Skip to content

Latest commit

 

History

History
779 lines (586 loc) · 24.6 KB

NEWS.md

File metadata and controls

779 lines (586 loc) · 24.6 KB

RSiena 1.4.21

2024-12-18

Changes in RSiena:

New functionality

  • New functions selectionTable and influenceTable, with print methods.

Effects

  • New effect altHigherEgoX.
  • Effect higher also implemented for symmetric networks.
  • Used # in name of threshold effects.

Bug corrections

  • In siena.table, fixed parameter values are not reported as NA, but as their fixed values.

Messages

  • If includeInteraction is called with argument parameter, an error message appears that this keyword should not be given.
  • Extension of message in sienaTimeTest given in the case of collinearities.

Help pages

  • Improved explanation of the use of interaction1 and interaction2 in the help page for includeInteraction.

RSiena 1.4.20

2024-11-10

Changes in RSiena:

Effects

  • New effects varAlt and avSimVarAlt.

Bug corrections

  • Interaction effects for continuous behavior now turned off. The R side of includeInteraction for continuous behavior had been implemented but not the C++ side, so now an error message is given.

Error messages

  • If `includeInteraction' is called for a continuous behavior effect, an error message is given that interaction effects are not yet implemented for continuous behavior.

Coding

  • For the new effects, lvariance, the behavior variance over all but the last wave, was included as member data of BehaviorLongitudinalData together with the corresponding member functions.

RSiena 1.4.19

2024-09-03

Changes in RSiena:

Effects

  • New effects outThreshold and outThreshold2.
  • outActIntn is an ego effect (allEffects.csv).

New functionality:

  • Network option 11 = NETCONTEMP for use of contemporaneous statistics for estimating all evaluation effects of the network variable.

Bug corrections

  • Error corrected that occurred for estimation by the GMoM if some effects are fixed.
  • List of effect names when thetaBound is exceeded corrected (phase2.r).

Error messages

  • If setEffect is called for an effect with type=gmm, an error message is given that the function called should be includeGMoMStatistics.

RSiena 1.4.18

2024-07-31

Changes in RSiena:

Effects

  • New gmm effects for co-evolution of multiple networks: crprod_gmm, to_gmm, from_gmm.

Bug corrections

  • Bug corrected in sienaGOF which occurred for models with tested effects if iterations is less than sienaFitObject$n3.

Coding

  • The new gmm effects required the extension of the function classes AlterFunction, NetworkAlterFunction, and MixedNetworkAlterFunction to allow making estimation statistics depend totally on the simulated state.
  • Function fixUpEffectNames(effects, defaultEffects) moved from initializeFRAN.r to sienaEffects.r.

RSiena 1.4.13

2024-06-06

Changes in RSiena:

Effects:

  • New effect homXOutAct2.

Bug corrections:

  • Function setEffect corrected (it did not give the proper internal parameters in the effectName).
  • Function updateSpecification corrected (it did not work properly for including interactions).

Improved functionality:

  • The handling of internal effect parameters in the columns effectName and functionName of sienaEffects objects is improved. This was achieved by changes in functions setEffect and includeInteraction.
    Effectnames as reproduced by sienaFit objects should now contain the correct values of internal effect parameters.
  • New parameter thetaBound for siena07, which has the effect of stopping the estimation process if some parameters become too large (which would signal divergence).
  • Display of deviations in 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).

RSiena 1.4.12

2024-04-27

Changes in RSiena:

Improved coding:

  • All objects created by functions, if not print or summary, now have an attribute "version", which is the package version.

Miscellanea:

  • New RSiena logo inst/rsienalogo-2.png

RSiena 1.4.11

2024-04-23

Changes in RSiena:

Effects:

  • Effect name outOutDist2AvIntn changed to avAlt.2M.tot.
  • New effects avAlt.2M.tie, avAlt.2M.tot, avAltU.2M.tie, dist2OutInActIntn, nDist2ActIntn, sharedToU.
  • Changed sqrt treatment in outOutDist2ActIntn and outOutDist2AvIntn / avAlt.2M.tot.

New functionality:

  • Method print.sienaEffects has an extra parameter includeShortNames to do what the name of this parameter suggests.
  • Improved error message for function updateSpecification.

RSiena 1.4.10

2024-03-25

Changes in RSiena:

Effects:

  • Effects sameXV and sameXVInPop added for symmetric networks, and restricted to integer-valued variables in the range from 0 to 20.

New functionality:

  • Parameter silent (new in version 1.4.8) in sienaAlgorithmCreate activated.

Improved coding:

  • Actor covariates in sienaData have a new attribute lowIntegers used for in/excluding effects sameXVInPop and sameXV in getEffects.

RSiena 1.4.9

2024-03-21

Changes in RSiena:

Effects:

  • New effects crossXOutAct, outOutDist2ActIntn, outOutDist2AvIntn, inPopOutW.
  • New effect group doubleCovarNetObjective.
  • New effects sameXV and sameXVInPop for bipartite networks.
  • sameXCycle4 added for one-mode and symmetric networks.
  • sharedTo gets default internal effect parameter p=3.

Improved functionality:

  • Function updateSpecification now also updates interaction effects and initialValues.

Improved coding:

  • Internal functions numberIntn, numberBehIntn, checkVersion defined in file initializeFRAN.r.
  • The Covariate class and its descendants (all actor covariates) now have functions min and max.

RSiena 1.4.8

2024-02-29

Changes in RSiena:

Bug corrections:

  • Correction of memory leak in siena07setup.ccp for ML estimation.

New functionality:

  • New parameter silent in sienaAlgorithmCreate.

RSiena 1.4.7

2024-02-20

Changes in RSiena:

Bug corrections:

  • Correction (again) of error message in siena07utilities::Rterminate.

RSiena 1.4.6

2024-02-19

Changes in RSiena:

New functionality:

  • New parameter 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.
  • If the data contains a continuous dependent behavioral variable and the algorithm specifies conditional estimation, the estimation stops with a clear error message.

Bug corrections:

  • R_NO_REMAP included, and "\Rf_" prepended to all function names used from 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").
  • Corrected wrong length of lprobabilityArray in MLSimulation.h, and cleaned up a bit.
  • In MLSimulation.cpp, various sets of "delete" commands reordered so as to be in opposite order of the corresponding "new" commands.
  • Correction of error message in BehaviorVariable::accumulateDerivatives and in siena07utilities::Rterminate.
  • Allow sienaDataCreate to work with a single variable defined as a dependent network given as a list of sparse matrices.
  • Allow getEffects to construct effects of more than one dependent network on continuous behavior dependent variables.
  • Added some "drop=FALSE" in initializeFRAN.r to guard against dimension loss in the construction of sparse matrices.
  • Change check for constant dyadic covariates for sparse matrices (issue #88).
  • Some of the recently added effect groups were missing from effectsDocumentation. This led to an incomplete listing of the effects. They are now included.

Dropped functionality:

  • sienaRI temporarily disabled because of a memory leak.
  • The option 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:

  • List of changes in the code before 2022 moved from NEWS.md to ONEWS_gh.

RSiena 1.4.5

2024-02-14

Changes in RSiena:

Package

  • Migrated package repository to "stocnet" organisation.

Bug corrections:

  • Put #include <Rinternals.h> as the last of the include commands in various .cpp files (Tomas Kalibera).

RSiena 1.4.2

2023-12-14

Changes in RSiena:

Effects:

  • New effects outXMore, outMore3.
  • Interactiontype of altLThresholdX and altRThresholdX is dyadic.
  • Interactiontype of degAbsDiffX, degPosDiffX, and degNegDiffX is "" (blank).
  • Corrected effect outMore.

Improved coding:

  • bxeffects initialized to 0 in ContinuousVariable::accumulateScores.
  • All private variable declarations in the C++ *.h files were initialized using braces.
  • In 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:

  • New parameter iterations in sienaGOF to allow shorter computations.

RSiena 1.4.1

2023-11-01

New CRAN version.

Changes in help files:

  • Changes in accordance with "Guidelines for Rd files".

RSiena 1.4.0

2023-10-31

Changes in RSiena:

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" (for testing).

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 and before

Earlier changes:

  • See file ONEWS_gf in the source code at GitHub for changes in versions 1.2-26 to 1.3.5.

RSiena 1.2-25 and before

Earlier changes:

  • See file ONEWS in the source code at GitHub for changes in versions 17 to 1.2-25 (when the code was hosted at R-forge).