add
	  -ed dependency for MASS, sna, vioplot for sienaGOF.
	* R/sienaTimeTest.r: added functionality for behavioral dummies
	  but they will not work until behavioral interaction effects
	  are supported.
	* R/sienaGOF.r: removed dependency on snopgof (runs standalone)
	  and a number of smaller features like being able to run a
	  joint test across all waves or break them out, having control
	  over the centrality measure (mean, median, etc.), and not
	  requiring that the auxiliary statistics are non-collinear
	  (this is where MASS's ginv comes in). I also moved the
	  relevant functionality from snopgof directly into the code.
	* man/sienaGOF.Rd: Changes to reflect the above

2011-02-21 R-forge revision 136

	* R/initializeFRAN.r: fix bug in bipartite networks: diagonals
	were being zeroed.
	* R/siena01.r: correct test for maximum degree in display

2011-02-05 R-forge revision 135

	* R/siena08.r: fix bug in summary method. Just layout, caused crash.

2011-02-05 R-forge revision 134

	* R/phase2.r, R/siena08.r, man/siena08.Rd, man/print.sienaMeta.Rd:
	changes as in revision 133 copied to RSiena.
	* R/siena08.r, man/siena08.Rd, man/print.sienaMeta.Rd: changes to
	format of new code, reinstate object in summary method  help page.
	* R/iwlsm.r, man/iwlsm.Rd: correct calculation of variance estimate
	* R/sienaDataCreate.r: minor amendments
	* R/sienaDataCreateFromSession.r: message from siena01Gui if
	changing dyadic covariates do not match number of observations.
	* R/sienaTimeTest.r: message that timedummies are not implemented
	for structural rate effects.
	* src/model/ml/MLSimulation.cpp, src/model/ml/NetworkChange.cpp,
	src/model/variables/NetworkVariable.cpp: changes for ML, should now run OK
	for bipartite networks.
	* src/model/variables/DependentVariable.cpp: added some error trapping.
	* tests/parallel.R, tests/parallel.Rout.save: removed multiple
	processes from tests as they were failing on R-forge.

2011-01-25 R-forge revision 133 (RSienaTest only)
        * R/phase2.r: comment out two test lines causing a crash of the ML
        estimation when model specifications get so large that subphases
        exceed 1000 iterations.
        * R/siena08.r: debugging and adding of functionalities to the meta-
        analysis.
        * man/siena08.Rd: explain new features in help function
        * man/print.sienaMeta.Rd: explain new features in help function

2011-01-17 R-forge revision 132
	* Changing revision 131 to conform with coding standards
2011-01-17 R-forge revision 131
	* Changes to RSienaTest Only
	* R/gof.r: Added. Contains the function sienaGof and other functions
	for performing basic goodness of fit tests from arbitrary functions.
	This function requires the snopgof package to perform the Monte
	Carlo test. There are also plotting facilities.
	* man/gof.rd: Added. Contains basics of how to use sienaGof
	* NAMESPACE: Added sienaGof functions to namespace for proper operation
	* DESCRIPTION: Added snopgof to the recommended packages.

2011-01-16 R-forge revision 130

	* R/phase3.r: correct number of iterations in field Phase3nits
	* R/robmon.r, R/siena07.r, man/siena07.Rd: make initC=TRUE the
	default
	* src/model/variables/NetworkVariable.cpp: fix array bound error in
	initialisation for bipartite networks and reverse order of tests
	for symmetric model types to avoid problem with bipartite no
	change.
	* src/model/effects/generic/GenericNetworkEffect.cpp: edits to
	comments
	* src.model/tables/MixedConfigurationTable.cpp,
	MixedConfigurationTable.h: make size of table big enough for any
	of the senders or receivers.
	* doc/s_man400.tex, doc/RSiena.bib: various edits.
	* tests/parallel.R, test/parallel.Rout.save: added test with bipartite
	network and multiple processes.

2011-01-08 R-forge revision 129

	* R/sienaTimeTest.r, doc/sienaTimeFix.tex: added interactions
	types for requested effect in call to includeInteraction.
	* R/siena07.r: suppress warning message when loading snow
	package. (Ineffective in sub processes)

2010-12-02 R-forge revision 128

	* data/allEffects.csv: removed to effect from bipartite bipartite,
	added altDist2W and simDist2W to group covarNetNetObjective.
	* R/effects.r: fixed bug meaning covNetNet effect was not added
	for behavior variables. Altered code for covarNetNetEff to cope
	with new effects.
	* R/effectsMethods.r: now interaction names may be expanded even
	in the absence of time dummies.
	* R/initializeFRAN.r: make targets2 for maximum likelihood a
	matrix of the correct size, containing zeros.
	* R/initializeFRAN.r, R/sienaModelCreate, man/sienaModelCreate.Rd:
	Add multiplication factor, altered default ML probabiltities
	* R/sienaEffects.r: added period and group to setEffect so can set
	initial values on basic rates.
	* src/model/effects/CovariateDistance2AlterEffect.cpp: fixed a bug
	in calculation with parameter set to 2.
	* src/model/effects/EffectFactory.cpp,
        src/model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp
	src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h
	src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
	src/model/effects/generic/CovariateDistance2NetworkFunction.h
	src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.
	cpp
	src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.h
	src/model/effects/generic/CovariateNetworkAlterFunction.cpp
	src/model/effects/generic/CovariateNetworkAlterFunction.h
	src/model/effects/generic/MixedNetworkAlterFunction.cpp
	src/model/effects/generic/MixedNetworkAlterFunction.h
	src/model/effects/generic/MixedTwoPathFunction.cpp
	src/model/effects/generic/MixedTwoPathFunction.h
	src/model/effects/generic/NetworkAlterFunction.h
	src/model/tables/MixedConfigurationTable.cpp
	src/model/tables/MixedConfigurationTable.h
	src/model/tables/MixedEgocentricConfigurationTable.cpp
	src/model/tables/MixedEgocentricConfigurationTable.h
	src/model/tables/MixedTwoPathTable.cpp
	src/model/tables/MixedTwoPathTable.h
	src/model/tables/TwoNetworkCache.cpp
	src/model/tables/TwoNetworkCache.h
	src/model/tables/Cache.cpp
	src/model/tables/Cache.h
	added new effects: to, altDist2W, simDist2W. Altered altDist2 and
	simDist2 to  be generic effects which use same functions as
	altDist2W, simDist2W. New two-network cache with mixed-two-path
	table.
	* src/model/ml/MLSimulation.cpp: changes to ML routines
	* src/model/variables/DependentVariable.cpp,
	 src/model/variables/DependentVariable.h: added calculation loop
	for rate effects depending on behavior variables, and stored
	the product term for the scores. Also stored product term for
	model type B scores.
	* src/model/variables/NetworkVariable.cpp: fixed bug in
	calculation of symmetric model type BFORCE scores.
	* R/sienaTimeTest.r: added code for finitedifferences and ML fits.
	* doc/sienaTimeFixDoc.tex: added to RSienaTest

2010-11-25 R-forge revision 127

	* man/s_man400.tex: updated examples of sienaTimeTest.
	* R/initializeFRAN.r: (RSiena only): forgotten new file

2010-11-25 R-forge revision 126

	* DESCRIPTION: new main version number for RSiena, 1.0.12
	* R/sienaTimeTest.r, R/effects.r, R/sienaeffects.r,
	R/effectsMethods.r, man/sienaTimeTest.Rd, plot.sienaTimeTest.Rd,
	man/print.sienaEffects.Rd, man/includeInteraction.Rd:
	amendment and extension of sienaTimeTest and sienaTimeFix.
	includeInteraction now adds rows if necessary and has parameter to
	suppress printing. Time dummy rows can optionally be added to
	print and summary of sienaEffects object.
	* src/siena07internals.cpp, src/model/ml/MLSimulation.cpp,
        src/model/ml/MLSimulation.h, src/model/variables/DependentVariable.cpp,
        src/model/variables/DependentVariable.h: return values for rates
	for multiple dependent variables.
	* doc/RSiena.bib: minor updates
	* man/sienaNet.Rd, getEffects.Rd, siena07.Rd, sienaDataCreate.Rd,
	doc/RSIENAspec.tex: documentation
	* tests/parallel.Rout.save: minor changes for compatibility
	* R/terminateFRAN.r, R/simstatsc.r, R/maxlikec.r: new function
	terminateFRAN in separate file.
	* R/Sienatest.r: added traps for matrix inversion failure
	* R/sienaDataCreate.r, R/initializeFRAN: minor amendments
	* R/phase1.r, R/phase3.r, R/maxlikec.c: return contributions to
	dfra for maximum likelihood and finite differences by wave

2010-11-06 R-forge revision 125

	* data/allEffects.csv,
	src/model/effects/InStructuralEquivalenceEffect.cpp,
	src/model/effects/InStructuralEquivalenceEffect.h,
	src/model/effects/EffectFactory.cpp,src/model/effects/AllEffects.h,
	src/data/OneModeNetworkLongitudinalData.cpp,
	src/data/OneModeNetworkLongitudinalData.h,
	R/sienadataCreate.r, R/initializeFRAN.r, src/siena07internals.cpp:
	new in-structural equivalence effect (RSienaTest only)
	* data/allEffects.csv, R/sienaModelCreate.r, R/initializeFRAN.r,
	R/sienaprint.r, man/sienaModelCreate.Rd, R/printDataReport.r,
	src/model/variables/NetworkVariable.cpp,
	src/model/variables/NetworkVariable.h,
	src/model/variables/DependentVariable.cpp,
	src/model/variables/DependentVariable.h,
	src/model/variables/BehaviorVariable.cpp,
	src/model/EpochSimulation.cpp, src/model/Model.h,
	doc/simstats0c.tex: symmetric models
	(RSienaTest only)
	* R/robmon.r, man/siena01Gui.Rd : minor textual corrections
	* R/sienaDataCreate.r: sorted networks before behavior variables
	* doc/RSienaDeveloper.tex, doc/Siena_algorithms4.tex:
	documentation (RSienaTest only)
	* R/phase1.r: do finite difference calculations for fixed
	parameters during phase 3.
	* R/print07Report.r, R/phase3.r: fix typos in printing of report.
	* R/sienaTimeTest.r: fix bugs with missing interaction effects,
	multiple dependent networks and multiple groups.
	* src/model/effects/DenseTriadsEffect.cpp: add parentheses to remove a
	compiler warning.
	* src/model/ml/MLSimulation.cpp: commented a problem (RSienaTest only)
	* src/siena07models.cpp: return chains as dataframe not list.
	(RSienaTest only)
	* cleanup.win: remove siena01.exe part

2010-10-22 R-forge revision 124

	* R/sienaTimeTest.r: fix bug causing error when only one effect
	(added multiple drop=FALSE)
	* src/win32/(all), configure.win, R/siena01.r: removed siena.exe,
	install function now gives a message.
	* doc/classdesign.tex (RSienaTest only) updated documentation

2010-10-13 R-forge revision 123 RSienaTest only

	* doc/RSienaDeveloper.tex: added details about change logs etc

2010-10-09 R-forge revision 122

	* src/siena07models.cpp: corrected loop for return of MH
	acceptances and rejections. (RSienaTest only)
	* doc/RSienaDeveloper.tex, doc/RSiena.bib, doc/s_man400.tex,
	doc/siena_algorithms4.tex, doc/simstats0c.tex: documentation
	updates.
	(RSienaTest only)
	* R/effects.r: fixed bug in starting values for behavior
	variables when all changes were in one direction (in revision 120
	for RSienaTest)
	* src/data/various, src/model/ml: ML code (RSienaTest only)
	* src/model/effects/AltersCovariateAverageEffect.cpp,
	CovariateDistance2AlterEffect.cpp: implemented new parameter.
	* data/allEffects.csv: removed effects added in error (revision
	120)
	* data/allEffects.csv: added dyadic/ego to various effects to
	allow inclusion of interaction effects.

2010-10-08 R-forge revision 121 RSienaTest only

	* src/model/ml/chain.cpp: commented out a rogue "Rprintf" command

2010-09-20 R-forge revision 120

	* data/allEffects.csv: added alter average distance 2 effects for
	behavior variables
	* R/sienaDataCreate.r: fixed bug in names of dyadic covariates
	when converted to varying covariates for groups
	* R/effects.r: fixed bug in starting values for behavior
	variables when all changes were in one direction (missed this in RSiena)
	* R/phase3.r: minor correction to text in siena07 report.
	* R/print01Report: minor correction to text.
	* R/simstatsc.r (RSiena only): make sure types are available to
	multiple processes.

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
