2023-10-31

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

2023-10-31

`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.

2023-10-11

`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).

2023-09-29

- 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`

.

2023-08-15

- 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`

).

2023-08-01

- 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”.

2023-06-29

- 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).

2023-05-11

- 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`

).

2023-04-22

`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.

2023-02-07

`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.

2023-01-29

- 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`

.

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...).
```

- All occurrences of
`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`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`

.

2022-11-04

- CRAN version.

- Update
`configure`

and`configure.ac`

(with help from Brian Ripley).

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 default 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\generic`

, 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.