RSiena 1.4.1

2023-10-31

New CRAN version.

Changes in help files:

• Changes in accordance with “Guidelines for Rd files”.

RSiena 1.4.0

2023-10-31

Changes in meta-data:

• Author field omitted in DESCRIPTION, because Author@R is sufficient. ### Changes in inst directory:
• Superfluous files in inst directory omitted.
• New CITATION. ### Small changes in coding:
• Superfluous “lsimulatedDistance” in SdeSimulation.h deleted.
• In PrimarySettingEffect.cpp, used to_string for converting a number to string in an error message.

RSiena 1.3.28

2023-10-11

Changes in RSiena:

Changed effect:

• threshold, threshold2, threshold3, `threshold4’ changed to work with non-centered parameters (not backward-compatible). ### Improved documentation:
• Descriptions of effects altInDist2W and totInDist2W added to the manual (the effects had been there since a long time, but not documented).

RSiena 1.3.27

2023-09-29

Changes in RSiena:

Coding:

• Corrected one line in 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:
• Some explanation is given in the manual about internal effect parameters for interactions created by includeInteraction.

RSiena 1.3.26

2023-08-15

Changes in RSiena:

Coding:

• Improved Phase 1 derivative matrix computation for basic SDE parameters.
• Added continuous behavior to returned simulated data. ### Corrections:
• Period/groupwise tests in 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).

RSiena 1.3.24

2023-08-01

Changes in RSiena:

Corrections:

• In 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.)
• Corrections of implementation of acceptance by sienaGOF of a list of sienaFit objects (was not correct in version 1.3.23). ### Additional testing:
• function includeInteraction used in “parallel.R”.

RSiena 1.3.23

2023-06-29

Changes in RSiena:

New effects:

• New effects diffWXClosure, sameWWClosure, diffWWClosure, diffXWClosure, sameXWClosure, unequalX.
• JoutMix made available for bipartite dependent networks.
• For continuous behavior variables depending on a bipartite dependent network, the effect group continuousBipartiteObjective was created, with effects outdeg, outdegSqrt, and isolateOut.
• sameXOutAct and diffXOutAct now have a parameter 2 for sqrt. ### Corrections:
• In initializeFRAN, the call of getEffects now is dependent on the value of attribute “onePeriodSde”.
• The error was corrected that occurred if useStdInits = TRUE in sienaAlgorithmCreate and the effects object includes interaction effects.
• In sienaDataCreate, the warning message that there is at least one upOnly period now is made for each dependent variable instead of only the last.
• In getEffects, the effects object was given an attribute onePeriodSde and an attribute version.
• In 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:
• The model for continuous behavior variables seems to work now, because of the first correction mentioned above.
• sienaGOF now also accepts a list of sienaFit objects. ### Improved coding:
• Better text for stop in initializeFRAN when there is a mismatch between effects objects disabling the creation of interaction effects.
• Warning in 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).
• Better error message in sienaGOF if groupName or varName is incorrect.
• Use default bandwidth selection in violin plot for sienaGOF (the use of “nrd” sometimes led to absent plots because of negative bw).

RSiena 1.3.22

2023-05-11

Changes in RSiena:

Coding:

• Corrected and cleaned up virtual definitions in AlterFunction and its descendants, in particular CovariateNetworkAlterFunction.
• Added const to virtual specification of value in AlterFunction.h and all of its descendants.
• Replaced ambiguous call to std::abs in AbsDiffFunction.cpp. ### New functionality:
• For one-mode networks, new model options DOUBLESTEP25, DOUBLESTEP50, DOUBLESTEP75, DOUBLESTEP100. ### Corrections:
• The first item in “Coding” implies correction of several distance-2 network effects such as altDist2, totDist2 and altInDist2.
• In 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).

RSiena 1.3.20

2023-04-22

Changes in RSiena:

Corrections:

• updateSpecification (in effectsMethods) now also updates internal parameter values.
• In TriadCensus, the empty network will not lead to an error but be reported with the correct triad census.
• For reciAct, check whether internal parameter ==2 replaced by check whether absolute difference from 2 is less than 0.001.
• In phase2.r, z$sd is calculated using sqrt(pmax(..., 0)) to avoid the extremely rare case of a negative calculated variance.
• In sienaDataCreate, handling of structurally determined values in checkConstraints corrected (thanks to issue raised by Jos Elkink). ### Improvements of functionality:
• The keyword 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.
• The column dimnames of the Simulations array returned by sienaGOF are set to the names of the elements of the auxiliary function.
• Standard deviations added to output of descriptives.sienaGOF.
• Improved error message in initializeFRAN in the case of mismatch between effects objects.
• Warning in sienaAlgorithmCreate if (maxlike && (!is.null(MaxDegree))). This is now also mentioned in the help page for sienaAlgorithmCreate. ### Documentation:
• Reference about score-type test added to Wald.Rd.
• In the help page for sienaDependent, it is mentioned that if there are one-mode as well as two-mode dependent networks, the one-mode networks should come first.

RSiena 1.3.19

2023-02-07

Changes in RSiena:

Coding:

• siena07internals.cpp adapted to be compatible with new clang 16 C++ compiler (thanks to Brian Ripley). ### New effects:
• New effect inPop_dya.
• Parameter 2 for sameXInPop and diffXInPop. ### Corrections:
• Help page for 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.

RSiena 1.3.18

2023-01-29

Changes in RSiena:

Improvements of functionality:

• Additional step type move for MH proposal distribution for likelihood estimation (thanks to Charlotte Greenan).
• Accordingly, parameters changed that are used in sienaAlgorithmCreate for probabilities of MH steps, now summarized in prML; with a new default.
• List elements accepts, rejects, aborts for sienaFit objects produced by ML estimation improved/corrected by reorganizing them in C++.
• List element ac3 added to sienaFit object if maxlike.

RSiena 1.3.17

2023-01-06

Changes in RSiena:

Improvements of functionality:

• 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.

RSiena 1.3.16

2023-01-02

Changes in RSiena:

Corrections:

Effects:

`inPopIntnX`, `inActIntnX`, `outPopIntnX`, `outActIntnX`, `sameXInPopIntn`, 
`sameXOutPopIntn`, `sameXInActIntn`, `sameXOutActIntn` restored
(these had got lost in some way...).

Updates:

• All occurrences of http in R and Rd files changed to https.
• seq_len used and superfluous c() omitted in various R files.

RSiena 1.3.15

2022-11-27

Changes in RSiena:

Corrections:

• siena08: correct p-value pTsq for overall test statistic Tsq
• print.summary.sienaMeta, siena07, print01Report: drop RForge revision.
• Correct “objname” to “projname” in meta.table (siena08.r).
• Simplify LaTeX output of meta.table.
• seq_along and seq_len used in print01Report.

RSiena 1.3.14

2022-11-04

Changes in RSiena:

Note:

• CRAN version.

Corrections:

• Update configure and configure.ac (with help from Brian Ripley).

RSiena 1.3.13

2022-10-07

Changes in RSiena:

Updates:

• Replacements in EffectFactory.cpp of single | operator by ||.

RSiena 1.3.12

2022-10-06

Changes in RSiena:

Updates:

• Changes to comply with new version of Matrix package.
• Replacements in some C++ functions of single & and | operators by && and ||. ### Corrections:
  
• universalOffset initialized as 0; it was earlier initialized as the maximum real number (NetworkLongitudinalData.cpp).
• thetaStore deleted (was trash in phase2.r).
• Various comparisons for vectors with 0 changed to using all to avoid warnings (initializeFRAN.r). ### Code modifications:
• sigmas and meansigmas added to sienaRI object.
• Print of standard deviations in the sienaRI object for printSigma=TRUE changed to using averages at the variance level.
• If returnThetas in the call of siena07, also simulated estimation statistics during Phase 2 (deviations from targets) are returned. ### Effects:
• Several new effects related to primary setting: nonPCompress, primCompress, primary, primDegAct, primDegActDiff, primDegActDiffSqrt, primDegActSqrt, primDegActLog, primDegActInv.
• gwdspFB effect added for two-mode networks.
• New effects outAct_ego, inAct_ego,reciAct_ego, toAny.
• For effects to, toBack, toRecip, mixedInXW, internal effect parameter 3 now specifies truncation of the number of twosteps (change to MixedTwoStepFunction). ### Improvements of documentation:
• Modified help page for sienaRI.
• Small modifications of help page for sienaGOF.

RSiena 1.3.11

2022-05-30

Changes in RSiena:

Corrections:

• Correction in effects.r of error that led to warning for multivariate networks.
• Correction of help page for sienaGOF (groupName).
• Correction of igraphNetworkExtraction in the help page for sienaGOF-auxiliary.

Improvements of functionality:

• Further explanation of mixedTriadCensus in the help page for sienaGOF-auxiliary.

RSiena 1.3.10

2022-04-28

Changes in RSiena:

Corrections:

• Bug corrected that occurred when several two-mode networks were included in the dependent variables, with an order restriction between them. (Correction of HigherFilter and DisjointFilter).

Effects:

• New effects avInAltW, avWInAlt, totInAltW, totWInAlt (with help from Robert Krause).
• Corrected implementation of sharedTo.

Code modifications:

• Several modifications to enable traceback of errors occurring in checkSenderRange called in inTies.

RSiena 1.3.9

2022-03-18

Changes in RSiena:

Effects:

• Corrected implementation of simAllNear and simAllFar.

Corrections:

• small correction of summary.sienaGOF.
• small correction of sienaTimeTest.

RSiena 1.3.8

2022-03-07

Changes in RSiena:

Effects:

• Changed default internal effect parameter for simAllNear to 2 and for simAllFar to 4.

Improvements of functionality:

• In sienaTimeTest, added warn=FALSE to varCovar() to avoid warnings.
• Small improvements to help pages for sienaGroupCreate and sienaGOF.

Corrections:

• corrected sienaRI for behavioral variables. This required changes in StatisticCalculator::calculateBehaviorStatistics and StatisticCalculator::calculateBehaviorGMMStatistics.
• dropped exclusion of bipartite for sienaRI (only continuous excluded), but only if there are fewer second-mode nodes than actors. This required changes in StatisticCalculator::calculateNetworkEvaluationStatistics and in `siena07internals::getChangeContributionStatistics’.

RSiena 1.3.7

2022-02-18

Changes in RSiena:

Effects:

• New effect avDeg.

RSiena 1.3.6

2022-02-16

Changes in RSiena:

Effects:

• New effects simAllNear,simAllFar, absOutDiffIntn, avDegIntn.
• New effects recipRateInv, recipRateLog (Steffen Triebel).
• Default internal effect parameter for outOutActIntn, outOutAvIntn, and both changed from 2 to 1.

Improvements of functionality:

• Function 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.
• Small clarifications of help pages for includeInteraction and setEffect.

RSiena 1.3.5

2021-12-15

Changes in RSiena:

Bug corrections

• Corrected the check for effects in initializeFRAN.r which led to errors if interaction effects are included, because of the changes to includeInteraction in version 1.3.4.

RSiena 1.3.4

2021-12-08

Changes in RSiena:

Effects:

• New effects inRateInv, inRateLog (Steffen Triebel).

Improvements of functionality:

• When an effects object with interaction effects is printed, the names of the interacting effects are mentioned, and prefixes “int.” and “i3.” were dropped.
• The check of whether an interaction effect is allowed now is done immediately when creating the interaction effect instead of waiting for its use in siena07.
• For function sienaGroupCreate some changes were made:
  if it is applied to a list of length 1, attributes of the single group are not recomputed;
  if it is applied to a list of length larger than 1, the attributes “range” and “range2” of behavioral variables of individual groups are computed as the range of the unions of the ranges of all the groups. The same is done for covariates.
• print.sienaGroup slightly extended.
• Creation of covariates gives a warning (optional) if all values are missing, and also if all non-missing values are the same.

Bug corrections

• if a sienaGroup object is given to sienaBayes and some of the covariates are constant in one or more of the groups, the `simX effect will not run into an error any more; this is achieved by the first change mentioned above for sienaGroupCreate.
• sienaFitThetaTable in sienaprint.r was corrected for from sienaBayes.
• siena.table was corrected for sienaBayes objects, and this possibility was mentioned in the help file.

Coding changes:

• In sienaprint.r, methods and functions relating to sienaBayes omitted.

Tests:

• Test 18, a test for `sienaGroupCreate, added to parallel.R.

RSiena 1.3.3

2021-10-09

Changes in RSiena:

Effects:

• internal effect parameter for diffusion rate effects (‘at least p’).
• New effect outOutAvIntn.
• outOutActIntn also made available for non-directed explanatory networks and for two-mode dependent networks.

Improvements of functionality:

• toggleProbabilities added to output of sienaRI.
• Trial values of theta used during Phase 2 of siena07 added to the sienaFit object ans as ans$thetas.
• warnings if a data object contains only missings, or only the same value.

Bug corrections

• if a data set contains a constant covariate, the simX effect will not run into an error any more; this is obtained by defining the range attribute of the covariate as 1 to prevent division by zero, and the simMean attribute as 0 instead of NaN (sienaDataCreate). This is relevant especially for sienaGroup data sets, where covariates might be constant for some of the groups.`

Corrections of documentation:

• In sienaAlgorithmCreate, the default values of diagonalize for MoM is 0.2; this was corrected in the help file.

RSiena 1.3.2

2021-07-29

Changes in RSiena:

Improvements of functionality:

• Effects of type creation or endow represented in siena.table by creation and maintenance, respectively.
  This was erroneously omitted in 1.3.1.

RSiena 1.3.1

2021-07-27

Effects:

• New effects: crprodInActIntn (Nynke Niezink), XXW.

Improvements of functionality:

• Effects of type creation or endow represented in siena.table by creation and maintenance, respectively.
• updateTheta also accepts sienaBayesFit objects as prevAns.

Small corrections:

• If upOnly or downOnly, the (out)degree (density) effect is also excluded for symmetric networks (this was reported in print01Report, but not carried out). This happens in effects.r.
• Message corrected in sienaDataCreate if there is an attribute higher.

RSiena 1.3.0

2021-05-02

• Drop testthat in tests.

RSiena 1.2.34

2021-04-30

New functions:

• testSame.RSiena.

Effects:

• New effects: avInSim (thanks to Steffen Triebel), totInSim, avInSimPopAlt, totInSimPopAlt, constant, avAttHigher, avAttLower, totAttHigher, totAttLower.
• Changed effects: endowment and creation types for avInSim (brought in line with these types for avSim).

Improvements of functionality:

• funnelPlot adapted to lists of sienaFit objects containing missing estimates or standard errors.
• plot.sienaGOF: new parameter position.
• Small improvements (length of effect names) in meta.table and siena.table.

Bug corrections

• Restore backward compatibility with respect to checks of x$gmm.
  
• In test functions: correct names reported for tested effects by using ans$requestedEffects instead of ans$effects.

Code improvements

• Improved coding of SimilarityEffect, using new parts of NetworkDependentBehaviorEffect.
  
• Changed unsigned actors to int in Continuousvariable and EpochSimulation;
  int …EffectCounts to unsigned in BehaviorVariable, to avoid warnings in C++ compilation.
• Changed name of similarity(int i, int j) to actor_similarity in order to avoid confusion with similarity(double v1, double v2).

Corrections

• Took out of NAMESPACE a few imported functions from graphics, stats, utils that were not used.
  
• Correction of footer of CovariateDistance2EgoAltSimNetworkFunction.h.

RSiena 1.2.33

2021-03-19

• Adjusted configure, cleanup and Makevars files for just C++ checks.
• Pandoc dropped as a system requirement.

RSiena 1.2.32

2021-03-16

Effects:

• New effects: homXTransRecTrip, toU.
• This implied creation of a new effect class dyadANetNetObjective.
• sqrt versions for parameter 2 for the effects to, toBack, toRecip, from, fromMutual.
• Effects to, toU, toBack, toRecip, MixedInXW are dyadic.
• Reinstated effect MixedInXW, also with sqrt version for parameter 2.
• Dropped effect to.2 (identical to to) and MixedInWX (identical to toBack).

Improvements of functionality:

• effectsDocumentation now also includes gmm effects (at the bottom).
• Improved fromObjectToLaTeX in meta.table and siena.table.
• Display of deviations from targets changed to after subtraction of targets.
• Stop if no parameters are estimated and simOnly is FALSE (initializeFRAN).

Reduction of functionality:

• Vignette basicRSiena.Rmd dropped (available at website).

Documentation:

• Extended description of GMoM in the manual.
• Description of toBack and toRecip in manual.
• Changed keyword for some help pages.

Corrections / safeguards

• Correction in phase3.2 of a bug that sometimes led to an error message if simOnly.
• oneModeNet in effects.r: some further cases where the comparison of types with behavior is replaced by comparison with c(behavior, continuous).
• Extra check in phase1.2.
• Temporarily drop the final part of test16, in view of an irreproducible error.

More neat code:

• Dropped MixedOutStarFunction, MixedInStarFunction, MixedTwoPathFunction, (their functionality replaced by MixedTwoStepFunction).
• Dropped MixedTwoStepFunction from effects (its place is in effects\generic, and that’s were it is).

RSiena 1.2-31

2021-02-27

• Generalized method of Moments implemented (Viviana Amati): see docs_RSiena_GMoM.tex; new function includeGMoMStatistics, extended functionality of siena07.
• Require R >= 3.5.0.
• xtable added to Imports (used to be in Suggests).
• dyadicCov made to accept also changing dyadic covariates.
• Used verbose condition in sienaGOF also for last console output.
• new arguments plotAboveThreshold and verbose for funnelPlot.

RSiena 1.2.30

2021-02-23

• Resolved issue with continuous dependent behavior variables (Nynke Niezink).

RSiena 1.2-29

2020-12-10

• New effects (due to Christoph Stadtfeld): transtrip.FR, transtrip.FE, transtrip.EE, WWX.EE, WWX.FR, WXX.FE, WXX.ER, XWX.ER, XWX.FE, to.2, toBack, toRecip.
• New effect transtripX.
• New functions meta.table and funnelPlot.
• For effect from.w.ind, option parameter=-1 added.
• The to effect is an ego effect.
• New parameter tested in sienaGOF.
• For siena.table, some of the effectNames changed to nice strings, so that LaTeX can run without errors if type=tex.
• The object produced by siena08 now has IWLS estimates more easily accessible, as object$muhat and object$se.muhat.
• Error message in sienaTimeTest for sienaFit objects produced with lessMem=TRUE.
• More extensive error message for error in named vectors in algorithm object (checkNames in initializeFRAN).
• For sienaDataCreate: more extensive error message, and class(...) replaced by class(...)[1].
• multiplication factor added to print.sienaAlgorithm if maxlike.
• In sienaAlgorithmCreate: requirements for mult corrected in help page.
• In sienaAlgorithmCreate, use the definitions for projname=NULL also if any environment variable _R_CHECK* is set.

RSiena 1.2-28

2020-09-30

• Adapted filter disjoint so that it operates correctly also when the network is symmetric. Consequence: constraint that two networks are disjoint operates correctly also when one of the networks is symmetric and the other is not.
• Adapted filter higher so that it operates correctly also when the other network is symmetric. Consequence: constraint that one network is at least as high as another network operates correctly also when the higher networks is symmetric and the other is not.
• In CheckConstraints, used in sienaDataCreate, the requirement was dropped that the two networks have the same symmetry property; and for higher it is required that if the lower network is symmetric, the higher network is also symmetric.
• In sienaDataConstraint, if type is disjoint or atLeastOne, the constraint is also implemented for the pair (net2, net1).
• Vignette basicRSiena added (was earlier available as a script); thanks to James Hollway.

RSiena 1.2-26

2020-09-17

• Changed requirement for tcltk to Suggests, and further modified / cleaned up DESCRIPTION.
• In siena07: if (!requireNamespace(tcltk)) set batch to TRUE.
• In NAMESPACE drop tcltk.
• In sienaAlgorithmCreate, use the definitions for projname=NULL also if any environment variable _R_CHECK* is set.