[Rsiena-commits] r270 - in pkg: RSiena RSiena/inst/doc RSiena/man RSienaTest RSienaTest/inst/doc RSienaTest/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Apr 13 23:58:27 CEST 2014
Author: tomsnijders
Date: 2014-04-13 23:58:25 +0200 (Sun, 13 Apr 2014)
New Revision: 270
Added:
pkg/RSiena/ChangeLog
pkg/RSienaTest/ChangeLog
Removed:
pkg/RSiena/changeLog
pkg/RSienaTest/changeLog
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/inst/doc/RSiena_Manual.tex
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/sienaRI.Rd
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/doc/RSiena_Manual.tex
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/sienaRI.Rd
Log:
Small change to sienaRI.Rd to prevent opening a graphical window.
Copied: pkg/RSiena/ChangeLog (from rev 269, pkg/RSiena/changeLog)
===================================================================
--- pkg/RSiena/ChangeLog (rev 0)
+++ pkg/RSiena/ChangeLog 2014-04-13 21:58:25 UTC (rev 270)
@@ -0,0 +1,2835 @@
+2014-04-13 R-Forge Revision 270
+Changes in RSiena and RSienaTest:
+ * Moved plot(RI) in sienaRI.Rd to dontrun{...}.
+ * File changeLog renamed ChangeLog.
+
+2014-04-13 R-Forge Revision 269
+Changes in RSienaTest:
+ * 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).
+Changes in RSiena:
+ * sienaRIDynamics with plot and print methods temporarily left out.
+ * Small changes in sienaRI.r and sienaRI.Rd.
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSiena:
+ * 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
+Changes in RSiena:
+Added R-files that contain functionalities to calculate, print and plot relative importances of effects
+ * sienaRI.r: new
+ * sienaRIDynamics.r: new
+Changes in RSiena and RSienaTest:
+ * Model.cpp: bugfix
+
+2014-03-17 R-Forge Revision 266
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSiena: Included exactly the same changes in RSiena
+as have been included in RSienaTest in Revision 255
+
+2014-03-14 R-Forge Revisions 255-260
+Changes in RSienaTest:
+ * 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<double> > * lpChangeContributions (MiniStep.h, MiniStep.cpp)
+ public map<const EffectInfo *, vector<double> >* changeContributions() (MiniStep.h, MiniStep.cpp)
+ public void changeContributions(map<const EffectInfo *, vector<double> > * contributions) (MiniStep.h, MiniStep.cpp)
+ * Added field to class DependentVariable (DependentVariable.h, DependentVariable.cpp)
+ protected map<const EffectInfo *, vector<double> > * 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 od 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
+Changes in RSiena and RSienaTest:
+ * Give the capital P to HomCovariateMixedTwoPathFunction.cpp
+ and HomCovariateMixedTwopathFunction.h.
+
+2014-02-16 R-Forge Revision 253
+Changes in RSiena and RSienaTest:
+ * Give the capital E to HomCovariateTransitiveTripletsEffect.h
+ and HomCovariateTransitiveTripletsEffect.cpp.
+
+2014-02-15 R-Forge Revision 252
+Changes in RSiena:
+ * Set eoln property to "native" for HomCovariateTransitiveTripletsEffect.h
+ and HomCovariateTransitiveTripletsEffect.cpp.
+Changes in RSienaTest:
+ * Small change to sienaBayes (mustUpdate).
+
+2014-02-13 R-Forge Revision 251
+Changes in RSiena and RSienaTest:
+ * 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.
+Changes in RSiena:
+ * Ported effects outRateLog and outTrunc2 from RSienaTest.
+ * Ported changes (new folders and files: \layers, \iterators, etc.)#
+ in \src\network\ from RSienaTest.
+Changes in 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
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSiena and RSienaTest:
+ * 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
+Changes in RSienaTest:
+ * 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
+Changes in RSienaTest:
+ * Corrected DistanceTwoLayer.cpp
+
+2013-09-17 R-forge revision 243
+Changes in RSiena and RSienaTest:
+ * 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().
+Changes in RSiena:
+ * Add functions AntiIsolateEffect.h and AntiIsolateEffect.cpp
+ which were forgotten to include in revision 242.
+
+2013-09-10 R-forge revision 242
+Changes in RSiena and RSienaTest:
+ * 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).
+Changes in RSienaTest:
+ * Small additions to Siena_algorithms4.
+
+2013-08-23 R-forge revision 241
+Changes in RSiena and RSienaTest:
+ * 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.
+Changes in RSienaTest:
+ * Small unimportant changes in sienaeffects.r, robmon.r, sienaprint.r
+
+2013-08-08 R-forge revision 240
+Changes in RSienaTest:
+ * Added the parameter reduceg to siena07()
+ (sienaModelCreate.r, phase2.r, robmon.r, printDataReport.r, sienaprint.r)
+Changes in RSienaTest and RSiena:
+ * 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
+Changes in RSiena:
+ * Drop the possibility to use obsolete package snow and rlecuyer
+ if Rversion < 2.14.0; functionality replaced by
+ package parallel (siena07.r).
+ * Correct DESCRIPTION file to satisfy CRAN requirements.
+ * Correct lines in various help pages that were too long
+ in the pdf version.
+
+2013-06-15 R-forge revision 231
+Changes in RSiena as well as RSienaTest:
+ * Make the "cumulative" option operational in BehaviorDistribution()
+ (sienaGOF.r).
+ * Correct bug in treatment of missing values in sparseMatrixExtraction()
+ (sienaGOF.r).
+ * Allow sparse observed data matrices, and structural zeros and ones, in
+ sparseMatrixExtraction() and networkExtraction(),
+ and bipartite networks in networkExtraction() (sienaGOF.r).
+ * In case prevAns exists, recalculate z$dinvv instead of taking it
+ from prevAns (initializeFRAN.r) (parameter diag may have changed)
+ * Report correct centering (by overall means) of individual
+ covariates for multi-group objects (print01Report.r).
+ * in sienaTimeTest: string in toTest$effectName set to "chisq="
+ instead of "p=" (sienaTimeTest.r)
+ * In print method for sienaAlgorithm, report of conditional corrected
+ in case !x$cconditional (sienaprint.r)
+ * If there is a composition change object, MoM estimation is forced
+ to be non-conditional (initializeFRAN.r). This is reported in the help file
+ (sienaCompositionChange.Rd).
+ * Small changes in help files sienaAlgorithm.Rd, plot.sienaTimeTest.Rd,
+
+
+2013-05-10 R-forge revision 230
+Changes in RSiena as well as RSienaTest:
+ * Add attribute maxObsOutDegree to <object of class siena>$depvars[[.]]
+ (sienaDataCreate.r).
+ * Check whether this maximum observed degree is not higher than maxDegree
+ (printDataReport.r).
+ * Fix bug in implementation of maxDegree (initializeFRAN.r)
+ * Fix bug in print.siena and extend print.siena (sienaprint.r).
+ * Make print method for sienaDependent (sienaprint.r).
+Changes only in RSienaTest:
+ * File
+ \pkg\RSienaTest\inst\doc\effects.pdf
+ was updated.
+
+2013-05-10 R-forge revision 229
+Changes only in RSiena:
+ * Korean translation of R messages is updated: changed file
+ \pkg\RSiena\po\R-RSiena.pot
+
+2013-04-20 R-forge revision 228
+Changes only in RSiena:
+ * Files
+ \pkg\RSiena\src\model\variables\DiffusionEffectValueTable.cpp
+ \pkg\RSiena\src\model\variables\DiffusionEffectValueTable.h
+ \pkg\RSiena\man\sienaGOF-auxiliary.Rd
+ \pkg\RSiena\man\sienaGOF.Rd
+ were erroneously not committed in revision 227.
+ Therefore this was done now.
+ * Also, file
+ \pkg\RSiena\inst\doc\effects.pdf
+ was updated.
+
+2013-04-19 R-forge revision 227
+Changes in RSiena as well as RSienaTest;
+both now are very similar; sienaBayes, algorithms, and profileLikelihoods
+are the only functions in RSienaTest not in RSiena.
+Available effects now are the same.
+
+I hope the list of changes indicated here is complete.
+
+For Siena only:
+ * function bayes() was removed (still under development in RSienaTest).
+ * Attributes "allowOnly" and "simOnly" ported from RSienaTest.
+ * Improved error messages in includeEffects ported from RSienaTest.
+ * sienaGOF ported from RSienaTest.
+ * siena.table() ported from RSienaTest, in file sienatable.r.
+ * Changes of revision 226 ported from RSienaTest.
+
+For RSienaTest only:
+ * bayes() renamed to sienaBayes() and considerably changed.
+ * Added function print.sienaBayesFit to sienaprint.r, with
+ new documentation file printsienaBayesFit.Rd.
+ * Some invisible developments for settings model.
+
+For RSiena and RSienaTest:
+ * Changes to sienaGOF: new use structure with auxiliary functions
+ sparseMatrixExtraction, networkExtraction, behaviorExtraction,
+ allowing to test any dependent variable;
+ commented out some superfluous lines.
+ * The function sienaModelCreate() is now called sienaAlgorithmCreate(),
+ but the earlier name is still retained as an alias;
+ the class name of the object created by this function is now called
+ sienaAlgorithm.
+ * The function sienaNet() is now called sienaDependent(),
+ but the earlier name is still retained as an alias;
+ the class name of the object created by this function is now
+ sienaDependent.
+ * The function effectsDocumentation() now has an extra argument "effects";
+ if this points to an effects object, all available effects
+ in this effects object are listed with shortName,
+ with a variety of other often used characteristics.
+ * Effect type "covarBehaviorOneModeRate" was added.
+ * Added effects (some existed already in RSienaTest):
+ average exposure effect on rate xxxxxx, avExposure
+ susceptibility to av. exp. by indegree effect on rate xxxxxx,
+ susceptAvIn
+ total exposure effect on rate xxxxxx, totExposure,
+ infection by indegree effect on rate xxxxxx, infectIn,
+ infection by outdegree effect on rate xxxxxx, infectOut,
+ susceptibility to av. exp. by zzzzzz effect on rate xxxxxx,
+ susceptAvCovar
+ infection by zzzzzz effect on rate xxxxxx, infectCovar,
+ WW=>X cyclic closure of xxxxxx, cyWWX
+ WW=>X shared incoming xxxxxx, InWWX
+ WW=>X shared outgoing xxxxxx, OutWWX
+ xxxxxx alter at distance 2 (#), altDist2
+ xxxxxx similarity at distance 2, simDist2
+ transitive triplets xxxxxx similarity, simXTransTrip
+ transitive triplets same xxxxxx, sameXTransTrip
+ transitive triplets jumping xxxxxx, jumpXTransTrip
+ transitive reciprocated triplets, transRecTrip
+ GWESP I -> K -> J (#), gwespFF
+ GWESP I <- K <- J (#), gwespBB
+ GWESP I <- K -> J (#), gwespFB
+ GWESP I -> K <- J (#), gwespBF
+ GWESP I <> K <> J (#), gwespRR
+ isolate - popularity, isolatePop
+ in-isolate Outdegree, inIsDegree
+ network-isolate, isolateNet
+ outdegree^(1/#) xxxxxx popularity, outPopIntn xxxxxx
+ closure jumping yyyyyy, jumpWWClosure
+ mixed xxxxxx closure jumping yyyyyy, jumpWXClosure
+ cyclic closure of xxxxxx, cyClosure
+ shared incoming xxxxxx, sharedIn
+ * Outdegree-popularity effect: multiplication by n dropped.
+ * GWESP effects: default parameter changed from 25 to 69
+ (corresponding to alpha = log(2).) See the manual.
+ * Added to siena07:
+ option "Dolby" for variance reduction.
+ Correlations between scores and statistics are reported in output file;
+ this is a measure for the amount of variance reduction.
+ * Added to siena07:
+ option "diagonalize" for having more possibilities for
+ tuning the algorithm
+ (extent of diagonalization of matrix D in Robbins-Monro update).
+ * sienaTimeTest() updated; now also contains effect-wise tests,
+ groupwise tests (for group objects), automatic exclusion of
+ collinear effects, and has prettier output and improved summary.
+ * Truncation of update steps in phase2.r modified.
+ * Overall maximum convergence ratio, x$tconv.max
+ (maximum value of t-ratio for convergence, for any linear combination)
+ added to result of siena07.
+ * The print method for objects of class siena (created by sienaDataCreate)
+ has been extended with printing "uponly" and "downly" attributes,
+ if these are TRUE.
+ * A bug in the starting values for two-mode networks was corrected.
+ * Small bug fixed in print01Report() for reporting of uponly and downonly,
+ in the case where this does not affect all periods.
+ * Changed almost all .Rd documentation files: sometimes to make them
+ better understandable or complete, sometimes to make more appropriate
+ examples, sometimes only minor prettifications.
+ * Updated:
+ pkg\RSiena(Test)\inst\scripts\Rscript01DataFormat.R,
+ pkg\RSiena(Test)\inst\scripts\Rscript02VariableFormat.R,
+ pkg\RSiena(Test)\inst\scripts\Rscript03SienaRunModel.R,
+ pkg\RSiena(Test)\inst\scripts\Rscript04SienaBehaviour.R.
+ (of pkg\RSiena(Test)\inst\scripts\RSienaDescriptives
+ only the date was changed.)
+ * Updated tests\scriptfile.Rout.win to current version
+ (scriptfile.Rout.save).
+ * Manual and siena.bib updated.
+
+2013-04-17 R-forge revision 226 RSienaTest only
+
+ * changed:
+ pkg/RSienaTest/src/model/effects/generic/AlterPredicate.h
+ pkg/RSienaTest/src/model/effects/generic/CovariatePredicate.h
+ pkg/RSienaTest/src/model/filters/PermittedChangeFilter.
+ Note: changes:
+ base classes have always a virtual destructor
+ reduced visibility of abstract class constructors
+
+2013-03-12 R-forge revision 225
+
+ * Removed files and directories that were put in, at the highest directory
+ level, by mistake at revision 220.
+
+2013-02-14 R-forge revision 224 RSiena only
+
+ * Added pkg//RSiena/po/R-ko.mo and pkg//RSiena/po/R-ko.po
+
+2013-01-01 R-forge revision 223
+
+ * R/sienaDataCreateFromSession.R: change assignments to frame of
+ function rather than using global environment.
+
+2012-12-24 R-forge revision 222 mostly RSienaTest only
+
+ * tests/slowtest.R (added), R/document.R, .Rbuildignore: Created function
+ to concatenate all examples and run them, including the dontrun ones.
+ * R/bayes, R/algorithms.r, man/sienaGOF.Rd,
+ man/sienaNet.Rd (also RSiena): minor changes to make the new test
+ run sensibly.
+ * tests/effectsTest.R: edited comments
+
+2012-12-23 R-forge revision 221 RSiena and RSienaTest
+
+ * R/robmon.r, siena07.r, simstatsc.r: corrected check for R version
+ so will work with R version 3.0.0.
+
+2012-09-10 R-forge revision 220
+
+ * Unintended changes in highest directory (i.e., without effect on packages);
+ undone in revision 225.
+
+2012-07-06 R-forge revision 219
+ For RSiena and RSienaTest:
+ * Added matrices N3401, N3403, N3404, N3406, and HN3401, HN3403, HN3404,
+ HN3406 to RSiena.Rda, with associated documentation files
+ N3401.Rd and HN3401.Rd.
+ * Updates to manual and RSiena.bib.
+ For RSienaTest only:
+ * Further serious changes in bayes.r and documentation bayes.tex.
+ * Added function print.sienaBayesFit to sienaprint.r, with
+ new documentation file printsienaBayesFit.Rd
+ * Small changes to sienaGOF: commented out some superfluous lines.
+ * Made all siena07 calls in tests and examples to batch=TRUE:
+ this affected tests\effectsTest.R, man\plot.sienaTimeTest.Rd,
+ man\sienaTimetest.Rd.
+ * Changed documentation files bayes.Rd, sienaGroupCreate.Rd,
+ siena08.Rd, siena07.Rd, sienaDataCreate.Rd, sienaModelCreate.Rd.
+ * Updated tests\scriptfile.Rout.win to current version (scriptfile.Rout.save
+ still needs to be done!)
+ * New and changed effects: changes to
+ \src\AllEffects.h, \data\allEffects.csv,
+ in \src\model\effects : \EffectFactory.cpp, AllEffects.h,
+ SameCovariateTransitiveTripletsEffect.cpp,
+ new files JumpCovariateTransitiveTripletsEffect.cpp and .h
+ in \src\model\effects\generic : MixedNetworkAlterFunction.cpp and .h,
+ SameCovariateMixedTwoPathFunction.cpp and .h,
+ SameCovariateTwoPathFunction.cpp and .h,
+ CovariateMixedNetworkAlterFunction.cpp and .h.
+ * Removed some extra documentation producing a warning in R CMD check.
+
+2012-06-07 R-forge revision 216
+
+ All for RSienaTest only.
+ * R/bayes.r: considerable update (no known errors now,
+ except multigroup does not work for dyadic covariates.)
+ * R/print07report.r: small cosmetic change
+ * data/allEffects.csv,
+ src/model/effects/AllEffects.h, src/model/effects/effectFactory.cpp,
+ src/model/effects/InIsolateDegreeEffect.h,
+ src/model/effects/InIsolateDegreeEffect.cpp,
+ src/model/effects/IsolateNetEffect.h,
+ src/model/effects/IsolateNetEffect.cpp,
+ src/model/effects/IsolatePopEffect.h,
+ src/model/effects/IsolatePopEffect.cpp,
+ src/model/effects/WWXClosureEffect.h,
+ src/model/effects/WWXClosureEffect.cpp,
+ src/model/effects/generic/OutStarFunction.h,
+ src/model/effects/generic/OutStarFunction.cpp,
+ src/model/effects/generic/ReverseTwoPathFunction.h,
+ src/model/effects/generic/ReverseTwoPathFunction.cpp:
+ new effects.
+ * R/printInitialDescription.r: minor rewriting.
+ * Manual correspondingly updated.
+
+2012-05-18 R-forge revision 213
+
+ All for RSienaTest only.
+ * R/effects.r and R/printInitialDescription.r:
+ protect against situations where matrix matchange has zero rows or columns
+ (i.e., prevent runtime error)
+ * R/sienaprint.r, R/print07Report.r, R/phase3.r, R/terminateFRAN.r,
+ R/robmon.r, R/sienaModelcreate.r, man/siena07.Rd, man/sienaModelCreate.r:
+ incorporate argument simOnly in sienaModelCreate() to facilitate
+ simulation without estimation.
+ * R/initializeFRAN.r, R/sienaDataCreate.r, R/sienautils.r, man/sienaNet.Rd:
+ incorporate argument allowOnly in sienaNet() to permit
+ ignoring monotonicity in data and its consequences for upOnly and downOnly.
+ * data/allEffects.csv,
+ src/model/effects/AllEffects.h, src/model/effects/effectFactory.cpp,
+ src/model/effects/SameCovariateTransitiveTripletsEffect.cpp,
+ src/model/effects/SameCovariateTransitiveTripletsEffect.h,
+ src/model/effects/TransitiveReciprocatedTripletsEffect.h,
+ src/model/effects/TransitiveReciprocatedTripletsEffect.cpp,
+ src/model/effects/SimilarityTransitiveTripletsEffect.h,
+ src/model/effects/SimilarityTransitiveTripletsEffect.cpp:
+ new effects
+
+2012-03-29 R-forge revision 212
+
+ * update of RSiena_Manual.tex, RSiena.bib (both packages)
+
+2012-03-29 R-forge revision 211
+
+ * doc/RSiena_Manual.tex, doc/siena1.png, doc/siena2.png,
+ doc/siena3.png, doc/ilcampo.jpg, doc/RSiena.bib moved to inst/doc/
+ and copied to RSiena to comply with GPL. Both packages now include
+ these files in the tarball but not the binary.
+ * .Rinstignore: added
+ * .Rbuildignore: added to RSiena and updated in RSienaTest to
+ exclude temporary latex files from the tar ball.
+ * R/effectsDocumentation.r: bug fix for newly added groups.
+ * inst/doc/effects.pdf: updated
+
+2012-03-29 R-forge revision 210 NB new version number sequence. 1.1.210
+
+ * src.siena07utilities.cpp, siena07setup.cpp: changes to R/C++
+ interface code. Moved a call to PutRNGstate to _before_ the
+ UNPROTECT to fix an intermittent error.
+ * tests/effectsTest.R: changes to comments only
+ * doc/RSienaDeveloper.tex, tests/scripts.Rout.save: updated output
+ file, minor additions to documentation.
+ * tests/testrefs/M44compare.out, tests/testrefs/M45compare.out:
+ updated test outputs. (RSienaTest only)
+ * tests/testrefs/*compare.out: some files got missed last time
+
+2012-03-28 R-forge revision 209 (RSienaTest only)
+
+ * src/model/effects/DiffusionRateEffect.cpp: bug fix
+
+2012-03-25 R-forge revision 208
+
+ * src/data/BehaviorLongitudinalData.cpp: fix memory leak
+ * src/model/effects/generic/CovariateDistance2NetworkFunction.cpp:
+ fix memory leak
+ * src/model/variables/NetworkVariable.cpp: fix bug in endowment
+ and creation effect scores for no change.
+ * data/allEffects.csv, R/effects.r, R/effectsDocumentation.r:
+ split behavior network effects between symmetric and other networks.
+ * src/model/model.cpp (RSiena only),
+ src/model/variables/DependentVariable.cpp,
+ src/model/variables/EffectValueTable.h (RSiena only): added
+ comments, formatting
+ * src/model/effects/DiffusionRateEffect.cpp: bug fix (RSienaTest
+ only)
+ * doc/RSienaDeveloper.tex: updated doc (RSienaTest only)
+ * doc/MCMCandRM.pdf: added
+ * tests/effectsTest.R, tests/sampson.r, testrefs/*,
+ .Rbuildignore: new testing files added, not to be included in tar
+ ball. (RSienaTest only)
+ * inst/examples/Sampson_t2.txt, inst/examples/Sampson_t3.txt,
+ inst/examples/Sampson_t4.txt, inst/examples/vtextexoreal.dat:
+ added.
+ * src/effects.r: correct bug causing crash with sparse matrices
+ with changes all in one direction.
+ * src/model/EpochSimulation.cpp: added comments
+ * src/model/ml/MLSimulation.cpp: correct test when storing
+ rejection numbers.
+ * src/model/StatisticCalculator.h: formatting (RSienaTest only)
+ * src/model/ml/chain.cpp: initialize finalReciprocalRate explicitly.
+
+2012-03-21 R-forge revision 207 (RSienaTest only)
+ * siena07internals.cpp, DependentVariable.h,
+ DependentVariable.cpp: changed calculation of scores for diffusion
+ rate effects
+ * StatisticCalculator.h, StatisticCalculator.cpp, DependentVariable.h,
+ DependentVariable.cpp, DiffusionRateEffect.h,
+ DiffusionRateEffect.cpp: added a function to calculate value of
+ a type of diffusion rate effect
+
+2012-03-16 R-forge revision 206 (RSienaTest only)
+
+ * R/effects.R, R/effectsDocumentation.R: added a new behavior rate
+ effectGroup covarBehaviorOneModeRate
+ * data/allEffects.csv, siena07internals.cpp,
+ StatisticCalculator.cpp, DependentVariable.cpp,
+ DependentVariable.h, DiffusionRateEffect.cpp,
+ DiffusionRateEffect.h: added new diffusion behavior rate effects
+ susceptAvIn, susceptAvCovar, infectIn, infectOut, infectCovar,
+ totExposure
+
+2012-03-07 R-forge revision 205
+
+ * src/model/effects/CovariateDistance2AlterEffect.cpp,
+ src/model/effects/CovariateDistance2AlterEffect.h,
+ src/model/effects/CovariateDistance2NetworkEffect.cpp,
+ src/model/effects/CovariateDistance2NetworkEffect.h,
+ src/model/effects/CovariateDistance2SimilarityEffect.cpp,
+ src/model/effects/CovariateDistance2SimilarityEffect.h: removed as
+ no longer used
+ * src/model/effects/allEffects.h: remove the .h's from previous
+ entry
+ * src/model/effects/CovariateAndNetworkBehaviorEffect.cpp: correct
+ memory leak.
+ * src/model/effects/generic/CovariateDistance2NetworkFunction.cpp:
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 270
More information about the Rsiena-commits
mailing list