2024-02-20

- Correction (again) of error message in
`siena07utilities::Rterminate`

.

2024-02-19

- 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 "_" 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`

.

2024-02-14

- Put
`#include <Rinternals.h>`

as the last of the include commands in various`.cpp`

files (Tomas Kalibera).

2023-12-14

- 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.

2023-11-01

- 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” (for testing).

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`

.

- See file
`ONEWS_gf`

in the source code at GitHub for changes in versions 1.2-26 to 1.3.5.

- 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`

).