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# RSiena 1.2-25
2020-04-08
R-Forge Revision 348
## Changes in RSiena and RSienaTest:
* Correction of `sienaDataCreate` for actor covariates (gave a warning).
* Auxiliary function `dyadicCov` now can handle missings,
does not return a named value for frequency of zeros,
and returns the frequencies without any division.
* `descriptives.sienaGOF` also shows the exceedance probabilities
of the observed statistics.
* `modelType` and `behModelType`, if NULL, get their defaults already in
`initializeFRAN` (checkNames) rather than in C++.
* Some extra information in help page for siena07.
## Changes in RSienaTest:
* `getNames` corrected for data with multiple periods
(used in `sienaBayes`, `extract.sienaBayes`, and `extract.posteriorMeans`)
check bayesTest.getNames, voor extract.sienaBayes en extract.posteriorMeans !!!
# RSiena 1.2-24
2020-02-16
R-Forge Revision 347
## Changes in RSiena and RSienaTest:
* New auxiliary function `dyadicCov`.
* Correction of error in `modelType` when one-mode as well as two-mode
networks are used (`initializeFRAN.r`).
## Changes in RSienaTest:
* Corrected `siena.table` for `sienaBayesFit` objects;
added `startingDate` in `sienaBayes` and `siena08` to the object produced.
# RSiena 1.2-23
2020-01-12
R-Forge Revision 346
* one error in dontrun part of `sienaGOF-auxiliary.Rd` was corrected.
## Changes in RSiena and RSienaTest:
* 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.
# RSiena 1.2-22
2020-01-10
## Changes in RSiena and RSienaTest:
* Changed extension names of output files from .out to .txt.
# RSiena 1.2-22
2020-01-04 R-Forge Revision 345
## Changes in RSiena and RSienaTest:
* 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).
# RSiena 1.2-21
2019-12-18
## Changes in RSiena and RSienaTest:
* Tests ended with deleting file `Siena.out` by `unlink` instead of `file.remove`.
# RSiena 1.2-20
2019-12-16
## Changes in RSiena:
* `dumpChain` (Chain) and `getChainProbabilities` (siena07models) dropped;
kept in RSienaTest.
* Configure line 2274 changed to `RBIN="${R_HOME}/bin"`
## Changes in RSiena and RSienaTest:
* Tests ended with deleting file `Siena.out`.
# RSiena 1.2-19
2019-12-16 R-Forge Revision 344
## Changes in RSiena and RSienaTest:
* `SienaTimeTest`: some corrections with consequences probably only if
one effect is being tested; or is left after automatic exclusion
of tested effects.
* Setting-related effects corrected.
* Some further changes in Settings model.
* New effects `avGroupEgoX`, `outIso`.
* `CovariateDependentNetworkEffect`: + `lSimulatedOffset` taken out of
definition missings for `ChangingCovariate` (seems wrong).
* Alphabetically ordered sources.list.
## Changes in RSienaTest:
* In `sienaBayes`: more precise check that
prevAns has same specification as effects;
`priorSigEta` added to `sienaBayesFit` object.
`dimnames(ThinParameters)[[3]]` defined as effect names;
ridge for prior variance of rate parameters if priorRatesFromData=1 or 2
decreased from 0.5 to 0.01.
* `sienaBayes`: `zm` and `zsmall` are removed at the end.
* `plotPostMeansMDS` also shows a title, and coordinates show the dimensions
of the MDS solution.
* The value returned by `plotPostMeansMDS` contains not only the
plot coordinates, but also the similarities (correlations)
between the groups.
* `glueBayes`: added `z$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.
# RSiena 1.2-18
2019-10-16 R-Forge Revision 341
In this R-forge revision, only RSienaTest was updated.
## Changes in RSiena and RSienaTest:
* 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`.
## Changes in RSienaTest:
* Corrected error in names of array returned by `extract.posteriorMeans`.
* New parameter `excludeRates` in `extract.posteriorMeans`, `plotPostMeansMDS`.
* Use parameter `pmonly` also in `plotPostMeansMDS`.
# RSiena 1.2-17
2019-05-20 R-Forge Revision 340
## Changes in RSiena and RSienaTest:
* 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`).
## Changes in RSienaTest:
* `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.
# RSiena 1.2-16
2019-02-26 R-Forge Revision 339
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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
# RSiena 1.2-15.
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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
# RSiena 1.2-14.
## Changes in RSiena and RSienaTest:
* Check for length of parameter mult for ML estimation (initializeFRAN),
extend explanation of mult in help page for sienaAlgorithmCreate.
## Changes in RSienaTest:
* 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
# RSiena 1.2-13.
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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
# RSiena 1.2-12.
2018-05-07 R-Forge Revision 336
# RSiena 1.2-12.
## Changes in RSiena and RSienaTest:
* Change default parameter of reciAct to 1 (implies changes only in
output, not computationally).
* Internal effect parameter carried through in sienaTimeFix.
## Changes in RSiena:
* Shorter examples for sienaGOF and sienaGOF-auxiliary help pages.
2018-05-06 R-Forge Revision 335
# RSiena 1.2-11.
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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
# RSiena 1.2-10.
## Changes in RSiena and RSienaTest:
* Example in help page siena07 for accessing generated networks for ML.
2018-03-21 R-Forge Revision 332
# RSiena 1.2-9.
## Changes in RSiena and RSienaTest:
* 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).
## Changes in RSiena:
* siena07internals.cpp, siena07model.cpp, and siena07setup.cpp brought
in line with RSienaTest.
## Changes in 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
## Changes in RSienaTest:
* 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
## Changes in RSienaTest:
* Added \R\formula.R and \tests\formula.R.
2017-09-18 R-Forge Revision 325
## Changes in RSienaTest:
* Added \doc\tutorial-effect.tex
2017-09-18 R-Forge Revision 323
## Changes in RSienaTest:
* StatisticCalculator.cpp: delete Network clones not owned by State.
2017-09-18 R-Forge Revision 322
## Changes in RSiena:
* StatisticCalculator.cpp: delete Network clones not owned by State.
2017-09-10 R-Forge Revision 321
## Changes in RSiena:
* Merge RSienaTest changes r319-r320. Renamed init.c to init.cpp.
2017-09-10 R-Forge Revision 320
## Changes in RSienaTest:
* 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
## Changes in RSienaTest:
* init.cpp: Register native routines.
* *.R: Apdapt .Call statements.
2017-09-09 R-Forge Revision 318
# RSiena 1.2-4.
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* Extra line in example for sienaBayes.Rd.
2017-09-09 R-Forge Revision 317
## Changes in RSienaTest:
* 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).
# RSiena 1.2-3
2017-09-08
R-Forge Revision 316
## Changes in RSiena and RSienaTest:
* totAlt also for non-directed networks
* Added cran-comments.md, .Rbuildignore for comments about cran submission.
2017-09-07 R-Forge Revision 315
## Changes in RSiena:
* Merge RSienaTest changes r311-r314.
2017-09-07 R-Forge Revision 314
## Changes in RSienaTest:
* 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
## Changes in RSienaTest:
* DependentVariable.cpp: Fix null pointer in accumulateRateScores when
called on BehaviorVariable.
2017-09-04 R-Forge Revision 312
## Changes in RSienaTest:
* configure.win: adapt windows configuration script
2017-09-04 R-Forge Revision 311
## Changes in RSienaTest:
* configure.ac: add openmp test for macOS El Capitan compatibility
2017-09-03 R-Forge Revision 310
## Changes in RSiena:
* effects.r: remove hard coded number of types of interactions
* NetworkDependentBehaviorEffect.cpp: fix uninitialized network pointer
# RSiena 1.2-1 (not accepted)
2017-09-03
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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).
## Changes in RSiena:
* 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
## Changes in RSienaTest:
* configure.ac: don't compile with openmpi if orted is missing
2017-08-30 R-Forge Revision 308
## Changes in RSienaTest:
* 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
## Changes in RSiena and RSienaTest:
* Operation of option 'absorb' (behModelType=2) corrected.
## Changes in RSienaTest:
* BothDegreesEffect.h and .cpp added to repository.
2017-05-10 R-Forge Revision 306
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSiena:
* test13 dropped from parallel.R (using clusters undesirable
for basic testing).
## Changes in RSienaTest:
* 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
## Changes in RSienaTest:
* BehaviorEffect, NetworkDependentBehaviorEffect, StatisticCalculator:
initialize() with simulated state for GMM.
* Other effects: Fix [-Wreorder] warings.
2016-10-14 R-Forge Revision 304
## Changes in RSiena and RSienaTest (George Vega Yon):
* 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
## Changes in RSiena and RSienaTest (George Vega Yon):
* 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
## Changes in RSiena and RSienaTest:
* Capitalization error corrected in CovariateDegreeFunction.cpp.
2016-10-09 R-Forge Revision 301
## Changes in RSiena and RSienaTest:
* 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
## Changes in RSiena:
* buildsystem: added Makefile and src/sources.list
2016-08-17 R-Forge Revision 296
## Changes in RSiena and RSienaTest:
* 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
## Changes in RSienaTest (Felix Schoenenberger):
* buildsystem: added Makefile and src/sources.list
unitTests: removed sink('/dev/null')
2016-05-28 R-Forge Revision 294
## Changes in RSiena and RSienaTest:
* In SimilarityEffect.cpp and SimilarityWEffect.cpp, changed
abs to std::abs to avoid ambiguity, dropping #include <cmath>.
## Changes in RSienaTest:
* Mac line endings given to configure file.
2016-05-23 R-Forge Revision 293
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSiena:
* siena01Gui and associated functions dropped.
* sienaDataCreateFromSession dropped.
## Changes in RSienaTest:.
* Change in endowment effect estimation for avAlt effect.
* New effects simmelian, simmelianAltX, avSimmelianAlt, totSimmelianAlt.
2016-02-22 R-Forge Revision 292
## Changes in RSienaTest:
* Fixed permission filter for 2-mode networks (NetworkVariable.cpp).
2016-02-03 R-Forge Revision 291
## Changes in RSienaTest:
* Fixed include order.
* Removed `using namespace` from all headers.
2016-01-31 R-Forge Revision 290
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSienaTest:
* 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
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSiena:
* 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.".
## Changes in RSienaTest:
* 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
## Changes in RSiena and RSienaTest:
* 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.
## Changes in RSiena:
* Correction of error for two-mode networks in sienaGOF.
## Changes in RSienaTest:
* 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...)
## Changes in RSienaTest:
* Correction of error for two-mode networks in sienaGOF.
2015-05-21 R-Forge Revision 286
## Changes in RSiena and RSienaTest:
* test11 dropped from \tests\parallel.R.
* print.xtable.sienaFit exported as S3method in Namespace.
## Changes in RSienaTest:
* Larger dontrun part in examples for SienaRIDynamics
(there still is an error).
## Changes in RSiena:
* SienaRIDynamics not exported from RSiena only (there still is an error),
SienaRIDynamics.Rd dropped.
2015-05-20 R-Forge Revision 285
## Changes in RSiena and RSienaTest:
* 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
## Changes in RSienaTest:
* Small changes in HowToCommit.tex.