[Rsiena-commits] r278 - in pkg: RSiena RSiena/R RSiena/data RSiena/inst/doc RSiena/man RSiena/src/model/effects RSiena/src/model/effects/generic RSienaTest RSienaTest/R RSienaTest/data RSienaTest/doc RSienaTest/inst/doc RSienaTest/man RSienaTest/src/model/effects RSienaTest/src/model/effects/generic RSienaTest/src/model/variables
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jul 24 12:00:53 CEST 2014
Author: tomsnijders
Date: 2014-07-24 12:00:52 +0200 (Thu, 24 Jul 2014)
New Revision: 278
Added:
pkg/RSiena/man/s50s.Rd
pkg/RSiena/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.cpp
pkg/RSiena/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.h
pkg/RSienaTest/man/s50s.Rd
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.h
Modified:
pkg/RSiena/ChangeLog
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/effects.r
pkg/RSiena/R/phase1.r
pkg/RSiena/R/phase3.r
pkg/RSiena/R/print01Report.r
pkg/RSiena/R/robmon.r
pkg/RSiena/R/sienaDataCreate.r
pkg/RSiena/R/sienaprint.r
pkg/RSiena/R/sienautils.r
pkg/RSiena/data/RSiena.rda
pkg/RSiena/data/allEffects.csv
pkg/RSiena/inst/doc/RSiena.bib
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/inst/doc/RSiena_Manual.tex
pkg/RSiena/inst/doc/effects.pdf
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/effectsDocumentation.Rd
pkg/RSiena/man/s50.Rd
pkg/RSiena/man/s501.Rd
pkg/RSiena/man/s502.Rd
pkg/RSiena/man/s503.Rd
pkg/RSiena/man/s50a.Rd
pkg/RSiena/man/sienaDependent.Rd
pkg/RSiena/src/model/effects/BehaviorEffect.h
pkg/RSiena/src/model/effects/CovariateAndNetworkBehaviorEffect.cpp
pkg/RSiena/src/model/effects/CovariateAndNetworkBehaviorEffect.h
pkg/RSiena/src/model/effects/EffectFactory.cpp
pkg/RSiena/src/model/effects/FourCyclesEffect.cpp
pkg/RSiena/src/model/effects/IsolatePopEffect.cpp
pkg/RSiena/src/model/effects/IsolatePopEffect.h
pkg/RSiena/src/model/effects/SameCovariateTransitiveTripletsEffect.cpp
pkg/RSiena/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp
pkg/RSiena/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h
pkg/RSiena/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
pkg/RSiena/src/model/effects/generic/CovariateDistance2NetworkFunction.h
pkg/RSiena/src/model/effects/generic/GwespFunction.cpp
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/effects.r
pkg/RSienaTest/R/phase1.r
pkg/RSienaTest/R/phase3.r
pkg/RSienaTest/R/print01Report.r
pkg/RSienaTest/R/robmon.r
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaDataCreate.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/R/sienautils.r
pkg/RSienaTest/data/RSiena.rda
pkg/RSienaTest/data/allEffects.csv
pkg/RSienaTest/doc/RSIENAspec.tex
pkg/RSienaTest/inst/doc/RSiena.bib
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/doc/RSiena_Manual.tex
pkg/RSienaTest/inst/doc/effects.pdf
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/bayesTest.Rd
pkg/RSienaTest/man/effectsDocumentation.Rd
pkg/RSienaTest/man/s50.Rd
pkg/RSienaTest/man/s501.Rd
pkg/RSienaTest/man/s502.Rd
pkg/RSienaTest/man/s503.Rd
pkg/RSienaTest/man/s50a.Rd
pkg/RSienaTest/man/sienaBayes.Rd
pkg/RSienaTest/man/sienaDependent.Rd
pkg/RSienaTest/src/model/effects/CovariateAndNetworkBehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateAndNetworkBehaviorEffect.h
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp
pkg/RSienaTest/src/model/effects/generic/CovariateDistance2NetworkFunction.h
pkg/RSienaTest/src/model/variables/BehaviorVariable.cpp
Log:
Version 1.1-278. See changelog.
Modified: pkg/RSiena/ChangeLog
===================================================================
--- pkg/RSiena/ChangeLog 2014-06-22 20:19:13 UTC (rev 277)
+++ pkg/RSiena/ChangeLog 2014-07-24 10:00:52 UTC (rev 278)
@@ -1,3 +1,25 @@
+2014-07-24 R-Forge Revision 278
+Changes in RSiena and RSienaTest:
+ * 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.
+Changes in RSienaTest:
+ * 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
Changes in RSiena and RSienaTest:
* Some documentation of returnChains in siena07.Rd.
@@ -38,7 +60,7 @@
Changes in RSiena and RSienaTest:
* NAMESPACE: removed entries sienaRIDynamics with the corresponding
print, summary, and plot methods (to be entered later when
- problems have been solved).
+ 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
@@ -109,9 +131,9 @@
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.
+ of behaviour variable.
* sienaModelCreate.r, initializeFRAN.r, setup07setup.cpp, Model.cpp, Model.h,
- MLSimulation.cpp, MLSimulation.h: added localML option to sienaAlgorithm.
+ 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
@@ -128,46 +150,46 @@
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)
+ 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)
+ 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.
+ 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;
+ 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
+ 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)
+ 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:
@@ -245,17 +267,17 @@
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
+ * 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
+ * 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:
@@ -263,7 +285,7 @@
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.
+ variables.
2013-10-16 R-Forge Revision 245
Changes in RSienaTest:
@@ -313,11 +335,11 @@
* 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$targets but if dolby,
- the regression on the scores is subtracted.
+ this is colMeans(z$sf) + z$targets but if dolby,
+ the regression on the scores is subtracted.
* Correction to Dolby option for the case of more than 2 waves:
in phase1.r and phase3.r, scores are added (instead of averaged)
- over waves. (Averaging was wrong, because in phase 2 they are added.)
+ over waves. (Averaging was wrong, because in phase 2 they are added.)
* All single quotes in .Rd files replaced by double quotes
(first seemed required by the disappearance of inconsolata.sty,
probably superfluous).
@@ -385,17 +407,17 @@
2013-05-10 R-forge revision 230
Changes in RSiena as well as RSienaTest:
- * Add attribute maxObsOutDegree to <object of class siena>$depvars[[.]]
+ * 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).
+ (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.
+ * File
+ \pkg\RSienaTest\inst\doc\effects.pdf
+ was updated.
2013-05-10 R-forge revision 229
Changes only in RSiena:
@@ -404,16 +426,16 @@
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.
+ * 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;
@@ -424,218 +446,218 @@
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.
+ * 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.
+ * 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.
+ * 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:
+ * 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.
+ * 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
+ * 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.
+ * 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
+ * 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.
+ * 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);
+ * 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 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.
+ * 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
+ * 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.
+ 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/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.
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 278
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