2020-04-08
R-Forge Revision 348
- Correction of
sienaDataCreatefor actor covariates (gave a warning). - Auxiliary function
dyadicCovnow can handle missings, does not return a named value for frequency of zeros, and returns the frequencies without any division. descriptives.sienaGOFalso shows the exceedance probabilities of the observed statistics.modelTypeandbehModelType, if NULL, get their defaults already ininitializeFRAN(checkNames) rather than in C++.- Some extra information in help page for siena07.
getNamescorrected for data with multiple periods (used insienaBayes,extract.sienaBayes, andextract.posteriorMeans) check bayesTest.getNames, voor extract.sienaBayes en extract.posteriorMeans !!!
2020-02-16
R-Forge Revision 347
- New auxiliary function dyadicCov.
- Correction of error in modelType when one-mode as well as two-mode networks are used (initializeFRAN.r).
- Corrected siena.table for sienaBayesFit objects; added startingDate in sienaBayes and siena08 to the object produced.
2020-01-15
R-Forge Revision 346
- one error in dontrun part of sienaGOF-auxiliary.Rd was corrected.
2020-01-12
- Option projname=NULL in sienaAlgorithmCreate. This option is used for all examples in RSiena where siena07 is called, to restrict file writing for examples to the temporary directory.
2020-01-10
- Changed extension names of output files from .out to .txt.
2020-01-04 R-Forge Revision 345
- Tested effects reported in print of Multipar.RSiena and score.Test.
- Reordered effects object so that reciAct comes after instead of before inAct and inAct.c.
- Operation of siena07 in Test 14 silenced (message Brian Ripley about apparently minor changes depending on the platform).
2019-12-18 packages version 1.2-21.
- Tests ended with deleting file Siena.out by unlink instead of file.remove.
2019-12-16 packages version 1.2-20.
- dumpChain (Chain) and getChainProbabilities (siena07models) dropped; kept in RSienaTest.
- Configure line 2274 changed to RBIN="${R_HOME}/bin"
- Tests ended with deleting file Siena.out.
2019-12-16 R-Forge Revision 344
- SienaTimeTest: some corrections with consequences probably only if one effect is being tested; or is left after automatic exclusion of tested effects.
- Setting-related effects corrected.
- Some further changes in Settings model.
- New effects avGroupEgoX, outIso.
- CovariateDependentNetworkEffect: + lSimulatedOffset taken out of definition missings for ChangingCovariate (seems wrong).
- Alphabetically ordered sources.list.
- In sienaBayes: more precise check that prevAns has same specification as effects; priorSigEta added to sienaBayesFit object. dimnames(ThinParameters)[[3]] defined as effect names; ridge for prior variance of rate parameters if priorRatesFromData=1 or 2 decreased from 0.5 to 0.01.
- sienaBayes: zm and zsmall are removed at the end.
- plotPostMeansMDS also shows a title, and coordinates show the dimensions of the MDS solution.
- The value returned by plotPostMeansMDS contains not only the plot coordinates, but also the similarities (correlations) between the groups.
- glueBayes: added z$varyingInEstimated, z$varyingNonRateInEstimated, z$ratesInVarying to the object produced. (Else extract.sienaBayes is not going to work properly.)
- glueBayes: if one of the sampling parameters is different, give a warning instead of a stop.
2019-10-16 R-Forge Revision 341
In this R-forge revision, only RSienaTest was updated.
- Continuous dependent behavior variables implemented (Nynke Niezink). This implies new effect types continuousFeedback, continuousIntercept, continuousOneModeObjective, continuousRate, continuousWiener, unspecifiedContinuousInteraction.
- imputationValues allowed in sienaDependent (Nynke Niezink)
- New effect outMore.
- component startingDate added to sienaFit object; this is reported in siena.table(..., type='tex', ...).
- Speeded up calculation of IndegreeDistribution and OutdegreeDistribution for sienaGOF if there are no missings or structurals.
- regrCoef and regrCor added to the sienaFit object also when !dolby.
- Some "warnings" changed back to "cat".
- EpochSimulation->totalRate renamed to grandTotalRate, to avoid confusion with DependentVariable->totalRate.
- stop if useCluster and returnChains (in this case, no chains would be returned anyway).
- sienaDataCreate: more informative message in case of constraints.
- Further explanation in help page for setEffect, and small extensions of help pages for getEffects, includeEffects, and includeInteraction.
- small clarification in help page for sienaDependent.
- small clarifications about node sets in help pages for coCovar, varCovar, coDyadCovar, varDyadCovar, and sienaDataCreate.
- small addition to help page for sienaTimeTest.
- Object names are given in sienaFit.print if simOnly.
- Settings model: corrected scores for rate parameters; stepType in NetworkCache; new class settingNetworkEffects; effect group nonSymmetricSymmetricObjective split in this and nonSymmetricSymmetricSObjective (also operating for primary setting effects); new effects settingSizeAct, settingSizeActSqrt, settingSizeActLog, settingOppAct, settingOppActSqrt, settingOppActLog, settingLogCreationAct, settingOppActD, settingOppActSqrtD, settingOppActLogD, settingLogCreationActD. These new effects are not yet operational (target statistics not calculated).
- inPopIntn and outActIntn dropped from effect group nonSymmetricSymmetricObjective.
- Corrected error in names of array returned by extract.posteriorMeans.
- New parameter excludeRates in extract.posteriorMeans, plotPostMeansMDS.
- Use parameter pmonly also in plotPostMeansMDS.
2019-05-20 R-Forge Revision 340
- New effects outAct.c, inAct.c, outPop.c., inPop.c, degPlus.c.
- Effects antiInIso and antiInIso2 implemented for non-directed networks.
- Effects outTrunc, outTrunc2, outSqInv, isolateNet, and degPlus got endowment effects.
- For inPopIntn, outPopIntn, inActIntn, and outActIntn, added "centered" to the statistic name.
- In plot.sienaGOF new parameter fontsize; ... will also accept parameters cex, cex.main, cex.lab, cex.axis.
- estMeans.sem added to object produced by siena07, if x$simOnly.
- Components regrCoef, regrCor, estMeans, and estMeans.sem mentioned in help page for siena07.
- Hidden options in siena07 with x$targets (initializeFRAN.r).
- Extra identifying information for "total probability non-positive" error (NetworkVariable.cpp).
- On various places replaced "cat" by "message" or "warning".
- Replaced && by any(.. & ..) to comply with R 3.6.0 new standard (sienaTimeTest).
- sienaBayes: do not allow prevAns and prevBayes objects simultaneously; omit partial averaging at the end of warming phase; "prevAns" now is allowed to have a different specification of random effects than "effects"; warming up lowest level reduced to 3 iterations of MCMCCycle, but applied also if newProposalFromPrev.
2019-02-26 R-Forge Revision 339
- New effects maxXAlt, minXAlt (thanks to Per Block, Marion Hoffman, Isabel Raabe, and Timon Elmer), outIsolate.
- Effect name of isolate effect (not shortName) changed to in-isolate.
- New parameter thetaValues in siena07, allowing simulations in Phase 3 with varying parameters according to matrix input. Corresponding changes in print.sienaFit.
- sienaRI: earlier check for bipartite dependent variables; if so, stop.
- Argument "verbose" added to includeEffects and setEffect. (It existed already for includeInteraction.)
- Wald.RSiena, Multipar.RSiena and score.Test also produce one-sided test statistic if df=1.
- objects produced by Wald.RSiena, Multipar.RSiena and score.Test have class "sienaTest".
- print method added for objects of class sienaTest.
- Changed/added some keywords and concepts in .Rd files.
- Allow arbitrary number of interactions in sienaBayes (via getEffects).
- simpleBayesTest and multipleBayesTest corrected; they were wrong for models with user-defined interactions.
- glueBayes extended (to allow good use for models with fixed parameters) and check for prior rates relaxed (to allow priorRatesFromData=2 leading to different prior rates.)
- New default (prevBayes$nwarm >= 1) for newProposalFromPrev in sienaBayes.
- siena.table for sienaBayes results extended with between-groups s.d.
- Argument "verbose" added to extract.posteriorMeans.
- sienaBayes: check that prevAns is a sienaFit object; totally skip initial multigroup estimation if prevAns is given with prevAns$n3 >= 500 and (!usePrevOnly).
2019-01-02 R-Forge Revision 338
- New effects sameXReciAct and diffXReciAct.
- Increased length of MLSimulation::preburnin.
- Changes in sienaFitThetaTable, averageTheta.last, sdTheta.last in sienaprint.r to enable change in extract.posteriorMeans (see below).
- siena.table adapted for sienaBayes results.
- New functions shortBayesResults and plotPostMeansMDS.
- extract.posteriorMeans works also for an object saved as PartialBayesResult (which has NA results for as yet unfinished runs) (this was achieved by changes in sienaprint.r, see above).
- Examples added to help page for print.sienaBayesFit (in dontrun...).
2018-12-05 R-Forge Revision 337
- Check for length of parameter mult for ML estimation (initializeFRAN), extend explanation of mult in help page for sienaAlgorithmCreate.
- extract.sienaBayes corrected.
- sienaBayes: subphases for initial global parameter estimation decreased to 2; prior variances for fixed parameters introduced; after initialization by MoM estimation of multi-group data set, a precision weighted mean (called "Kelley") of this estimate and the prior mean is used for initial parameter values; prewarming phase introduced before improveMH; in case prevBayes is used, also parameter nImproveMH in the function call of sienaBayes supersedes this parameter in the prevBayes object; checks for dimensions of prior mean and covariance matrix put earlier in the initialization phase.
2018-10-29 R-Forge Revision 336
- Correct error in print01Report that occurred for changing dyadic covariates given as lists of sparse matrices.
- Correct error in sienaGroupCreate for non-centered actor covariates.
- Drop dependence on utils (the packages did not depend on it).
- Also get simulated dependent behavior variables for siena07(,,, returnDeps=TRUE, ...) for ML estimation.
- siena.table corrected for data sets with several dependent variables.
- For siena08: new parameters which and useBound in plot.sienaMeta; new parameter reportEstimates in siena08, allowing to reduce the output produced.
- updateSpecification: also update randomEffects column.
- Change help page for sienaDependent.
- Some changes in sienaprint.r depending on sienaBayes, to keep the two packages the same when possible.
- sienaBayes: new parameters proposalFromPrev, which allows taking proposal distributions from prevBayes object; incidentalBasicRates resuscitated; allow fixed rate parameters, with priorRatesFromData=-1; changed initial values of scale factors for proposal distributions; new parameters target and usePrevOnly; in case prevBayes is used, parameters nrunMHBatches, nSampVarying, nSampConst, and nSampRates in the function call of sienaBayes supersede those in the prevBayes object; correct bug for three-effect interactions (projectEffects) copy parameters modelType, behModelType, MaxDegree, Offset, initML, from parameter algo to the algorithms created within sienaBayes; more extensive checking of smallest eigenvalue of covariance matrix (function correctMatrix); For priorRatesFromData = 1 or 2, the resulting matrix for priorKappa != 1 was incorrect; this was corrected. reported timing changed to elapsed system time; some reordering of parameters. This also required some corresponding changes in sienaprint.r.
- DESCRIPTION: Added 'Encoding: UTF-8' because sienaGOF.r complained about non-ASCII.
- Data.cpp: Add a new 'SimNetworkData' type: This is for variables that behave like dependent variable for effects but are not changed by the simulation. Currently used for the primary setting network.
- PrimaryLayer: A network layer holding the full primary setting as network.
2018-05-13 CRAN for RSiena
2018-05-07 R-Forge Revision 336
* Change default parameter of reciAct to 1 (implies changes only in
output, not computationally).
* Internal effect parameter carried through in sienaTimeFix.
* Shorter examples for sienaGOF and sienaGOF-auxiliary help pages.
2018-05-06 R-Forge Revision 335
- New effects gwdspFF and gwdspFB.
- Corrected effects simEgoInDist2 and simEgoInDist2W for two-mode networks. Perhaps simEgoDist2 and simEgoDist2W were broken in a previous version; if so, that was now corrected.
- Added sqrt version for reciAct, obtained for parameter = 2.
- Allowed the value parameter=NULL for setEffect and includeInteraction, meaning that no change is made for the internal effect parameter. For setEffect this is the new default, implying that when starting the default values from allEffects.csv are used, just like in includeEffects (where no parameter can be given).
- New auxiliary functions for sienaGOF: Triad Census and mixedTriadCensus (contribution by Christoph Stadtfeld).
- triad census from igraph added to help page of sienaGOF-auxiliary.
- sienatable output for type="html": added rules=none, frame = void to general options; changed minus to – ; added column for asterisks to have better alignment for estimates.
- Stop cluster also if (!z$OK || !z$Phase3Interrupt) (robmon.r).
- Extension of help page for siena07 by mentioning functions for accessing simulated networks for ML.
- extract.sienaBayes: error corrected that occurred if called with extracted="all" but there are no varying, or no non-varying parameters.
2018-03-24 R-Forge Revision 334
- Example in help page siena07 for accessing generated networks for ML.
2018-03-21 R-Forge Revision 332
- model/effects/generic: Remove const from some of the value methods (as it was in rev316).
- new effect group covarBehaviorSymmetricRate (effects.r, effectsDocumentation.r).
- Added effects avExposure, totExposure, infectDeg, susceptAvCovar, infectCovar for symmetric networks.
- New effects degAbsDiffX, degPosDiffX, degNegDiffX, degAbsContrX, degPosContrX, degNegContrX,
- New effect group dyadBipartiteObjective (effects.r).
- Effects XWX, XWX1, and XWX2 enabled for bipartite networks.
- Added parameter=2 for FFDeg, BBDegm FBDeg, FRDeg, BRDeg.
- Corrected altInDist2, totInDist2 for two-mode networks.
- Dropped some duplications in effectsDocumentation.
- Modification of effect outTrunc2 (TruncatedOutdegreeEffect2). Perhaps this was superfluous.
- Export of last simulated state from ML simulations if returnDeps: new function gotoLastState() in MLSimulation, adaptation of mlPeriod() in siena07models.cpp, and some other small changes.
- Added endowment and creation effects for maxAlt and minAlt.
- Error messages for non-character nodeSets in sienaDependent, coCovar, varCovar.
- Improved way of handling missings for distance-2 network effects.
- Added components requestedEffects, theta, and se to siena08 (theta and se are the ML estimates).
- Error in summary of sienaMeta object corrected: for the Estimated mean parameter the two-sided p was announced but a one-sided p was given. Also the ML results under normality assumptions were copied from print.sienaMeta to print.summary.sienaMeta.
- Drop transTriads<-TRUE in effects.r, so that initial model for non-directed networks contains only basic rates and degree effect.
- Added reference to DESCRIPTION and citation info in \inst.
- The dropping of the exclusion in effects.r of effects if the variance of a covariate is 0, or a covariate has only two values, of version 1.1-306, is taken further (was incomplete).
- Message if attributes higher, disjoint, or atLeastOne are TRUE at the end of sienaDataCreate.
- Incomplete changes toward export of observed information matrix for MoM (derivative of score function): extensions to getStatistics in siena07internals, implying also changes in siena07models.cpp, Networkvariable.cpp, BehaviorVariable.cpp.
- Added altInDist2 test to parallel.R (test12, test13).
- siena07internals.cpp, siena07model.cpp, and siena07setup.cpp brought in line with RSienaTest.
- new function extract.posteriorMeans for sienaBayes results.
- Add z$fix to sienaBayes object, and use !z$fix in check of maximum estimated parameter value after initialization.
- Correct construction of groupwise effects object in sienaBayes so that this will work also when evaluation effects for density and/or reciprocity are not included; and when there are interaction effects for which the main effects are not included.
- Corrections for print and summary of sienaBayes objects. In print.sienaBayesFit: include fixed parameters and give credibility intervals for rate parameters; also give posterior means and credibility intervals for standard deviations of randomly varying parameters; allow shorter ThinParameters; print objects returned through partialBayesResult.RData.
- multipleBayesTest corrected (there was an error for testing 2 or more linear combinations simultaneously) and adapted for cases with fixed parameters; adapted help page text.
- All remaining parts of rsiena01gui removed.
- As a compensation of this, sienaDataCreateFromSession exported, with a more informative help page.
2017-09-18 R-Forge Revision 331
- simplify/harden configure.ac Compiling examples and trying to load them should prove more robust against the ongoing changes in the R-Forge build setup.
2017-09-18 R-Forge Revisions 328-330
- Added \R\formula.R and \tests\formula.R.
2017-09-18 R-Forge Revision 325
- Added \doc\tutorial-effect.tex
2017-09-18 R-Forge Revision 323
- StatisticCalculator.cpp: delete Network clones not owned by State.
2017-09-18 R-Forge Revision 322
- StatisticCalculator.cpp: delete Network clones not owned by State.
2017-09-10 R-Forge Revision 321
- Merge RSienaTest changes r319-r320. Renamed init.c to init.cpp.
2017-09-10 R-Forge Revision 320
- siena07*.h: Update method declarations.
- getTargets.R: getTheTargets renamed to getTargets to match with RSiena.
- R/algorithms.r: Uncomment doCreateChains (C side is missing). See change log for "2017-09-03 version 1.2-1" where it is mentioned as dropped.
- utils/Utils.cpp: Make log call unambiguous.
- R/, man/: Whitespace changes to ease the merging.
2017-09-10 R-Forge Revision 319
- init.cpp: Register native routines.
- *.R: Apdapt .Call statements.
2017-09-09 R-Forge Revision 318
- Longer Description field in DESCRIPTION, as per CRAN suggestions.
- Correction of print.sienaFit, repairing the option include=FALSE in setEffect and includeEffects.
- Included test of includeEffects in parallel.r.
- Extra line in example for sienaBayes.Rd.
2017-09-09 R-Forge Revision 317
- Effects: Move 'using namespace std' to cpp files. Make value() consistently 'const'. Use std::abs for integers. Remove unused fields.
- UniversalSetting.cpp: Do not hide GeneralSetting::terminateSetting().
- siena07models.cpp: Reduce state complexity (rchk test).
- siena07*.cpp: Fix unPROTECTed vars (rchk test).
2017-09-08
R-Forge Revision 316
- totAlt also for non-directed networks
- Added cran-comments.md, .Rbuildignore for comments about cran submission.
2017-09-07 R-Forge Revision 315
- Merge RSienaTest changes r311-r314.
2017-09-07 R-Forge Revision 314
- StatisticCalculator.cpp: Fix memory leak in deconstructor.
- Move some of the 'using namespace' from header to cpp files.
- Lots of whitespace changes to ease the merging process.
2017-09-06 R-Forge Revision 313
- DependentVariable.cpp: Fix null pointer in accumulateRateScores when called on BehaviorVariable.
2017-09-04 R-Forge Revision 312
- configure.win: adapt windows configuration script
2017-09-04 R-Forge Revision 311
- configure.ac: add openmp test for macOS El Capitan compatibility
2017-09-03 R-Forge Revision 310
- effects.r: remove hard coded number of types of interactions
- NetworkDependentBehaviorEffect.cpp: fix uninitialized network pointer
2017-09-03
- Score test and sienaGOF corrected for the case that some parameters are fixed and not tested.
- New function score.Test, and its output added to print.sienaFit (if any parameters fit the bill).
- Argument varName added to updateTheta.
- In sienaAlgorithmCreate, for parameters Offset, MaxDegree, modelType, and behModelType, require that these are named vectors with the names of the dependent variables, or NULL; this is checked in initializeFRAN.
- For networkModelType 3 (Initiative, AAGREE), an offset is added to the confirmation model; this is taken from Offset in the algorithm object.
- For effects inPopX, outPopX, inActX, outActX, sameXInPop, sameXOutAct, diffXInPop, diffXOutAct, homXInPop, homXOutAct, altXOutAct, diffXOutAct, changed interaction2 to '' (was '1') and default parameter to 1 (AllEffects.csv).
- New effects sameXInPopIntn, sameXOutPopIntn, sameXInActIntn, sameXOutActIntn,
- Additional parameter dropRates in print.sienaEffects (useful for sienaBayes with many groups).
- In print.sienaEffects, omit last remark about random effects if only one line is printed.
- Corrected use of modeltype (initializeFRAN.r, CInterface.r),
- Change in print.sienaAlgorithm for modelType.
- In CalculateDerivative (phase1.r) changed assignment for diag(dfra)[a][b] (which is wrong) to diag(dfra)[which(a)[b]] (avoids crash of sienaBayes in rare cases).
- Added stopCluster to robmon.r.
- Took out verbose reporting for sienaGOF with !is.null(cluster).
- Added an example for multiple processes in sienaGOF.Rd.
- Took out 'dontrun' for the example in sienaGOF.Rd and the first example in sienaTimeTest.Rd.
- Reduced running time of some of the algorithms used in examples.
- LF line endings for files configure, configure.ac, cleanup, also in Tortoise properties. CRLF line endings for configure.win, cleanup.win, also in Tortoise properties.
- To avoid confusion with the C++ function, renamed getActorStatistics() in getActorStatistics.R to getTheActorStatistics, and renamed getTargets() in getTargets.R to getTheTargets. For similarity between RSiena and RSienaTest, added getActorStatistics.R to RSienaTest, even if it is not used.
- Completed heading for getTargets() in siena07setup.h, and used these additional parameters in getTheTargets.
- Error fixed in sienaBayes for definition of z$rateParameterPosition, which could lead to errors in the case of more than one dependent variable with an interaction effect specified for some other than the last dependent variable.
- Parameter UniversalOffset of sienaAlgorithmCreate renamed to Offset.
- Added posterior variances to print.sienaBayesFit.
- Added stopCluster to sienaBayes.r.
- Dropped doCreateChains from algorithms.r.
- Terminated open connection at the end of sienacpp (CInterface.r).
- New parameter OffSet in sienaAlgorithmCreate.
- Registration of native routines (init.c, using tools::package_native_routine_registration_skeleton, \fixes in NAMESPACE, changed specifications of arguments of .Call, and with help from Brian and Ruth Ripley).
2017-09-01 R-Forge Revision 309
- configure.ac: don't compile with openmpi if orted is missing
2017-08-30 R-Forge Revision 308
- effects.r: remove hard coded number of types of interactions
- Model.cpp: allow gmm type interaction effects
- NetworkDependentBehaviorEffect.cpp: fix uninitialized network pointer
Some forking here: RSienaTest and RSiena went their own ways, reunited in 1.2-2.
2017-05-12 R-Forge Revision 307
- Operation of option 'absorb' (behModelType=2) corrected.
- BothDegreesEffect.h and .cpp added to repository.
2017-05-10 R-Forge Revision 306
- Added updateSpecification (effectsMethods)
- New effects inPopX, outPopX, inActX, outActX, sameWXClosure, degPlus, absDiffX, avAltPop, totAltPop, egoPlusAltX, egoPlusAltSqX, egoRThresholdX, egoLThresholdX, altRThresholdX, altLThresholdX.
- New effect group covarABipNetObjective.
- outActIntn added to effect group nonSymmetricSymmetricObjective.
- outOutAss dropped for symmetric networks; only outInAss remains.
- egoX effect has interactionType='ego' also for symmetric networks.
- The exclusion in effects.r of effects if the variance of a covariate is 0, or a covariate has only two values, is dropped (these effects have no meaning, but their exclusion was a potential nuisance for meta-analyses).
- Description of gwespFB and gwespBF corrected (allEffects.csv and manual).
- includeInteraction has an additional parameter random.
- siena08 now also accepts a list for ...
- somewhat extended help page for siena08.
- Longer example in sienaTimeTest.Rd.
- Indication of effect parameters dropped in names for altInDist2 and totInDist2 (they have no effect parameters).
- ModelType now is specific to the dependent variable: given as a named integer vector in sienaAlgorithmCreate, defined in Dependentvariable.h and NetworkVariable.h as networkModelType.
- ModelTypeStrings now is a function instead of a string vector.
- behModelType added (sienaAlgorithmCreate, siena07setup.cpp, BehaviorLongitudinalData, BehaviorVariable), and enum type BehaviorModelType specified in BehaviorVariable.cpp.
- New option 'absorb' for behModelType=2.
- sienaAlgorithmCreate, siena07: new option lessMem, reducing storage in siena07 by leaving out z$ssc and z$sf2; but these are used by sienaTimeTest and sienaGOF, so running those functions will be impossible for sienaFit object obtained with lessMem=TRUE.
- modified print.sienaAlgorithm: added behModelType, n2start.
- small cosmetic change print.siena.
- Modified check for singular covariance matrix (phase3.2 in phase3.r).
- Warning if includeEffects is used with parameter random.
- Warning for impossible or zero changes if maximum likelihood.
- siena07: z$phase1devs, z$phase1dfra, z$phase1sdf, z$phase1sdf2, z$phase1scores, z$phase1accepts, z$phase1rejects, z$phase1aborts, z$sfl, z$msfinv, z$sf.invcov dropped from object produced.
- Checks for named vectors in initializeFRAN made more systematic.
- Check of effects object in mlInit (maxlike.r) does not use is.data.frame any more.
- test13 dropped from parallel.R (using clusters undesirable for basic testing).
- sienaBayes: various changes to save memory (thanks to Ruth Ripley); lessMem=TRUE in operation of siena07; z$candidates removed, place of storing z$acceptances changed; improved report of groups with no changes; warning for impossible changes; if priorRatesFromData=2, change to different robust covariance matrix estimator when this is necessary (i.e., for small number of groups); in print.summary, also report nImproveMH; a few lines added to help page.
- test14 dropped from parallel.R (using clusters undesirable for basic testing) and replaced by a test using maxlike.
2016-10-20 R-Forge Revision 305
- BehaviorEffect, NetworkDependentBehaviorEffect, StatisticCalculator: initialize() with simulated state for GMM.
- Other effects: Fix [-Wreorder] warings.
2016-10-14 R-Forge Revision 304
- tests/parallel.R: Changing makeForkCluster to makeCluster.
- man/siena07.Rd: Adding a description of the -cl- option + examples.
2016-10-13 R-Forge Revision 303
- R/robmon.r: New argument -cl- allows users passing their own cluster, creating a new cluster only if length(cl) == 0.
- R/siena07.r: Same as in robmon. Now, if the user passes -cl-, the cluster is closed only if length(cl) == 0.
- man/siena07.Rd: Including the new -cl- option in the manual.
- tests/parallel.R: Adding new test using the new -cl- option.
2016-10-10 R-Forge Revision 302
- Capitalization error corrected in CovariateDegreeFunction.cpp.
2016-10-09 R-Forge Revision 301
- Warning if includeEffects is used with parameter initialValue - corrected.
- New effect: sameXCycle4, homCovNetNet, contrastCovNetNet, covNetNetIn, homCovNetNetIn, contrastCovNetNetIn, inPopIntnX, inActIntnX, outPopIntnX, outActIntnX
- Changed type of lcounters and counters in FourCyclesEffect to long int, permitting the 4-cycles effects for larger and denser networks.
- Dropped cl.XWX effect from two-mode - one-mode coevolution (did not belong).
- egoSqX is an ego effect (CovariateEgoSquared.cpp and .h).
- Added cycle4 for one-mode networks.
- Added outAct, outInAss for symmetric networks.
- SienaRI: Structural zeros and ones are excluded from the calculations; added option getChangeStatistics; row names given to matrices that have rows corresponding to effects; adapted so that it runs for models with only 1 parameter; adapted so that for a bipartite dependent variable it does not crash.
- Warning if includeEffects is used with parameter 'parameter'.
- Small additions to print.sienaAlgorithm.
- Clearer output for MaxDegree in print.sienaFit.
- Indication '^(1/2)' for outInAss for 2-mode networks changed to '^(1/#)', where # is the effect parameter (allEffects.csv). Changes RSienaTest:
- simulatedOffset changed from int to double (NetworkLongitudinalData)
2016-09-12 R-Forge Revision 300 Changes RSienaTest:
- doc/RSienaDeveloper.tex: Build system documentation.
2016-08-30 R-Forge Revision 299 Changes RSienaTest:
- network/Simmelian: Cleaned dependencies.
2016-08-28 R-Forge Revision 297
- buildsystem: added Makefile and src/sources.list
2016-08-17 R-Forge Revision 296
- Warning if includeEffects is used with parameter initialValue - did not work.
- Warning if includeInteraction is used for more interactions than available given parameters nintn and behNintn.
- Deleted session parameter from print01Report.
- Corrected cycle4 effect for parameter=2 (sqrt version).
- Additional auxiliary function CliqueCensus in help page sienaGOF-auxiliary.
- Error corrected in DyadicCovariateAvAltEffect.cpp.
2016-07-23 R-Forge Revision 295
- buildsystem: added Makefile and src/sources.list unitTests: removed sink('/dev/null')
2016-05-28 R-Forge Revision 294
- In SimilarityEffect.cpp and SimilarityWEffect.cpp, changed abs to std::abs to avoid ambiguity, dropping #include .
- Mac line endings given to configure file.
2016-05-23 R-Forge Revision 293
- Removed manual and bibliography from installation; still available in \RSienaTest\doc.
- Added functions initializeStatisticCalculation() and cleanupStatisticCalculation() to class BehaviorEffect.
- New effects totAltEgoX, totAltAltX, egoSqX, diffX, diffSqX, egoDiffX, avAltW, totAltW, avSimW, totSimW, jumpFrom, jumpSharedIn, mixedInXW, mixedInWX, avWalt, totWAlt.
- New effect class DyadicCovariateDependentBehaviorEffect corresponding to group dyadBehaviorNetObjective (effects.r, effectsDocumentation.r).
- added endowment and creation effects for inAct, inActSqrt, outAct, outActSqrt.
- inActIntn also implemented for two-mode dependent networks.
- New argument 'matrices' in print.summary.sienaFit.
- Changes to NAMESPACE and DESCRIPTION files to satisfy R3.3.0 for external functions from base packages.
- siena01Gui and associated functions dropped.
- sienaDataCreateFromSession dropped.
- Change in endowment effect estimation for avAlt effect.
- New effects simmelian, simmelianAltX, avSimmelianAlt, totSimmelianAlt.
2016-02-22 R-Forge Revision 292
- Fixed permission filter for 2-mode networks (NetworkVariable.cpp).
2016-02-03 R-Forge Revision 291
- Fixed include order.
- Removed
using namespacefrom all headers.
2016-01-31 R-Forge Revision 290
- New effects FBDeg, FRDeg, BRDeg (RFDeg was mentioned earlier but was not implemented; its place is now taken by FRDeg), gwespFFMix, gwespBBMix, gwespBFMix, gwespFBMix, gwespRRMix, gwespMix.
- Corrected check for positive derivative matrix at the end of phase 1 omitted for effects with fixed parameters (phase1.r, CalculateDerivative(); phase3.r).
- Added parameters fix, test, parameter to includeInteraction().
- More helpful error message for incorrect nodesets in sienaDataCreate; extended help pages sienaDataCreate.Rd and sienaDependent.Rd.
- Correction of diag(diag(..)) to allow estimation with p=1 (phase1.r, initializeFRAN.r)
- fromBayes bug corrected.
- sienacpp added (programmed by Felix Schoenenberger); this includes gmm estimation (Amati - Snijders); and implies a lot of changes in other functions to enable this.
- settings model added (Snijders - Preciado; programmed by Mark Ortmann); not yet documented. Also implies a lot of changes.
- sienaBayes(): option initML added; check for zero distances. corrected function improveMH() in initialization; check for dimensions priorMu and priorSigma done earlier.
- print.multipleBayesTest(): option descriptives added.
- glueBayes(): add p1 and p2 to created object.
2015-09-10 R-Forge Revision 289
- New defaults for siena07() in sienaAlgorithmCreate(): doubleAveraging=0, diagonalize=0.2 (for MoM).
- Improved one-step approximations to expected Mahalanobis distances in sienaGOF() (control variates for score function).
- Permit 3-way interactions with one ego and two dyadic effects (initializeFRAN.r) (this was erroneously not allowed).
- New effects Jin, Jout, JinMix, JoutMix, altXOutAct, doubleInPop, doubleOutAct.
- print01Report() now reports in-degrees also for two-mode networks.
- Better error handling for sienaTimeTest and scoreTest (EvaluateTestStatistic() in Sienatest.r).
- inOutAss is dyadic.
- Check for positive derivative matrix at the end of phase 1 omitted for effects with fixed parameters (phase1.r, CalculateDerivative()).
- Corrected effectName and functionName of inPopIntn, outPopIntn, inActIntn, and outActIntn ('in' and 'out' were missing).
- Extended error message for "invalid effect" in initializeFRAN().
- Console message when allowOnly=TRUE is active in sienaDependent().
- Some change in includeInteraction.Rd.
- New effects homXOutAct, FFDeg, BBDeg, RFDeg, diffXTransTrip (ported from RSienaTest).
- sameXInPop and diffXInPop also added for two-mode networks; but they are not dyadic!
- In names of behavior effects and statistics dropped the (redundant) parts "behavior" and "beh.".
- New function extract.sienaBayes() (bayesTest.r).
- sienaBayes(): options diagonalize=0.2, doubleAveraging=0 for estimation of initial models in initialization phase; save initial results in case of divergence during initialization phase; check for initialEstimates done only for non-rate parameters.
2015-07-18 R-Forge Revision 288
- plot.sienaRI: new parameter "actors"; proportions with piechart improved; function of parameter radius changed.
- fra2 constructed only if findiff (phase3.r).
- siena.table does no more produce the double minus sign in html output.
- Correction of error for two-mode networks in sienaGOF.
- New effects homXOutAct, FFDeg, BBDeg, RFDeg, diffXTransTrip.
- sameXInPop and diffXInPop also added for two-mode networks; but they are not dyadic!
- In names of behavior effects and statistics dropped the (redundant) parts "behavior" and "beh.".
- sienaBayes: new parameter nSampRates; correction in use of prevBayes (with extra createStores()); more efficient calculation of multivariate normal density.
- Small changes in HowToCommit.tex.
2015-06-02 R-Forge Revision 286 (Version number was kept the same...)
- Correction of error for two-mode networks in sienaGOF.
2015-05-21 R-Forge Revision 286
- test11 dropped from \tests\parallel.R.
- print.xtable.sienaFit exported as S3method in Namespace.
- Larger dontrun part in examples for SienaRIDynamics (there still is an error).
- SienaRIDynamics not exported from RSiena only (there still is an error), SienaRIDynamics.Rd dropped.
2015-05-20 R-Forge Revision 285
- tmax added to sienaFit objects and tconv.max mentioned in print.sienaFit().
- sienaAlgorithmCreate() has new arguments n2start, truncation, doubleAveraging, standardizeVar; this leads to various changes in phase2.r.
- Diagonalization corrected (matrix transpose: for defining changestep, fra %% z$dinvv replaced by z$dinvv %% fra in phase2.r).
- Truncation based on multivariate deviation if diagonalize < 1 (phase2.r).
- When there are missings in constant or changing monadic covariates, and centered=FALSE for their creation by coCovar() or varCovar(), the mean will be imputed (used to be 0, which was an error). For changing covariates, this is the global mean.
- In coCovar() and varCovar() there is a new argument imputationValues, which are used (if given) for imputation of missing values. Like all missings, they are not used for the calculation of the target statistics in the Method of Moments, but only for the simulations.
- For non-centered covariates, averageAlter and averageInAlter values for zero degrees were replaced by the observed covariate mean.
- New effects: outOutActIntn, sharedTo, from.w.ind
- New effectGroup tripleNetworkObjective (allEffects.csv, effects.r) (see the manual or effects.r for its characteristics).
- In the target statistic for the 'higher' effect, contributions for value(ego)=value(alter) are now set appropriately at 0.5 (was 0).
- Decent error message when there are (almost) all NA in the dependent behavioural variable (effects.r, function getBehaviorStartingVals()).
- The centering within effects for similarity variables at distance 2 now is done by the same similarity means just as for the simX effect (attr(mydata$cCovars$mycov, "simMean"), etc.). (Background: this was done earlier by "simMeans", the implementation of which contained an error; but the differentiation between "simMean" and "simMeans" is not important, so "simMeans" was dropped for simplicity.) The object "simMeans" was not yet dropped from the data structure transmitted to C++ (siena07internals.cpp. initializeFRAN.r)
- z$positivized changed from matrix to vector (not important enough for so much memory use).
- test7 renamed test 5, test6 and new test7 added in \tests\parallel.R
- Small changes in HowToCommit.tex.
2015-04-02 R-Forge Revision 284
- New effects: simEgoDist2, simEgoInDist2, simEgoDist2W, simEgoInDist2W, sameXOutAct, diffXInPop, diffXOutAct.
- New effectGroups covarABNetNetObjective, covarANetNetObjective, and covarBNetNetObjective (allEffects.csv, effects.r).
- Bug corrected that occurred in print01Report for a sienaGroup object where the component objects have constant dyadic covariates (sienaDataCreate.r).
- When a statistic is not plotted in plot.sienaGOF() because its variance is 0, a note about this is printed to the screen.
- Minimum and maximum of plotted region in plot.sienaGOF() is calculated without taking into account non-plotted statistics.
- Bug corrected with includeTimeDummy for timeDummy greater than or equal to 10 (sienaTimeTest.r).
- In case of collinear parameter estimates, standard errors are reported as NA (phase3.r, print07Report.r).
- At the end of subphases of phase 2, add condition ((!is.na(z$minacor)) & (!is.na(z$maxacor))) to avoid NA errors.
- Arguments main and ylab dropped from plot.sienaGOF(); they did not work, and their functionality now is covered by the ... argument (so using main and ylab as arguments now should work). (Thanks to David Kavaler.)
- Various changes in DESCRIPTION and NAMESPACE files with respect to Suggests and Depends; for packages in "Depends", require(packageName) was dropped in all R functions; for package "network", suppressPackageStartupMessages() was added to require(); for packages in "Suggests", the package name was everywhere added as packageName:: before the function name.
- GPL requirement changed to >= 3.
- sienaBayes: correction in initialization of truncation rate parameters based on prior; correction of sampleConstantParameters() (MCversion=0 used the wrong MH ratio, now was dropped altogether).
- reduceg parameter added (sienaAlgorithmCreate, siena07)
2014-12-11 R-Forge Revision 282
- Effects cl.XWX and cl2.XWX corrected (thanks to Christoph Stadtfeld) (MixedTwoPathTable.cpp).
- interactionType of gwesp.. effects was made dyadic (allEffects.csv)
- Some layout changes in warning message, phase3.r.
- New effects reciPop, reciAct, in3Plus, maxAlt, minAlt, transTrip1, transTrip2.
- Effect antiInIsolate2 got alias in2Plus.
- inPop is dyadic effect (except for symmetric networks) (it is sum_j x_{ij} (sum_{h \neq i} x_{hj} + 1)).
- egoX added as effect for non-directed networks (can be important for representing effects of group-level covariates in multi-group analyses).
- Components IActors and expectedI added to sienaRI() and print.sienaRI().
- The check for MaxDegree when running siena07 now works properly also for sienaGroup objects (initializeFRAN).
- Manual introduces the term 'elementary effects'.
- sienaBayes: the stop caused by singularity of the precision matrix after the multi-group estimation now is circumvented; still a warning is printed to the screen. This allows the use of more than one elementary effects having the same target statistic.
- sienaBayes: option priorRatesFromData changed to values 0-1-2, with 0 = former FALSE, 1 = former TRUE, 2 = robust estimation of prior for rate parameters from estimates at the end of initialization phase.
- sienaBayes: correction thetaMati (not important, only for output to screen).
- sienaprint: correction of print.summary.sienaBayesFit for models with more than one dependent variable.
2014-11-22 R-Forge Revision 281
- Translation of R messages was updated: changed file \pkg\RSiena\po\R-RSiena.pot
2014-11-19 R-Forge Revision 280
- Small changes in help pages for sienaGOF and for sienaCompositionChange.
- New parameters nSampVarying and nSampConst in sienaBayes().
2014-11-13 R-Forge Revision 279
- Effect AltsAvAlt renamed to avXAlt (with error message).
- effects object no longer used as argument for print01Report (with error message).
- New effects sameXInPop, transRecTrip2, totAlt, avInAlt, totInAlt, totRecAlt, totXAlt, avXInAlt, totXInAlt, avAltDist2, totAltDist2, avTAltDist2, totAAltDist2, avXAltDist, totXAltDist2, avTXAltDist2, totAXAltDist2, avInAltDist2, totInAltDist2, avTInAltDist2, totAInAltDist2, avXInAltDist2, totXInAltDist2, avTXInAltDist2, totAXInAltDist2, XWX1, XWX2, cl.XWX1, cl.XWX2.
- gwesp.. effects get endowment=TRUE in allEffects.csv, and thereby obtain endowment and creation effects.
- In effect group behaviorBipartiteObjective, the following meaningless effects were dropped: avAlt, avSim, totSim, avSimPopEgo, avSimPopAlt, behDenseTriads, simDenseTriads.
- Effect class covarBehaviorBipartiteObjective split into covarABehaviorBipartiteObjective (for covariates on first mode) and covarBBehaviorBipartiteObjective (for covariates on second mode) (allEffects.csv, effects.r).
- Added effect class covarABehaviorBipartiteObjective and covarBBehaviorBipartiteObjective to effectsDocumentation.R.
- Undid duplication of covarNetNetObjective.
- For non-invertible covariance matrices, give diagnostic for the linear combination that gives trouble at the end of the algorithm (phase3.r).
- Correction of igraphNetworkExtraction() in sienaGOF-auxiliary.Rd (the earlier version dropped isolated nodes from simulated networks).
- In sienaGOF-auxiliary.Rd, the example of constraint is replaced by the example of eigenvector centrality (because constraint is undefined for isolated nodes, leading to computational problems).
- sienaRIDynamics restored, after corrections.
- "file" parameter of sienaRI dropped (implied platform dependence).
- Parameter showAll added to descriptives.sienaGOF.
- Small correction of print.siena (reporting uponly/downonly).
- Some changes in print.sienaAlgorithm.
- Check in siena07 for incorrect MaxDegree specification.
- Correction of printing errors arising when result of score-type test is NA.
- maxRatio checked for NA or NaN in phase2.r.
- Section in manual about user-defined interaction effects updated.
- Siena_algorithms4.tex renamed Siena_algorithms.tex.
- Set diagonal of observed networks to 0 in sparseMatrixExtraction (sienaGOF.r).
- Some improvement of error messages for sienaTimeTest.
- p-value for goodness of fit rounded to 3 decimal places (sienaGOF.r)
- Longer string length for output of z$requestedEffects$effectName in print to output file (print07Report.r).
- File effects.pdf dropped from \inst\doc (it can be created by effectsDocumentation() so the separate file is superfluous).
- AverageAlterEffect.cpp simplified.
- sienaBayes(): new parameters nImproveMH and priorRatesFromData; truncate initial rate parameters depending on prior. Small change in example in help page.
- glueBayes() corrected so that it can be applied sequentially.
- Small improvement in print.summary.sienaBayesFit().
- multipleBayesTest now allows matrix parameter to test linear combinations.
- Improved plot.multipleBayesTest (shows truncation at 0).
2014-07-24 R-Forge Revision 278
- Added s50s to RSiena.rda.
- Corrected se component of sienaFit objects (should be standard error, was its square).
- new effects totDist2, altInDist2, totInDist2, totDist2W, altInDist2W, totInDist2W.
- Warnings turned off for calculation of z$regrCoef and z$regrCor in phase1.r and phase3.r.
- print01Report() improved for changing dyadic covariates, and some layout improvement for long variable names, and bug corrected for reporting upOnly/downOnly cases.
- Adapted sienaBayes and glueBayes and print.sienaBayes to allow inclusion of interaction effects without the corresponding main effects (use $requestedEffects instead of $effects).
- glueBayes(): checks of equality of prior parameters restricted to !ratesInVarying; parameter nwarm2 added (sienaBayes.r).
- sienaBayes: Multiplied priorSigma for rate parameters by priorKappa; changed z$nwarm to 0 if !is.null(prevBayes); change result of dmvnorm() to -Inf if cov. matrix singular; dropped plotit functionality.
2014-06-22 R-Forge Revision 277
- Some documentation of returnChains in siena07.Rd.
- Added function simpleBayesTest() (bayesTest.r, bayesTest.Rd).
- Added function multipleBayesTest() with print and plot methods (bayesTest.r, bayesTest.Rd).
- Small changes in various functions in sienaBayes.r.
- Corrected starting printing sienaBayesFit at nfirst (sienaprint.r).
2014-06-02 R-Forge Revision 275, but version predated 1.1-276
- Higher writefreq for batch operation (phase2.r, phase3.r)
- Error check for name of dependent variable to condition upon (initializeFRAN.r)
- Some corrections to allow behavior dependent variables that are not coded as integer (in initializeFRAN and unpackBehavior, initializeFRAN.r)
- Parameters fix and test now used in includeEffects() (sienaeffects.r)
- Small bug fix in CalculateDerivative3 (phase3.r)
- Avoidance of ":::" in siena01.r and document.r by small changes.
- Changes in sienaBayes.r and its print and summary methods; new function glueBayes.
2014-05-05 R-Forge Revision 275
- Error message and stop in case of mismatch variable names in algorithm object and in data (initializeFRAN.r).
- Force behavior and its attribute "change" to be integer in function unpackBehavior() (initializeFRAN.r).
- Some tabs in .Rd files change to spaces.
2014-04-26 R-Forge Revision 274
- Replaced (!strcmp...) by (!(strcmp...)) one more time in sienainternals07.cpp.
2014-04-25 R-Forge Revision 273
- NAMESPACE: removed entries sienaRIDynamics with the corresponding print, summary, and plot methods (to be entered later when problems have been solved).
- Removed sienaRIDynamics.Rd (ditto).
- Some changes in sienaRIDynamics.r but not enough to make it work.
- Duplication of outInv and outSqInv effects for two-mode networks canceled (allEffects.csv).
- Correction of effect homWXClosure.
- Small change in print01Report.r to improve reporting two files of composition change.
- sienaRI.r: require that <> argument is not NULL for non-Windows operating systems.
- Minor changes in sienaBayes.r.
2014-04-17 R-Forge Revision 272
- sienaRIDynamics.Rd: added
- sienaRIDynamics.r: small changes
- NAMESPACE: added entries sienaRIDynamics with the corresponding print, summary, and plot methods.
2014-04-17 R-Forge Revision 271
- Added component se (standard errors) to sienaFit objects
- Replaced
(!strcmp...)by(!(strcmp...))several times insienainternals07.cpp.
2014-04-13 R-Forge Revision 270
- Moved plot(RI) in sienaRI.Rd to dontrun{...}.
- File changeLog renamed ChangeLog.
2014-04-13 R-Forge Revision 269
- In one line in sienaRIDynamics.r, "intervalsPerPeriods" CHANGED TO "intervalsPerPeriod" (this was a misprint).
- Changes of version 1.1.268 in sienaRIDynamics ported from RSiena to RSienaTest.
- Small changes in sienaRI.r.
- sienaRI.Rd ported from RSiena to RSienaTest, with small changes.
- NAMESPACE: added entry sienaRI with the corresponding print, summary, and plot methods.
- sienaBayes.r, sienaprint.r: updates to let sienaBayes.r accept a wider range of data and models (e.g., user-defined interactions).
- sienaRIDynamics with plot and print methods temporarily left out.
- Small changes in sienaRI.r and sienaRI.Rd.
- sienaDataCreate.r, sienautils.r, print01Report.r: In coDyadCovar() and varDyadCovar(), centering now also is optional by the new option "centered" (like it was done for coCovar() and varCovar() in revision 1.1-251).
- sienaprint.r: correct bug when printing siena object with symmetric network.
- varDyadCovar: repaired bug occurring when calling it with a named list.
2014-04-08 R-Forge Revision 268
- sienaRI.Rd: added
- sienaRIDynamics.r: bugfix
- NAMESPACE: added entries sienaRI and sienaRIDynamics with the corresponding print, summary, and plot methods.
2014-03-30 R-Forge Revision 267
Added R-files that contain functionalities to calculate, print and plot relative importances of effects
- sienaRI.r: new
- sienaRIDynamics.r: new
- Model.cpp: bugfix
2014-03-17 R-Forge Revision 266
- getTargets.r: Added actorTargets function for use with multiple imputation of behaviour variable.
- sienaModelCreate.r, initializeFRAN.r, setup07setup.cpp, Model.cpp, Model.h, MLSimulation.cpp, MLSimulation.h: added localML option to sienaAlgorithm.
- allEffects.csv: added "local" column for use with localML option.
2014-03-14 R-Forge Revisions 261-265
as have been included in RSienaTest in Revision 255
2014-03-14 R-Forge Revisions 255-260
- Modified getTargets(...) such that it is possible to return target statistics of individual actors as well as change contributions necessary for calculating relative importances of effects (siena07setup.cpp).
- Call of getTargets(...) is correspondingly adapted (initializeFRAN.r).
- Modified simstats0c(...) such that it is possible to return statistics of individual actors in simulated networks as well as statistic contributions of all potential tie flips or behavior changes for all simulated micro-steps (simstatsc.r).
- Modified model(...) such that it calculates and returns the statistics newly needed in simstats0c(...) (siena07model.cpp)
- Added methods, functions, constructors, and fields needed due to changes in getTargets(...) and model(...): public void needChangeContributions(bool flag) (Model.h, Model.cpp) public bool needChangeContributions() (Model.h, Model.cpp) private bool lneedChangeContributions2 (Model.h) SEXP getChangeContributionsList(...) (siena07utilities.h, siena07utilities.cpp) SEXP createRObjectAttributes(...) (siena07utilities.h, siena07utilities.cpp) void getChangeContributionStatistics(...) (siena07internals.h, siena07internals.cpp) void getActorStatistics(...) (siena07internals.h, siena07internals.cpp) public StatisticCalculator(..., bool) (StatisticCalculator.h, StatisticCalculator.cpp) public StatisticCalculator(..., bool, bool) (StatisticCalculator.h, StatisticCalculator.cpp) public vector<double *> staticChangeContributions(...) (StatisticCalculator.h, StatisticCalculator.cpp) public double * actorStatistics(...) (StatisticCalculator.h, StatisticCalculator.cpp) private bool lneedActorStatistics (StatisticCalculator.h, StatisticCalculator.cpp) private bool lcountStaticChangeContributions (StatisticCalculator.h, StatisticCalculator.cpp) private map<EffectInfo *, double * > lactorStatistics (StatisticCalculator.h, StatisticCalculator.cpp) private map<EffectInfo *, vector<double *> > lstaticChangeContributions (StatisticCalculator.h, StatisticCalculator.cpp)
- Modifications of functions calculateNetworkEvaluationStatistics(...) (StatisticCalculator.cpp) calculateBehaviorStatistics(...) (StatisticCalculator.cpp) Specifically, assignments of form "this->lstatistics[pInfo] = pEffect->evaluationStatistic()" are extended in order to also store actor statistics and change contributions.
- Added a field and corresponding get-and set-methods to class MiniStep for storing potential statistic contributions of changes in micro-steps private map<const EffectInfo *, vector > * lpChangeContributions (MiniStep.h, MiniStep.cpp) public map<const EffectInfo , vector > changeContributions() (MiniStep.h, MiniStep.cpp) public void changeContributions(map<const EffectInfo *, vector > * contributions) (MiniStep.h, MiniStep.cpp) * Added field to class DependentVariable (DependentVariable.h, DependentVariable.cpp) protected map<const EffectInfo *, vector > * lpChangeContribution;
- Modifications of functions makeChange() and calculateTieFlipProbabilities() in class NetworkVariable (NetworkVariable.cpp) calculateProbabilities(), totalEvaluationContribution(), totalEndowmentContribution(), and totalCreationContribution() in class BehaviorVariable (BehaviorVariable.cpp) in order to store statistic contributions of effects to all possible choices of an actor in the current micro-step
- Added functions to classes NetworkEffect and BehaviorEffect (NetworkEffect.h, NetworkEffect.cpp, BehaviorEffect.h, BehaviorEffect.cpp) such that, in addition to the sum of statistics ovar all actors, individual actor statistics can be returned public virtual pair <double, double * > statistic(..., bool needActorStatistics) public virtual pair <double, double * > evaluationStatistic(...,bool needActorStatistics) public virtual pair <double, double * > endowmentStatistic(..., bool needActorStatistics) public virtual pair <double, double * > creationStatistic(..., bool needActorStatistics)
2014-02-17 R-Forge Revision 254
- Give the capital P to HomCovariateMixedTwoPathFunction.cpp and HomCovariateMixedTwopathFunction.h.
2014-02-16 R-Forge Revision 253
- Give the capital E to HomCovariateTransitiveTripletsEffect.h and HomCovariateTransitiveTripletsEffect.cpp.
2014-02-15 R-Forge Revision 252
- Set eoln property to "native" for HomCovariateTransitiveTripletsEffect.h and HomCovariateTransitiveTripletsEffect.cpp.
- Small change to sienaBayes (mustUpdate).
2014-02-13 R-Forge Revision 251
- Also cater for behavior user-specified interactions in includeInteraction and setEffect (sienaeffects.r).
- New effects: "cl.XWX", "homXTransTrip", "homWXClosure", and "sharedPop".
- Effect "cycle4" extended to non-directed one-mode networks
- (for directed one-mode networks it is "sharedPop").
- Effects "gwesp.." modified; extended to non-directed networks.
- Correction: Effect "to" is not a dyadic effect (allEffects.csv)
- sienaGOF: added the name of the siena fit object as attribute "sienaFitName" to each of the sienaGofTest objects.
- Manual: added paragraph about how to import results from xtable() and siena.table() into MS-Word.
- Correction in sparseNetworkExtraction() to avoid errors occurring when the extracted network has no edges (sienaGOF.r).
- In the help page for sienaGOF-auxiliary, geodesic distances changed to non-directed; which avoids a further error when the extracted network has no edges.
- Correction of an error in print.siena for data sets including other types than "oneMode".
- Changed bandwidth selector for violin plots in plot.sienaGOF to "nrd", to avoid long violins in cases where all simulations have the same outcome.
- Added parameter "includeRandoms" to print.sienaEffects.
- sienaGOF checks that the sienaFitObject object was not made by maximum likelihood estimation.
- Ported effects outRateLog and outTrunc2 from RSienaTest.
- Ported changes (new folders and files: \layers, \iterators, etc.)# in \src\network\ from RSienaTest.
- Major changes to sienaBayes and print.sienaBayes, to permit estimation of multilevel stochastic actor-oriented model with effects varying between groups for only a subset of the effects.
2013-12-04 R-Forge Revision 250
- New option "centered" in coCovar and varCovar (sienautils.r, sienaDataCreate.r, print01Report.r, sienaprint.r).
- setEffect, updateTheta, and prevAns in siena07() now also cater for user-specified interactions (sienaeffects.r, initializeFRAN.r).
- Wald.RSiena and Multipar.RSiena added (Sienatest.r).
- Error occurrence with message about cvalue in EvaluateTestStatistic corrected (Sienatest.r).
- Divergent parameters in siena07() get NA for their rows and columns in the covariance matrix (function phase3.2 in phase3.r). The following changes in revision 244 were ported from RSienaTest to RSiena:
- In siena08, also report Bonferroni combination of the two Fisher combinations.
- In phase2.r, rolled back change in truncation from version 1.1-227 to the earlier procedure.
- descriptives.sienaGOF added.
- Minor changes of output in siena.table, print07Report.r, print.siena, printInitialDescription.r, and in error message for includeEffects.
- Change artificial results from 999 to NA (robmon.r, phase3.r)
- For ML estimation: added autocorrelations during phase 3 to print.summary.sienaFit (sienaprint.r)
2013-11-29 R-Forge Revision 249
* Fix warning in EpochSimulation regarding String-plus-int.
Once RSiena moves to C++11 this can be replaced by std::to_string
2013-11-28 R-Forge Revision 247
* Fix problem with std::map<int,int>::const_iterator constructor
call in IncidentTieIterator.cpp
* Fix ambiguous call of abs in AlterCovariateAv/TotSimEffect by
replacing cmath by cstdlib
* Fix problem with using namespace std in DiffusionEffectValueTable
and EffectValueTable
2013-10-31 R-Forge Revision 246
- New behavior objective function effects avSimAltX, totSimAltX and avAltAltX to differentiate sources of peer influence in directed networks.
- Added effect class covarBehaviorNetObjective to effectsDocumentation.R.
- Fix of a bug that occurred in the case of on average decreasing behavior variables.
2013-10-16 R-Forge Revision 245
- New structural rate effect outRateLog (allEffects.csv, StatisticCalculator.cpp, DependentVariable.cpp, siena07Internals.cpp, StructuralRateEffect.cpp, Utils.h, Utils.cpp, RSiena_Manual.tex).
- In siena08, also report Bonferroni combination of the two Fisher combinations.
- In phase2.r, rolled back change in truncation from version 1.1-227 to the earlier procedure.
- descriptives.sienaGOF added.
- outTrunc2 effect added.
- Minor changes of output in siena.table, print07Report.r, print.siena, printInitialDescription.r, and in error message for includeEffects.
- Change artificial results from 999 to NA (robmon.r, phase3.r)
- For ML estimation: added autocorrelations during phase 3 to print.summary.sienaFit (sienaprint.r)
- Small addition to siena_Algorithms4.tex (statistics for rate effects).
- Bit of cleaning up (phase3.r)
- Start of the manual reorganized and partially rewritten (with help from Zsofia Boda and Andras Voros); instructions for siena01Gui separated in siena01gui.pdf.
- Larger example for sienaCompositionChange.Rd.
2013-10-16 R-forge revision 244
- Corrected DistanceTwoLayer.cpp
2013-09-17 R-forge revision 243
- Correct bug in EffectFactory for isolatePop effect.
- Improved plotting of sienaGOF objects so that observed values outside of the range of simulated values don't run off the chart.
- Improve treatment of structural values in sienaGOF by modifying sparseMatrixExtraction(); and simplify networkExtraction() by building it directly on sparseMatrixExtraction().
- Add functions AntiIsolateEffect.h and AntiIsolateEffect.cpp which were forgotten to include in revision 242.
2013-09-10 R-forge revision 242
- New effects: anti isolates, anti in-isolates, anti in-near-isolates.
- Effect inIsolatePop dropped (it was shortlived).
- Improved printing of results of siena07() in the case simOnly.
- Prettier response printed to console for includeEffects() and setEffect().
- z$estMeans added to siena objects z: vector of estimated expected values of statistics; this is colMeans(z$sf) + z$targets but if dolby, the regression on the scores is subtracted.
- Correction to Dolby option for the case of more than 2 waves: in phase1.r and phase3.r, scores are added (instead of averaged) over waves. (Averaging was wrong, because in phase 2 they are added.)
- All single quotes in .Rd files replaced by double quotes (first seemed required by the disappearance of inconsolata.sty, probably superfluous).
- Small additions to Siena_algorithms4.
2013-08-23 R-forge revision 241
- Corrected bug that occurred if there was only one option for choice of alter.
- Dropped scripts.r from \tests.
- Added "silent=TRUE" to various try statements (mainly associated with inversion of singular matrices) to avoid execution errors.
- Added various degree-related effects to bipartite networks.
- New effect inIsolatePop.
- Drop multiplication of the target statistic for the inPop effect by n.
- Small unimportant changes in sienaeffects.r, robmon.r, sienaprint.r
2013-08-08 R-forge revision 240
- Added the parameter reduceg to siena07() (sienaModelCreate.r, phase2.r, robmon.r, printDataReport.r, sienaprint.r)
- Added effects crprod and inPopIntn to bipartiteBipartiteObjective group (allEffects.csv, effects.pdf).
- Added tstat (t-statistic for convergence) to sienaFit objects.
- Clarification in sienaCompositionChange.Rd.
- Small change to siena07.Rd.
2013 July 26 - August 2 R-Forge revisions 232-239 Various changes by Mark Ortmann to RSienaTest.
2013-06-18 CRAN version 1.1-232
- 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
- 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 page (sienaCompositionChange.Rd).
- Small changes in help pages sienaAlgorithm.Rd, plot.sienaTimeTest.Rd,
2013-05-10 R-forge revision 230
* 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
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 pages 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 page 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