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. ### Dropped functionality: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. ### Other changes: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. ### Improved coding: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). ### New functionality:iterations in sienaGOF to allow shorter computations.2023-11-01
2023-10-31
Author field omitted in DESCRIPTION, because Author@R is sufficient. ### Changes in inst directory:inst directory omitted.CITATION. ### Small changes in coding: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). ### Improved documentation: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. ### New effects:avInSimDist2, totInSimDist2, sameEgoDist2,sameEgoInDist2, outMore2, divOutEgoIntn, divInEgoIntn, divOutAltIntn, divInAltIntn.avTAltDist2 and totTAltDist2 also implemented for behavior co-evolving with symmetric networks. ### Documentation: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). ### Additional testing: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. ### Corrections: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. ### New functionality:sienaGOF now also accepts a list of sienaFit objects. ### Improved coding: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. ### New functionality:DOUBLESTEP25, DOUBLESTEP50, DOUBLESTEP75, DOUBLESTEP100. ### Corrections: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$sd is calculated using sqrt(pmax(..., 0)) to avoid the extremely rare case of a negative calculated variance.sienaDataCreate, handling of structurally determined values in checkConstraints corrected (thanks to issue raised by Jos Elkink). ### Improvements of functionality:parameter in includeInteraction was dropped because it did not have any consequences. The help page for includeInteraction now explains how internal effect parameters for user-defined interactions are determined.dimnames of the Simulations array returned by sienaGOF are set to the names of the elements of the auxiliary function.descriptives.sienaGOF.initializeFRAN in the case of mismatch between effects objects.sienaAlgorithmCreate if (maxlike && (!is.null(MaxDegree))). This is now also mentioned in the help page for sienaAlgorithmCreate. ### Documentation:Wald.Rd.sienaDependent, it is mentioned that if there are one-mode as well as two-mode dependent networks, the one-mode networks should come first.2023-02-07
siena07internals.cpp adapted to be compatible with new clang 16 C++ compiler (thanks to Brian Ripley). ### New effects:inPop_dya.sameXInPop and diffXInPop. ### Corrections:siena07 corrected with respect to x$lessMem. ### Improvements of functionality: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). ### Code modifications: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. ### Effects: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). ### Improvements of documentation: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).