2022-10-07

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

2022-10-06

- 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`

.

2022-05-30

- 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`

.

- Further explanation of
`mixedTriadCensus`

in the help page for`sienaGOF-auxiliary`

.

2022-04-28

- 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`

).

- New effects
`avInAltW`

,`avWInAlt`

,`totInAltW`

,`totWInAlt`

(with help from Robert Krause). - Corrected implementation of
`sharedTo`

.

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

2022-03-18

- Corrected implementation of
`simAllNear`

and`simAllFar`

.

- small correction of
`summary.sienaGOF`

. - small correction of
`sienaTimeTest`

.

2022-03-07

- Changed internal effect parameter for
`simAllNear`

to 2 and for`simAllFar`

to 4.

- In
`sienaTimeTest`

, added`warn=FALSE`

to`varCovar()`

to avoid warnings. - Small improvements to help pages for
`sienaGroupCreate`

and`sienaGOF`

.

- 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’.

2022-02-18

- New effect
`avDeg`

.

2022-02-16

- 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.

- 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`

.

2021-12-15

- 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.

2021-12-08

- New effects
`inRateInv`

,`inRateLog`

(Steffen Triebel).

- 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.

- 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.

- In
`sienaprint.r`

, methods and functions relating to`sienaBayes`

omitted.

- Test 18, a test for `
`sienaGroupCreate`

, added to`parallel.R`

.

2021-10-09

- 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.

`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.

- 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.`

- In
`sienaAlgorithmCreate`

, the default values of`diagonalize`

for MoM is 0.2; this was corrected in the help file.

2021-07-29

- Effects of type
`creation`

or`endow`

represented in siena.table by`creation`

and`maintenance`

, respectively.

This was erroneously omitted in 1.3.1.

2021-07-27

- New effects:
`crprodInActIntn`

(Nynke Niezink),`XXW`

.

- Effects of type
`creation`

or`endow`

represented in siena.table by`creation`

and`maintenance`

, respectively. `updateTheta`

also accepts`sienaBayesFit`

objects as`prevAns`

.

- 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`

.

2021-05-02

- Drop
`testthat`

in tests.

2021-04-30

`testSame.RSiena`

.

- 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`

).

`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`

.

- 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`

.

- 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)`

.

- Took out of
`NAMESPACE`

a few imported functions from`graphics`

,`stats`

,`utils`

that were not used.

- Correction of footer of
`CovariateDistance2EgoAltSimNetworkFunction.h`

.

2021-03-19

- Adjusted
`configure`

,`cleanup`

and`Makevars`

files for just C++ checks. - Pandoc dropped as a system requirement.

2021-03-16

- 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`

).

- 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).

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

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

- 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.

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

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.

2021-02-23

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

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.

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.

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.