2024-02-20
siena07utilities::Rterminate.2024-02-19
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.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”).lprobabilityArray in
MLSimulation.h, and cleaned up a bit.MLSimulation.cpp, various sets of “delete” commands
reordered so as to be in opposite order of the corresponding “new”
commands.BehaviorVariable::accumulateDerivatives and in
siena07utilities::Rterminate.sienaDataCreate to work with a single variable
defined as a dependent network given as a list of sparse matrices.getEffects to construct effects of more than one
dependent network on continuous behavior dependent variables.initializeFRAN.r to guard
against dimension loss in the construction of sparse matrices.effectsDocumentation. This led to an incomplete listing of
the effects. They are now included. ### Dropped functionality:sienaRI temporarily disabled because of a memory
leak.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:NEWS.md to ONEWS_gh.2024-02-14
#include <Rinternals.h> as the last of the
include commands in various .cpp files (Tomas
Kalibera).2023-12-14
outXMore, outMore3.Interactiontype of altLThresholdX and
altRThresholdX is dyadic.Interactiontype of degAbsDiffX,
degPosDiffX, and degNegDiffX is “”
(blank).outMore. ### Improved coding:bxeffects initialized to 0 in
ContinuousVariable::accumulateScores.*.h files
were initialized using braces.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:iterations in sienaGOF to
allow shorter computations.2023-11-01
2023-10-31
Author field omitted in DESCRIPTION,
because Author@R is sufficient. ### Changes in
inst directory:inst directory omitted.CITATION. ### Small changes in coding:SdeSimulation.h
deleted.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:altInDist2W and
totInDist2W added to the manual (the effects had been there
since a long time, but not documented).2023-09-29
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:includeInteraction.2023-08-15
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
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.)sienaGOF
of a list of sienaFit objects (was not correct in version
1.3.23). ### Additional testing:includeInteraction used in “parallel.R” (for
testing).2023-06-29
diffWXClosure, sameWWClosure,
diffWWClosure, diffXWClosure,
sameXWClosure, unequalX.JoutMix made available for bipartite dependent
networks.continuousBipartiteObjective was
created, with effects outdeg, outdegSqrt, and
isolateOut.sameXOutAct and diffXOutAct now have a
parameter 2 for sqrt. ### Corrections:initializeFRAN, the call of getEffects
now is dependent on the value of attribute “onePeriodSde”.useStdInits = TRUE in sienaAlgorithmCreate and
the effects object includes interaction effects.sienaDataCreate, the warning message that there is
at least one upOnly period now is made for each dependent
variable instead of only the last.getEffects, the effects object was given an
attribute onePeriodSde and an attribute
version.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:sienaGOF now also accepts a list of
sienaFit objects. ### Improved coding:initializeFRAN when there is a
mismatch between effects objects disabling the creation of interaction
effects.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).sienaGOF if
groupName or varName is incorrect.sienaGOF (the use of “nrd” sometimes led to absent plots
because of negative bw).2023-05-11
AlterFunction and its descendants, in particular
CovariateNetworkAlterFunction.const to virtual specification of
value in AlterFunction.h and all of its
descendants.std::abs in
AbsDiffFunction.cpp. ### New functionality:DOUBLESTEP25,
DOUBLESTEP50, DOUBLESTEP75,
DOUBLESTEP100. ### Corrections:altDist2, totDist2 and
altInDist2.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.TriadCensus, the empty network will not lead to an
error but be reported with the correct triad census.reciAct, check whether internal parameter ==2
replaced by check whether absolute difference from 2 is less than
0.001.phase2.r, z$sd is calculated using
sqrt(pmax(..., 0)) to avoid the extremely rare case of a
negative calculated variance.sienaDataCreate, handling of structurally determined
values in checkConstraints corrected (thanks to issue
raised by Jos Elkink). ### Improvements of functionality:parameter in
includeInteraction was dropped because it did not have any
consequences. The help page for includeInteraction now
explains how internal effect parameters for user-defined interactions
are determined.dimnames of the Simulations
array returned by sienaGOF are set to the names of the
elements of the auxiliary function.descriptives.sienaGOF.initializeFRAN in the case of
mismatch between effects objects.sienaAlgorithmCreate if
(maxlike && (!is.null(MaxDegree))). This is now
also mentioned in the help page for sienaAlgorithmCreate.
### Documentation:Wald.Rd.sienaDependent, it is mentioned
that if there are one-mode as well as two-mode dependent networks, the
one-mode networks should come first.2023-02-07
siena07internals.cpp adapted to be compatible with new
clang 16 C++ compiler (thanks to Brian Ripley). ### New effects:inPop_dya.sameXInPop and diffXInPop.
### Corrections:siena07 corrected with respect to
x$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
move for MH proposal distribution
for likelihood estimation (thanks to Charlotte Greenan).sienaAlgorithmCreate for probabilities of MH steps, now
summarized in prML; with a new default.accepts, rejects,
aborts for sienaFit objects produced by ML
estimation improved/corrected by reorganizing them in C++.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...).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 Tsqprint.summary.sienaMeta, siena07,
print01Report: drop RForge revision.meta.table
(siena08.r).LaTeX output of meta.table.seq_along and seq_len used in
print01Report.2022-11-04
configure and configure.ac (with
help from Brian Ripley).2022-10-07
2022-10-06
Matrix
package.universalOffset initialized as 0; it was earlier
initialized as the maximum real number
(NetworkLongitudinalData.cpp).thetaStore deleted (was trash in
phase2.r).all to avoid warnings (initializeFRAN.r). ###
Code modifications:sigmas and meansigmas added to
sienaRI object.sienaRI object for
printSigma=TRUE changed to using averages at the variance
level.returnThetas in the call of siena07,
also simulated estimation statistics during Phase 2 (deviations from
targets) are returned. ### Effects:nonPCompress, primCompress,
primary, primDegAct,
primDegActDiff, primDegActDiffSqrt,
primDegActSqrt, primDegActLog,
primDegActInv.gwdspFB effect added for two-mode networks.outAct_ego,
inAct_ego,reciAct_ego,
toAny.to, toBack,
toRecip, mixedInXW, internal effect parameter
3 now specifies truncation of the number of twosteps (change to
MixedTwoStepFunction). ### Improvements of
documentation:sienaRI.sienaGOF.2022-05-30
effects.r of error that led to warning
for multivariate networks.sienaGOF
(groupName).igraphNetworkExtraction in the help page
for sienaGOF-auxiliary.mixedTriadCensus in the help
page for sienaGOF-auxiliary.2022-04-28
HigherFilter and
DisjointFilter).avInAltW, avWInAlt,
totInAltW, totWInAlt (with help from Robert
Krause).sharedTo.2022-03-18
simAllNear and
simAllFar.summary.sienaGOF.sienaTimeTest.2022-03-07
simAllNear to 2 and for simAllFar to 4.sienaTimeTest, added warn=FALSE to
varCovar() to avoid warnings.sienaGroupCreate
and sienaGOF.StatisticCalculator::calculateBehaviorStatistics and
StatisticCalculator::calculateBehaviorGMMStatistics.StatisticCalculator::calculateNetworkEvaluationStatistics
and in `siena07internals::getChangeContributionStatistics’.2022-02-18
avDeg.2022-02-16
simAllNear,simAllFar,
absOutDiffIntn, avDegIntn.recipRateInv, recipRateLog
(Steffen Triebel).outOutActIntn,
outOutAvIntn, and both changed from 2 to
1.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.includeInteraction and setEffect.ONEWS_gf in the source code at GitHub for
changes in versions 1.2-26 to 1.3.5.ONEWS in the source code at GitHub for changes
in versions 17 to 1.2-25 (when the code was hosted at
R-forge).