2024-12-18
selectionTable and influenceTable,
with print methods.altHigherEgoX.higher also implemented for symmetric networks.siena.table, fixed parameter values are not reported as NA,
but as their fixed values.includeInteraction is called with argument parameter,
an error message appears that this keyword should not be given.sienaTimeTest given in the case of
collinearities.interaction1 and interaction2
in the help page for includeInteraction.2024-11-10
varAlt and avSimVarAlt.includeInteraction for continuous behavior had been implemented but
not the C++ side, so now an error message is given.lvariance, the behavior variance over all but the
last wave, was included as member data of BehaviorLongitudinalData
together with the corresponding member functions.2024-09-03
outThreshold and outThreshold2.outActIntn is an ego effect (allEffects.csv).NETCONTEMP for use of contemporaneous statistics
for estimating all evaluation effects of the network variable.thetaBound is exceeded corrected (phase2.r).setEffect is called for an effect with type=gmm, an error message
is given that the function called should be includeGMoMStatistics.2024-07-31
crprod_gmm, to_gmm, from_gmm.sienaGOF which occurred for models with tested effects
if iterations is less than sienaFitObject$n3.AlterFunction, NetworkAlterFunction, and MixedNetworkAlterFunction
to allow making estimation statistics depend totally on the simulated state.fixUpEffectNames(effects, defaultEffects)
moved from initializeFRAN.r to sienaEffects.r.2024-06-06
homXOutAct2.setEffect corrected (it did not give the proper internal
parameters in the effectName).updateSpecification corrected (it did not work properly
for including interactions).effectName
and functionName of sienaEffects objects is improved.
This was achieved by changes in functions setEffect
and includeInteraction.sienaFit objects should now contain the
correct values of internal effect parameters.thetaBound for siena07, which has the effect of stopping
the estimation process if some parameters become too large (which would
signal divergence).siena07gui modified so that numbers larger
than or equal to 1e5 in absolute value are displayed in exponential format
(and use only one line in the gui) (function FormatString in siena07.r).2024-04-27
2024-04-23
outOutDist2AvIntn changed to avAlt.2M.tot.avAlt.2M.tie, avAlt.2M.tot, avAltU.2M.tie,
dist2OutInActIntn, nDist2ActIntn, sharedToU.outOutDist2ActIntn and
outOutDist2AvIntn / avAlt.2M.tot.print.sienaEffects has an extra parameter includeShortNames
to do what the name of this parameter suggests.updateSpecification.2024-03-25
sameXV and sameXVInPop added for symmetric networks,
and restricted to integer-valued variables in the range from 0 to 20.silent (new in version 1.4.8)
in sienaAlgorithmCreate activated.sienaData have a new attribute lowIntegers
used for in/excluding effects sameXVInPop and sameXV in
getEffects.2024-03-21
crossXOutAct, outOutDist2ActIntn,
outOutDist2AvIntn, inPopOutW.doubleCovarNetObjective.sameXV and sameXVInPop for bipartite networks.sameXCycle4 added for one-mode and symmetric networks.sharedTo gets default internal effect parameter p=3.updateSpecification now also updates interaction effects
and initialValues.numberIntn, numberBehIntn, checkVersion
defined in file initializeFRAN.r.Covariate class and its descendants (all actor covariates)
now have functions min and max.2024-02-29
siena07setup.ccp for ML estimation.silent in sienaAlgorithmCreate.2024-02-20
siena07utilities::Rterminate.2024-02-19
targets in siena07, used to supersede the targets
calculated from the data (not for use in estimation for regular data sets,
see the help file for siena07).effectsDocumentation reports to the console
the name of the file that was written.sienaDataCreate stops with an error message if there is a bipartite
network before a one-mode network.Rinternals.h and R_ext/Error.h (in siena07models.cpp,
siena07utilities.cpp, siena07setup.cpp and siena07internals.cpp)
and various other places
(in accordance with "Writing R Extensions").lprobabilityArray in MLSimulation.h,
and cleaned up a bit.MLSimulation.cpp, various sets of "delete" commands reordered so as
to be in opposite order of the corresponding "new" commands.BehaviorVariable::accumulateDerivatives
and in siena07utilities::Rterminate.sienaDataCreate to work with a single variable defined as
a dependent network given as a list of sparse matrices.getEffects to construct effects of more than one dependent network
on continuous behavior dependent variables.initializeFRAN.r to guard against
dimension loss in the construction of sparse matrices.effectsDocumentation. This led to an incomplete listing of the effects.
They are now included.sienaRI temporarily disabled because of a memory leak.prML=2 temporarily disabled because of a memory leak in the
move proposal distribution (sienaAlgorithmCreate).doMoreUpdates moved from maxlike.r to maxlikecalc.r.
The rest of maxlike.r as wel as maxlikefn.Rd deleted.
These were not used anywhere.NEWS.md to ONEWS_gh.2024-02-14
#include <Rinternals.h> as the last of the include commands
in various .cpp files (Tomas Kalibera).2023-12-14
outXMore, outMore3.Interactiontype of altLThresholdX and altRThresholdX is dyadic.Interactiontype of degAbsDiffX, degPosDiffX, and degNegDiffX
is "" (blank).outMore.bxeffects initialized to 0 in ContinuousVariable::accumulateScores.*.h files
were initialized using braces.mixedTriadCensus, the check of the condition about the matrix
dimensions was split into its two parts.TruncatedOutdegreeEffect2 dropped from src/model/effects
(was superfluous).iterations in sienaGOF to allow shorter computations.2023-11-01
2023-10-31
Author field omitted in DESCRIPTION, because Author@R is sufficient.inst directory:inst directory omitted.CITATION.SdeSimulation.h deleted.PrimarySettingEffect.cpp, used to_string for converting a number
to string in an error message.2023-10-11
threshold, threshold2, threshold3, threshold4 changed to
work with non-centered parameters (not backward-compatible).altInDist2W and totInDist2W added
to the manual (the effects had been there since a long time,
but not documented).2023-09-29
siena07models.cpp, which led to slowness of
siena07 since version 1.3.18.avInSimDist2, totInSimDist2, sameEgoDist2,sameEgoInDist2,
outMore2, divOutEgoIntn, divInEgoIntn, divOutAltIntn,
divInAltIntn.avTAltDist2 and totTAltDist2 also implemented for behavior co-evolving
with symmetric networks.includeInteraction.2023-08-15
sienaTimeTest corrected for the case of
non-saturated sets of dummy variables.plot.sienaTimeTest for "pairwise=TRUE" changed so that the warning
is avoided.sienaGOF corrected so that again it can handle auxiliary functions
referring to more than one varName (such as in mixedTriadCensus).2023-08-01
getEffects, the effects object was given an attribute version,
which was not done correctly in version 1.3.23.
(This led to always giving a warning if any interaction effects were
specified.)sienaGOF of a list of
sienaFit objects (was not correct in version 1.3.23).includeInteraction used in "parallel.R" (for testing).2023-06-29
diffWXClosure, sameWWClosure, diffWWClosure,
diffXWClosure, sameXWClosure, unequalX.JoutMix made available for bipartite dependent networks.continuousBipartiteObjective was created,
with effects outdeg, outdegSqrt, and isolateOut.sameXOutAct and diffXOutAct now have a parameter 2 for sqrt.initializeFRAN, the call of getEffects now is dependent on
the value of attribute "onePeriodSde".useStdInits = TRUE
in sienaAlgorithmCreate and the effects object includes
interaction effects.sienaDataCreate, the warning message that there is at least one
upOnly period now is made for each dependent variable instead of
only the last.getEffects, the effects object was given an attribute onePeriodSde
and an attribute version.initializeFRAN, the comparison between effects and
defaultEffects now is based on shortName instead of effectName
(effectName was changed if there are interaction effects),
excluding the lines in the effects object for unspInt and behUnspInt
to allow effects objects created
with non-default values of nintn and behNintn.sienaGOF now also accepts a list of sienaFit objects.initializeFRAN when there is a mismatch
between effects objects disabling the creation of interaction effects.initializeFRAN if the version of the effects object
is not current and the effects object contains interaction effects
(then it is possible that the interacting effects are chosen incorrectly,
even though the effectName of the interaction seems OK).sienaGOF if groupName or varName is incorrect.sienaGOF
(the use of "nrd" sometimes led to absent plots because of negative bw).2023-05-11
AlterFunction and its
descendants, in particular CovariateNetworkAlterFunction.const to virtual specification of value in AlterFunction.h
and all of its descendants.std::abs in AbsDiffFunction.cpp.DOUBLESTEP25, DOUBLESTEP50,
DOUBLESTEP75, DOUBLESTEP100.altDist2, totDist2 and altInDist2.sienaAlgorithmCreate, changed default prML=2 back to prML=1;
stop if Maximum Likelihood estimation is attempted for a data set
containing more than one dependent variable
with prML=2 (implemented in initializeFRAN.r).2023-04-22
updateSpecification (in effectsMethods) now also updates
internal parameter values.TriadCensus, the empty network will not lead to an error
but be reported with the correct triad census.reciAct, check whether internal parameter ==2 replaced by check
whether absolute difference from 2 is less than 0.001.phase2.r, z$sd is calculated using sqrt(pmax(..., 0)) to avoid the
extremely rare case of a negative calculated variance.sienaDataCreate, handling of structurally determined values
in checkConstraints corrected (thanks to issue raised by Jos Elkink).parameter in includeInteraction was dropped because it did
not have any consequences. The help page for includeInteraction now
explains how internal effect parameters for user-defined interactions
are determined.dimnames of the Simulations array returned by sienaGOF
are set to the names of the elements of the auxiliary function.descriptives.sienaGOF.initializeFRAN in the case of mismatch between
effects objects.sienaAlgorithmCreate if (maxlike && (!is.null(MaxDegree))).
This is now also mentioned in the help page for sienaAlgorithmCreate.Wald.Rd.sienaDependent, it is mentioned that if there are
one-mode as well as two-mode dependent networks,
the one-mode networks should come first.2023-02-07
siena07internals.cpp adapted to be compatible with new clang 16 C++
compiler (thanks to Brian Ripley).inPop_dya.sameXInPop and diffXInPop.siena07 corrected with respect to x$lessMem.coCovar and varCovar now can handle variables with only one
non-missing value, but will stop with an error message
if all values are missing.2023-01-29
move for MH proposal distribution
for likelihood estimation (thanks to Charlotte Greenan).sienaAlgorithmCreate
for probabilities of MH steps, now summarized in prML; with a new default.accepts, rejects, aborts for sienaFit objects
produced by ML estimation improved/corrected by reorganizing them in C++.ac3 added to sienaFit object if maxlike.2023-01-06
sienaGOF now accepts simulated auxiliary statistics containing missing
values. If there are any, this will be reported with a warning
if giveNAWarning is TRUE.sienaDataCreate now also accepts, as "...", a list of such objects.2023-01-02
`inPopIntnX`, `inActIntnX`, `outPopIntnX`, `outActIntnX`, `sameXInPopIntn`,
`sameXOutPopIntn`, `sameXInActIntn`, `sameXOutActIntn` restored
(these had got lost in some way...).
http in R and Rd files changed to https.seq_len used and superfluous c() omitted in various R files.2022-11-27
siena08: correct p-value pTsq for overall test statistic Tsqprint.summary.sienaMeta, siena07, print01Report: drop RForge revision.meta.table (siena08.r).LaTeX output of meta.table.seq_along and seq_len used in print01Report.2022-11-04
configure and configure.ac (with help from Brian Ripley).2022-10-07
2022-10-06
Matrix package.universalOffset initialized as 0; it was earlier initialized as
the maximum real number (NetworkLongitudinalData.cpp).thetaStore deleted (was trash in phase2.r).all
to avoid warnings (initializeFRAN.r).sigmas and meansigmas added to sienaRI object.sienaRI object for printSigma=TRUE
changed to using averages at the variance level.returnThetas in the call of siena07, also simulated estimation
statistics during Phase 2 (deviations from targets) are returned.nonPCompress, primCompress, primary, primDegAct,
primDegActDiff, primDegActDiffSqrt, primDegActSqrt,
primDegActLog, primDegActInv.gwdspFB effect added for two-mode networks.outAct_ego, inAct_ego,reciAct_ego, toAny.to, toBack, toRecip, mixedInXW,
internal effect parameter 3 now specifies truncation of the number of
twosteps (change to MixedTwoStepFunction).sienaRI.sienaGOF.2022-05-30
effects.r of error that led to warning
for multivariate networks.sienaGOF (groupName).igraphNetworkExtraction in the help page for
sienaGOF-auxiliary.mixedTriadCensus in the help page for
sienaGOF-auxiliary.2022-04-28
HigherFilter and DisjointFilter).avInAltW, avWInAlt, totInAltW, totWInAlt
(with help from Robert Krause).sharedTo.2022-03-18
simAllNear and simAllFar.summary.sienaGOF.sienaTimeTest.2022-03-07
simAllNear to 2 and for
simAllFar to 4.sienaTimeTest, added warn=FALSE to varCovar() to avoid warnings.sienaGroupCreate and sienaGOF.StatisticCalculator::calculateBehaviorStatistics and
StatisticCalculator::calculateBehaviorGMMStatistics.StatisticCalculator::calculateNetworkEvaluationStatistics
and in `siena07internals::getChangeContributionStatistics'.2022-02-18
avDeg.2022-02-16
simAllNear,simAllFar, absOutDiffIntn, avDegIntn.recipRateInv, recipRateLog (Steffen Triebel).outOutActIntn, outOutAvIntn,
and both changed from 2 to 1.includeInteraction now also can modify the initialValue
of an effect; and the order of parameters for this function was changed,
bringing it in line with setEffect.includeInteraction and
setEffect.ONEWS_gf in the source code at GitHub for changes
in versions 1.2-26 to 1.3.5.ONEWS in the source code at GitHub for changes
in versions 17 to 1.2-25 (when the code was hosted at R-forge).