2012-03-29 R-forge revision 212 * update of RSiena_Manual.tex, RSiena.bib (both packages) 2012-03-29 R-forge revision 211 * doc/RSiena_Manual.tex, doc/siena1.png, doc/siena2.png, doc/siena3.png, doc/ilcampo.jpg, doc/RSiena.bib moved to inst/doc/ and copied to RSiena to comply with GPL. Both packages now include these files in the tarball but not the binary. * .Rinstignore: added * .Rbuildignore: added to RSiena and updated in RSienaTest to exclude temporary latex files from the tar ball. * R/effectsDocumentation.r: bug fix for newly added groups. * inst/doc/effects.pdf: updated 2012-03-29 R-forge revision 210 NB new version number sequence. 1.1.210 * src.siena07utilities.cpp, siena07setup.cpp: changes to R/C++ interface code. Moved a call to PutRNGstate to _before_ the UNPROTECT to fix an intermittent error. * tests/effectsTest.R: changes to comments only * doc/RSienaDeveloper.tex, tests/scripts.Rout.save: updated output file, minor additions to documentation. * tests/testrefs/M44compare.out, tests/testrefs/M45compare.out: updated test outputs. (RSienaTest only) * tests/testrefs/*compare.out: some files got missed last time 2012-03-28 R-forge revision 209 (RSienaTest only) * src/model/effects/DiffusionRateEffect.cpp: bug fix 2012-03-25 R-forge revision 208 * src/data/BehaviorLongitudinalData.cpp: fix memory leak * src/model/effects/generic/CovariateDistance2NetworkFunction.cpp: fix memory leak * src/model/variables/NetworkVariable.cpp: fix bug in endowment and creation effect scores for no change. * data/allEffects.csv, R/effects.r, R/effectsDocumentation.r: split behavior network effects between symmetric and other networks. * src/model/model.cpp (RSiena only), src/model/variables/DependentVariable.cpp, src/model/variables/EffectValueTable.h (RSiena only): added comments, formatting * src/model/effects/DiffusionRateEffect.cpp: bug fix (RSienaTest only) * doc/RSienaDeveloper.tex: updated doc (RSienaTest only) * doc/MCMCandRM.pdf: added * tests/effectsTest.R, tests/sampson.r, testrefs/*, .Rbuildignore: new testing files added, not to be included in tar ball. (RSienaTest only) * inst/examples/Sampson_t2.txt, inst/examples/Sampson_t3.txt, inst/examples/Sampson_t4.txt, inst/examples/vtextexoreal.dat: added. * src/effects.r: correct bug causing crash with sparse matrices with changes all in one direction. * src/model/EpochSimulation.cpp: added comments * src/model/ml/MLSimulation.cpp: correct test when storing rejection numbers. * src/model/StatisticCalculator.h: formatting (RSienaTest only) * src/model/ml/chain.cpp: initialize finalReciprocalRate explicitly. 2012-03-21 R-forge revision 207 (RSienaTest only) * siena07internals.cpp, DependentVariable.h, DependentVariable.cpp: changed calculation of scores for diffusion rate effects * StatisticCalculator.h, StatisticCalculator.cpp, DependentVariable.h, DependentVariable.cpp, DiffusionRateEffect.h, DiffusionRateEffect.cpp: added a function to calculate value of a type of diffusion rate effect 2012-03-16 R-forge revision 206 (RSienaTest only) * R/effects.R, R/effectsDocumentation.R: added a new behavior rate effectGroup covarBehaviorOneModeRate * data/allEffects.csv, siena07internals.cpp, StatisticCalculator.cpp, DependentVariable.cpp, DependentVariable.h, DiffusionRateEffect.cpp, DiffusionRateEffect.h: added new diffusion behavior rate effects susceptAvIn, susceptAvCovar, infectIn, infectOut, infectCovar, totExposure 2012-03-07 R-forge revision 205 * src/model/effects/CovariateDistance2AlterEffect.cpp, src/model/effects/CovariateDistance2AlterEffect.h, src/model/effects/CovariateDistance2NetworkEffect.cpp, src/model/effects/CovariateDistance2NetworkEffect.h, src/model/effects/CovariateDistance2SimilarityEffect.cpp, src/model/effects/CovariateDistance2SimilarityEffect.h: removed as no longer used * src/model/effects/allEffects.h: remove the .h's from previous entry * src/model/effects/CovariateAndNetworkBehaviorEffect.cpp: correct memory leak. * src/model/effects/generic/CovariateDistance2NetworkFunction.cpp: adjust preprocessEgo method. * src/model/effects/InteractionCovariateEffect.cpp: amend test for missing as in revision 197. * src/model/variables/NetworkVariable.cpp: correct calculation of this->lalterProbability. 2012-02-29 R-forge revision 204 * src/model/effects/SimilarityEffect.cpp: fixed bugs in endowment/creation statistics. * src/model/ml/Chain.cpp: fixed bug causing failure in connect with constraints * src/model/EpochSimulation.cpp: allow for underflow of sigma2 when taking square root. * src/model/variables/NetworkVariable.cpp: fix bug in creation and endowment effect scores for pairwise symmetric network models. * R/simstatsc.r: fix bug which stopped chains being returned * R/sienaprint.r: amend model print * R/sienaDataCreate.r: amend error message for incorrect dyadic covariate. * R/siena08.r: suppress printed NULLS at end of summary. * R/robmon.r: remove cluster.out before using it again. * R/phase3.r: change format of report of autocorrelations in phase 3. * R/initializeFRAN.r: forbid maximum likelihood estimation with composition change, round calculation of number of MH steps. * R/bayes.r: fix incorrect condition, allow to work with non constant rates if a dfra is provided, minor reformatting. * doc/missingEtc.tex: minor update. * po/R-RSiena.pot, po/R-RSienaTest.pot: updated error message files 2012-02-19 R-forge revision 203 * src/siena07setup.cpp: initialize permutation length correctly in setup phase of ML. * R/robmon.r, R/zzz.r: add check for same package if using multiple processes. * doc/RSiena_manual.tex: 1) removed details about snow and rlecuyer packages 2) amended code to make sparse matrices. (RSienaTest only) * tests/scripts.Rout.save: update for reduced diffs. 2012-02-10 R-forge revision 202 (RSienaTest only) * doc/RSienaDeveloper.tex: updated various details. Reformatted pages 2012-02-08 R-forge revision 201 (RSienaTest only) * R/sienatable.r: added property eol-style=native. * src/model/StatisticCalculator.cpp, src/model/variables/DependentVariable.cpp, src/model/variables/NetworkVariable.cpp: fix some memory leaks in settings model. 2012-02-07 R-forge revision 200 * src/model/variables/DependentVariable.cpp: removing networkVariable conditions so score sum terms are calculated for behaviour rate effects. (As RSienaTest Revision 199) * src/model/EpochSimulation.cpp: remove automatic cast in call to log. * tests/scripts.R: alter order of testing so less output produced when scripts are not tested. * src/siena07setup.cpp, src/siena07internals.cpp, src/siena07internals.h, src/network/NetworkUtils.cpp, src/network/NetworkUtils.h, src/model/Model/cpp, src/model/Model.h, src/model/StatisticCalculator.cpp, src/model/StatisticCalculator.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/data/ChangingDyadicCovariate.cpp, src/data/ChangingCovariate.h, src/data/NetworkLongitudinalData.cpp, src/data/NetworkLongitudinalModel.h, R/initializeFRAN.r: settings Model. RSienaTest only * R/phase3.r: formatting, suppress error problems * R/phase1.r: stop if cannot get a derivative matrix in phase 1. * R/initializeFRAN.r, src/siena07utilities.cpp, src/siena07utilities.h, src/siena07setup.cpp, src/siena07setup.h, src/siena07models.cpp, src/siena07sinternals.cpp, src/siena07internals.h: remove redundant parameters * doc/RSienaDeveloper.tex: fix typo (RSienaTest only) 2012-02-07 R-forge revision 199 (RSienaTest only) * src/model/variables/DependentVariable.cpp, src/model/variables/EffectValueTable.h, src/model/variables/DiffusionEffectValueTable.h: removing backslashes from within comments. * src/model/variables/DependentVariable.cpp: removing networkVariable conditions so score sum terms are calculated for behaviour rate effects. * src/model/variables/DependentVariable.cpp, src/model/variables/DiffusionEffectValueTable.cpp: correction calculation of average exposure diffusion rate effect. * R/sienatable.r: removal of superfluous variables. 2012-01-29 R-forge revision 198 * src/siena07internals.cpp: fix a bug causing initialisation of ML to be done using the wrong rate parameter. Will change results slightly if there was a behavior variable or a bipartite variable. 2012-01-29 R-forge revision 197 * src/model/effects/CovariateDependentBehaviorEffect.cpp, src/model/effects/CovariateDependentBehaviorEffect.h, src/model/effects/MainCovariateEffect.cpp: fix bug in changing covariate in MainCovariate effect * src/model/variables/BehaviorVariable.cpp: fix bug in derivatives for maximum likelihood creation effects. 2012-01-28 R-forge revision 196 (RSienaTest only) * doc/Debugging.pdf, doc/RSiena_R20104up.pdf: added * doc/Siena_algorithms4.tex: amended maximum likelihood spec 2012-01-20 R-forge revision 195 * inst/scripts/Rscript01DataFormat.R, inst/scripts/Rscript02SienaVariableFormat.R, inst/scripts/Rscript03SienaRunModel.R, inst/scripts/Rscript04SienaBehavior.R: new versions now in RSiena too. Also one or two typos corrected. * tests/scriptfile.Rout.save, tests/scriptfile.Rout.win, tests/scripts.Rout.save, tests/parallel.Rout.save: updated targets for checks. * tests/scripts.R: Run sub process with --vanilla. Also some debugging code added. * src/sienaInternals.cpp: treat NaN in covariates the same as NA, as is done in the R part of RSiena. * src/siena07Models.cpp, src/siena07Utilities.cpp, src/model/EpochSimulation.cpp, src/model/Model.cpp, src/model/StatisticCalculator.cpp, src/ml/MLSimulation.cpp, src/ml/Chain.cpp: minor changes to remove compiler warnings. * doc/RSienaDeveloper.tex: revisions, additions * inst/examples/arclistdata.dat: added file * man/algorithms.Rd: corrected spelling * man/RSiena-package.Rd: new maintainer email address * R/sienaprint.r: leave fixed values of theta in the print 2012-01-17 R-forge revision 194 * doc/RSIENAspec.tex, man/coDyadCovar.Rd, man/varDyadCovar.Rd, R/effects.r, R/initializeFRAN.r, R/sienaDataCreate.r, R/sienautils.r, src/data/Data.cpp, src/data/NetworkLongitudinalData.cpp, src/data/NetworkLongitudinalData.h, src/data/OneModeNetworkLongitudinalData.cpp, src/model/filters/LowerFilter.cpp, src/model/ml/NetworkChange.cpp, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/model/network/Network.h: make treatment of bipartite networks and dyadic covariates consistent. * R/globals.r: make PrtOutMat cope with null matrices * R/initializeFRAN.r: fix to calculation of number of ML steps, relax restrictions on behavior interactions. 2012-01-17 R-forge revision 193. RSienaTest only. * R/sienatable.r: file added with siena.table function. * NAMESPACE: siena.table function added. 2012-01-17 R-forge revision 192. * minor but extensive changes to manual * inst/scripts/Rscript01DataFormat.R, inst/scripts/Rscript02SienaVariableFormat.R, inst/scripts/Rscript03SienaRunModel.R, inst/scripts/Rscript04SienaBehavior.R: minor changes to scripts (RSienaTest only) 2011-12-15 R-forge revision 191. * src/model/variables/BehaviorVariable.cpp, src/model/variables/NetworkVariable.cpp: altered calculations of probabilities to avoid overflow. * R/bayes.r: fix bug in accumulation of MII * src/model/filters/lowerfilter.cpp: fix bug which made no change not permitted * data/allEffects.csv: removed endowment effect for indTies for symmetric networks * R/algorithms.r, R/maxlikec.r, R/phase1.r, R/simstatsc.r, src/siena07utilities.cpp, src/siena07models.cpp, src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h: src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h, src/model/Model.cpp, src/model/Model.h, src/model/variables/BehaviorVariable.cpp, src/model/variables/NetworkVariable.cpp, src/model/variables/BehaviorVariable.h, src/model/variables/NetworkVariable.h, src/model/variables/DependentVariable.h: removed option (non-functioning) to store change contributions on ministeps * src/model/EpochSimulation.cpp, src/model/EpochSimulation.h, src/siena07Models.cpp, src/siena07models.h: remove some non-functioning options to do calculations for chains. * R/siena07.r: more attempts to reset the random number kind * tests/scripts.R: copied more data files to use for further scripts 2011-12-14 R-forge revision 190. * R/bayes.r: fix bugs from previous changes 2011-12-14 R-forge revision 189. * po/R-RSiena.pot, po/RSienaTest.pot added files for translators. * doc/RSienaDeveloper.tex: updated to reflect changes in algorithms and other minor details. * data/allEffects.csv: fixed typo in shortName for symmetric networks * man/sienaModelCreate.Rd: updated details * R/initializeFRAN.r, R/simstatsc.r, R/maxlikec.r, R/bayes.r, R/phase1.r, R/phase2.r, R/robmon.r, R/algorithms.r (RSienaTest only): rationalized and tidied code. * man/maxlikec.Rd: removed file, details now in man/simstatsc.Rd. * max/simstatsc.Rd: expanded to include maxlikec, initializeFRAN and terminateFRAN. * R/print01Report.r, R/printDataReport.r, R/sienaPrint.r, : minor changes to reports. * R/sienaeffects.r: fixed bug in error messages * src/model/ml/MLSimulation.cpp, src/model/Model.cpp, src/siena07Models.cpp: formatting source only. 2011-12-07 R-forge revision 188. * added directories po ready for translation files. 2011-12-06 R-forge revision 187. * src/siena07setup.cpp: correct change to name of included file in previous version: did not compile on case-sensitive systems. * doc/RSienaDeveloper.tex: fixed a latex error. (RSienaTest only) 2011-12-04 R-forge revision 186. * R/bayes.r, R/initializeFRAN.r, R/maxlikec.r, R/phase1.r, R/phase2.r, R/phase3.r, R/robmon.r, R/simstatsc.r, src/siena07models.cpp, src/siena07models.h, src/siena07setup.cpp, src/siena07utilities.cpp, src/model/EpochSimulation.cpp, src/model/EpochSimulation.h, src.model/Chain.cpp, src/model/Model.cpp, src/model/Model.h, src/model/State.cpp, src/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h: added facility to return log likelihood after simulation, stopped returning of chains every iteration. Bug fixes for ML. * R/algorithms.r: added to RSienaTest (from examples directory). * man/profileLikelihoods.Rd, man/algorithms.Rd: (RSien aTest only) help files for functions in algorithms.r. 2011-11-27 R-forge revision 185. * R/robmon.r, inst/examples/algorithms.r, inst/examples/runalg.r: minor changes to paths. Added parallel package to algorithm code (RSienaTest only for the algorithm code) * R/bayes.r: made functions internal to reduce copying. Replaced snow and Rlecuyer by parallel (non optionally) * src/model/ml/Chain.cpp, src/model/ml/MLSimulation.cpp, src/model/model.cpp: remove memory leaks. * src/siena07models.cpp: Ensure end state is on stored chain. Fix protection imbalance. * src/siena07utilities.cpp: correct copy of initial state to sub processes. * src/siena07setup.cpp: remove print of probabilities at start. * src/model/ml/Chain.h, src/model/MLSimulation.h, src/model/Model.h, src/model/tables/Cache.cpp, src/model/tables/Cache.h: altered comments only 2011-11-14 R-forge revision 184. * src/model/StatisticCalculator.cpp: fix memory leaks in network and behavior rate statistics. (Latter is long standing, former introduced in revision 181. 2011-11-11 R-forge revision 183. * R/initializeFRAN.r, R/phase1.r, R/phase3.r: fix minor bugs. Could not interrupt phase 1 or 3 of siena07, could use dfra from MOL with ML and vice versa. 2011-11-11 R-forge revision 182. * R/bayes.r, src/siena07models.cpp:correct return of acceptances etc. and new format of dff * R/sienaTimeTest.r: fix bug with multi groups and differing actor set sizes. 2011-11-04 R-forge revision 181. * src/data/BehaviorLongitudinalData.cpp, src/data/BehaviorLongitudinalData.h, src/data/NetworkLongitudinalData.cpp, src/siena07Setup.cpp, src/data/NetworkLongitudinalData.h, src/siena07Internals.cpp, src/model/StatisticCalculator.cpp, src/network/NetworkUtils.h, src/model/StatisticCalculator.h, src/network/NetworkUtils.cpp, R/initializeFRAN.r: Reorganised calculation of dependent variables with missing data removed. Hopefully speedier. * src.network/Network.cpp: added a doxygen commment for clone * R/siena07.r, R/robmon.r: reset the random number generator to * src/model/effects/behaviorInteractionEffect.h: correct properties to be eol-style not executable normal type after using parallel package. (RSiena only) 2011-11-04 R-forge revision 180. * R/phase1.r, R/phase3.r: revision to avoid time consuming copies * src/model/StatisticalCalculator.cpp: stop setting up of extra networks if no endowment or creation effects. (Diffusion rate effects were included in RSiena inadvertently: code removed in revision 181).. * src/model/effects/behaviorInteractionEffect.cpp: correct properties to be eol-style not executable (RSiena only) 2011-10-28 R-forge revision 179. * R/robmon.r: fix problem with forking clusters. * tests/scriptfile.Rout.save: updated version of script test output. 2011-10-27 R-forge revision 178. Fixes from rev 175 and rev 177 copied to RSiena. * R/phase3.r: correct covariance matrix for effects that have been fixed. Second attempt for RSienaTest * R/sienaGOF.r: RSienaTest only: back out change in rev 177. * R/effects.r: Rsiena only: remove out-of-date comments * R/sienaDataCreate.r: RSiena only. Remove inter-network constraints which relate a symmetric network to a non-symmetric network. * R/effectsMethods.r: RSiena only. make fix(myeff) return quietly with no change if session is not interactive. * man/bayes.Rd, man/maxlikec.Rd, R/bayes.r, NAMESPACE: bayes now exported in RSiena too (see rev 168) * man/updateTheta.Rd, R/initializeFRAN.r, NAMESPACE: new function: updateTheta (See rev 168/9) * inst/examples/s50e.dat, inst/scripts/*, tests/scripts.R, tests/scriptfile.Rout.save, tests/scripts.Rout.save, tests/scriptfile.Rout.win: added scripts, data file to use in script checking (see rev 175/6) * R/simstatsc.r, R/siena07.R, R/robmon.R, man.siena07.Rd: snow/rlecuyer or parallel used depending on R version. New argument for siena07 to allow option FORK as well as PSOCK. * man/sienaModelCreate.Rd, R/sienaModelCreate.r: altered multiplication factor from 4 to 5. * man/sienaTimeTest.Rd,R/sienaTimeTest.r: added tests for models fitted by finite differences or maximum likelihood. * R/simstatsc.r, R/maxlikec.r, R/phase1.r, R/phase3.r: simplified code, added new utility functions, changed format of stored derivative matrices and made the by wave set optional to save memory. Matrix objects are used for maxlike (as symmetric and this will save space) with minimal compatible changes to finite differences. Revert to normal matrix for dfra. (see rev 168) * R/sienaprint.r, NAMESPACE, man/xtable.Rd: added dummy xtable command to call real one. * src/model/ml/Chain.cpp, src/model/ml/MiniStep.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/siena07models.cpp, src/siena07setup.cpp, src/siena07models.h: maximum likelihood updates * src/model/variables/DependentVariable.cpp, src/model/variables/NetworkVariable.cpp: fix bug causing crashes with symmetric networks alongside either behavior variable or non-symmetric network. (see rev 175) * tests/parallel.Rout.save: updating the comparison file. * doc/_emacs, doc/.emacs: sample emacs initialization files 2011-10-27 R-forge revision 177 RSienaTest only (committed prematurely!) * inst/scripts/Rscript01DataFormat.R, inst/examples/s50e.dat, tests/scripts.R, tests/scriptfile.Rout.save, tests/parallel.Rout.save: added data file for testing scripts. Minor textual changes. Removed library commands for snow and rlecuyer as will not be necessary in 2.14.0. * src/model/variables/DependentVariable.cpp, R/sienaDataCreate.r: formatting changes * R/simstatsc.r, R/siena07.R, R/robmon.R, man.siena07.Rd: snow/rlecuyer or parallel used depending on R version. New argument for siena07 to allow option FORK as well as PSOCK. * R/phase3.r: correct covariance matrix for effects that have been fixed. * R/sienaTimeTest.r: fix bug since replaced arrays for derivatives by wave by lists of sparse matrices: the error trap failed. * doc/RSienaDeveloper.tex: added comments about emacs, debugging R, new parallel package, etc. * R/sienaGOF.r: local change committed in error: backed our in r178. 2011-10-14 R-forge revision 176 RSienaTest only * inst/scripts/RScriptDataFormat.R, inst/scripts/RScriptSienaVariable.R, inst/scripts/RScriptSienaRunModel.R, inst/scripts/RScriptSienaBehaviour.R, inst/scripts/RSienaSNADescriptives.R: removed sna and network code to separate file which is excluded from testing by containing 'SNA' in the name * R/siena07.r, tests/scripts.R, tests/scriptfile.Rout.save, tests/scripts.Rout.save, tests/scriptfile.Rout.win: amended to work better multi-platform, although linux not yet tested. * R/document.r, doc/auto.tex, RSienaDeveloper.tex: new function to automate construction of the function table in the manual. * src/model/variables/DependentVariable.cpp: fix bug in diffusion effects. 2011-10-06 R-forge revision 175 RSienaTest only * doc/RScriptDataFormat.R, doc/RScriptSienaVariable.R, doc/RScriptSienaRunModel.R, doc/RScriptSienaBehaviour.R: moved to inst/scripts. Renamed to have a numbering sequence so can concatenate in correct order for testing. Minimal changes to make the tests work within R CMD check sequence. * R/siena07.r: check for availability of X11 device on non-Windows and force batch=TRUE if necessary. Only set random seed if not testing scripts. * R/effectsMethods.r: make fix command for a sienaEffects object terminate return the object unchanged if called non-interactively. * R/sienaprint.r, NAMESPACE, man/xtable.Rd: added dummy xtable command to call real one. * tests/scripts.R, tests/scripts.Rout.save, tests/scriptfile.Rout.save: added file to test scripts, controlled by an environment variable. * doc/RSiena_Manual.tex: altered path to scripts and file names. * R/sienaDataCreate.r: remove inter-network constraints which relate a symmetric network to a non-symmetric network * src/model/variables/DependentVariable.cpp, src/model/variables/NetworkVariable.cpp, doc/simstats0c.tex, doc/RSienaSpec.tex: fix bug causing crashes with symmetric networks alongside either behavior variable or non-symmetric network. * src/model/effects/DiffusionRateEffect.cpp, src/model/StatisticCalculator.cpp, src/model/variables/DiffusionEffectValueTable.cpp: minor formatting 2011-10-04 R-forge revision 174 * doc/RSiena_Manual.tex, doc/Siena_algorithms4.tex: added meta-analysis, minor changes to manual. 2011-09-29 R-forge revision 173 * doc/RSiena_Manual.tex: some changes, explanation mainly * doc/RSiena.bib: very small updates. 2011-09-19 R-forge revision 172 RSienaTest only (NB version number did not match) * src/model/effects/DiffusionRateEffect.cpp, src/model/effects/DiffusionRateEffect.h, src/model/variables/DiffusionEffectValueTable.cpp, src/model/variable/DiffusionEffectValueTable.h: files created to implement diffusion rate effects. * data/allEffects.csv, src/siena07internals.cpp, src/model/StatisticCalculator.cpp, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h: diffusion rate effect averageExposure added. 2011-09-07 R-forge revision 171 * R/globals.r, R/siena08.r, man/siena08.Rd: fix bugs in siena08 which was using out of date effects object which included unselected underlying effects from interactions, and report would not print if it had previously been displayed. New parameter to control maximum numnber of iterations. * R/printInitialDescription.r: fix bug in description of more than two groups. * R/initializeFRAN.r: (RSienaTest only) add some validation to updateTheta. * R/globals.r: (To Rsiena also now) allow format of printed matrices to be controlled by an environment variable. Designed for use in testing as there are rounding incompatibilities between platforms. * man/simstats0c.Rd: (RSiena only) updated page. * R/sienaprint.r, R/printDataReport.r, R/print07report.r, R/robmon.r, R/siena07Gui.r: (RSiena only) as for revision 168 in RSienatest. 2011-08-22 R-forge revision 170 * doc/RSiena_Manual.tex: changes mainly for non-directed models * doc/RSiena.bib: small updates. 2011-08-09 R-forge revision 169 RSienaTest only * R/initializeFRAN.r: bug fix to order of sienaTimeFix and prevans etc. 2011-08-08 R-forge revision 168 RSienaTest only. * R/sienaprint.r: altered headings from 't-statistics for convergence' to 'convergence t-ratios' * doc/bayes.tex, doc/maxlikec.tex, doc/RSiena_Manual.tex, doc/RSienaDeveloper.tex, doc/RSIENAspec.tex, doc/simstats0c.tex: updates to the documentation. * R/bayes.r, R/maxlikec.r, R/initializeFRAN.r, R/printDataReport.r, R/print07Report.r, R/robmon.r, R/siena07Gui.r, R/sienaModelCreate.r, R/simstatsc.r, man/bayes.Rd, man/maxlikec.Rd, man/sienaModelCreate.Rd, man/simstats0c.Rd, NAMESPACE, src/siena07Models.cpp, src/siena07Models.h, src/siena07utilities.cpp, src/siena07setup.cpp, src/model/ml/MiniStep.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h: exported bayes, added help pages for maximum likelihood and bayes. Various changes to maximum likelihood: still in progress. * man/updateTheta.Rd, R/initializeFRAN.r: new function to update theta initial values from a sienaFit. Reordered adding time dummies to happen before prevAns processing in siena07. * R/effects.r, src/model/ml/chain.cpp: tidy up code. * R/globals.r: allow format of printed matrices to be controlled by an environment variable. Designed for use in testing as there were rounding incompatibilities between platforms. * R/maxlikec.r, R/phase1.r, R/phase3.r, R/sienaTimeTest.r, man/sienaTimeTest.Rd: simplified code, added new utility functions, changed format of stored derivative matricesand made the by wave set optional to save memory. Matrix objects are used for maxlike (as symmetric and this will save space) with minimal compatible changes to finite differences. Revert to normal matrix for dfra. * src/data/ConstantDyadicCovariate.cpp, src/data/ConstantDyadicCovariate.h, src/model/variable/NetworkVariable.cpp, src/model/variable/NetworkVariable.h: Added access method to map of row values. Also some commented out code eg to select alter from a smaller set. * tests/parallel.Rout.save: updated output from tests 2011-08-03 R-forge revision 167 * doc/RSiena_Manual.tex: minor changes * data/allEffects.csv, src.effects/effectFactory.cpp: renamed avSimX, totSimX, avAltX to avSimEgoX etc in preparation for avSimAlterX etc to appear soon! * R/effects.r: added network names to behavior effects if there is more than one network. * R/initializeFRAN.r: removed duplicate variable names from network interaction effects. * R/siena01.r, doc/RscriptDataFormat.R: change name of manual in model help function and script. * R/sienaDataCreate.r: trap missing Actors node set if node sets are supplied. (was crashing!) * DESCRIPTION: added BuildResaveData:no to stop allEffects.r being compressed in the build. 2011-08-02 R-forge revision 166 * doc/RSiena_Manual.tex: corrections * doc/RSiena.bib: small format corrections 2011-07-28 R-forge revision 165 * doc/RSiena_Manual.tex: corrections * doc/RSiena.bib: a few additions 2011-07-27 R-forge revision 164 * R/effects.r: change default behavior effects to include quadratic shape unless range is less than 2 (from less than or equal to 2). * R/siena01.r: change name of manual. * R/initializeFRAN.r: remove duplicate variable names from behavior interaction effects. * man/siena07.Rd: correct description of prevAns. 2011-07-23 R-forge revision 163 * R/effectsDocumentation.r: fix bug caused by changes to effects * R/phase1.r: avoid allocation of unnecessary storage for derivatives 2011-07-10 R-forge revision 162 * src/model/effects/OutTruncEffect.cpp, src/model/effects/OutTruncEffect.h, src/model/effects/allEffects.h, src/model/effects/EffectFactory.cpp: renamed effect to TruncatedOutDegree to comply with standards. * src/model/effects/BehaviorInteractionEffect.cpp: remove extraneous variable definitions to remove compiler warnings. 2011-07-02 R-forge revision 161 * man.siena08.Rd: add note that names of effects must match * man/siena07.Rd, man/simstats0c.Rd: minor edits. * R/effects.r, R/sienaDataCreate.r: minor edits of comments * R/bayes.r, R/maxlikec.r, inst/examples/algorithms.r: Bayesian routine was failing for single data objects. * R/RSienaRDocumentation.r: fix for internal functions of internal functions. Clumsy at present. * man/RscriptSienaRunModel.R: minor correction to text, many trailing spaces removed. 2011-06-24 R-forge revision 160 * src/model/effects/BehaviorInteractionEffect.cpp, src/model/effects/AltersCovariateAverageEffect.cpp, src/model/effects/LinearShapeEffect.cpp, src/model/effects/MainCovariateEffect.cpp, src/model/effects/IndegreeEffect.cpp, src/model/effects/OutdegreeEffect.cpp, src/model/effects/SimilarityEffect.cpp (this one was changed in the previous revision): make endowment and creation effects consistently subtract the previous value. Interactions now divide by minus the difference rather than the current value. 2011-06-23 R-forge revision 159 * src/model/effects/BehaviorInteractionEffect.cpp, src/model/effects/BehaviorInteractionEffect.h: forgotten in previous revision. 2011-06-22 R-forge revision 158 * data/allEffects.csv, R/effects.r, src/model/effects/InteractionCovariateEffect.cpp, src/model/effects/InteractionCovariateEffect.h, src/model/effects/SimilarityEffect.cpp, src/model/effects/SimilarityEffect.h: fix replication bug in unspecified interactions, remove influence 1-sided effects, replace influence interaction effects by 3 options. Tidy up covarBehaviorObjective group. * data/allEffects.csv, R/effectsMethods.r, R/initializeFRAN.r, src/model/effects/allEffects.h, src/model/effects/AltersCovariateAverageEffect.cpp, src/model/effects/AltersCovariateAverageEffect.h, src/model/effects/AverageAlterEffect.cpp, src/model/effects/AverageAlterEffect.h, src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h, src/model/EffectFactory.cpp, src/model/effects/IndegreeEffect.cpp, src/model/effects/indegreeEffect.h, src/model/effects/LinearShapeEffect.cpp, src/model/effects/LinearShapeEffect.h, src/model/effects/MainCovariateEffect.cpp, src/model/effects/MainCovariateEffect.h, src/model/effects/OutdegreeEffect.cpp, src/model/effects/OutdegreeEffect.h, src/model/variables/BehaviorVariable.cpp: behavior interactions * R/initializeFRAN.r: fix bug: underlying effects of interactions with include = FALSE were being included. * R/sienaTimeTest.r, doc/sienaTimeFix.doc (RSienaTest only): implement time dummies for behavior effects. 2011-06-18 R-forge revision 157 * R/phase2.r: corrected definition of standard deviation used to control maximum jump. Was incorrect if using prevAns as it had the deviations from phase 3 rather than phase 1. * R/phase1.r, R/maxlikec.r, R/siena08.r: reformatting, using complete object names * R/bayes.r: remove unused variables to avoid warnings * man/sienaFit.Rd, R/effectsDocumentation.r, R/RSienaRDocumentation.r, R/sienaprint.r, DESCRIPTION, NAMESPACE: alter interface to xtable to allow loading package without it. 2011-06-13 R-forge revision 156 * R/bayes.r, R/maxlikec.r, R/initializeFRAN.r, R/phase1.r, src/model/ml/chain.cpp, src/model/ml/chain.h, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h, src/model/model.cpp, src/model/model.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/siena07internals.cpp, src/siena07internals.h, src/siena07models.cpp, src/siena07models.h, src/siena07setup.cpp, src/siena07/utilities.cpp, src/siena07utilities.h: Bayesian routine now in R, calling normal maxlike routine. Also end state vector for chains. * R/effects.r: minor bug if up or down only for some waves only and bipartite. Density effect was removed. * R/sienaprint.r: new method to print initial and end states of chains: chains.data.frame. 2011-06-12 R-forge revision 155 * R/initializeFRAN.r: fix bug re behavior variables with values 10 or 11 * data/allEffects.csv: alter short name for egoXaltX for symmetric networks to match that for non-symmetric ones. 2011-06-05 R-forge revision 154 RSienaTest only * doc/missingsEtc.tex, doc/bayes.tex, doc.maxlikec.tex: added * doc/RSienaSpec.tex, doc/simstats0c.tex: updated * R/bayes.r, R/maxlikec.r, R/initializeFRAN.r: new Bayes routine 2011-06-04 R-forge revision 153 * R/effects.r, R/initializeFRAN.r, R/print07Report.r, R/sienaprint.r, src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h, src/model/effects/NetworkEffect.cpp, src/model/effects/NetworkEffect.h, src/model/EpochSimulation.cpp, src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h, src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h, src/model/model.cpp, src/model/model.h, src/model/StatisticCalculator.cpp, src/model/StatisticCalculator.h, src/model/variables/BehaviorVariable.cpp, src/model/variables/BehaviorVariable.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/siena07internals.cpp: creation effects (incomplete) * src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h: Minor changes to algorithm for model type B. * R/initializeFRAN.r, R/maxlikec.r, R/phase3.r, R/simstats0c.r src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h, src/model/ml/Chain.cpp, src/model/ml/Chain.h, src/model/ml/MiniStep.cpp, src/model/ml/MiniStep.h, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h, src/siena07models.cpp, src/siena07setup.cpp, src/siena07setup.h, src/siena07utilities.cpp, src/siena07utilities.h: ML work in progress. Includes corrections for bipartites, new parameter to return the chains, construction of initial chain corrected with constraints between networks, variable permutation lengths * R/bayes.r, src/model/effects/StructuralRateEffect.cpp, src/model/effects/StructuralRateEffect.h, src/model/EpochSimulation.cpp, src/model/EpochSimulation.h, src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/siena07internals.cpp, src/siena07models.cpp, inst/examples/algorithms.r, int/examples/runalg.r: Bayes, algorithms (still incomplete) * R/effectsMethods: fix bug which prevented time dummies showing on a print of the effects object. * R/phase3.r: minor change to code controlling iterations for multiple processors. Stop allocating unnecessary arrays. * R/siena07.r, R/siena01.r, R/sienatest.r, src/model/effects/OutTruncEffect.cpp: reformatting only * (RSienaTest only) src/model/effects/EffectFactory.cpp, src/model/effects/AllEffects.h, src/model/effects/generic/GwespFunction.cpp, src/model/effects/generic/GwespFunction.h: replaced GwespEffects by a generic one using a GwespFunction. * doc/RSiena_Manual.tex rename from doc/s_man400.tex *doc/RSienaDeveloper.tex: added C++ standards, notes about environment variables for use when checking packages. 2011-05-29 R-forge revision 152 RSienaTest only * R/sienaGOF.r: Fixed a few bugs, doc/s_400.tex: updated the script 2011-05-27 R-forge revision 151 * R/observationErrors.r: added various traps for vectors of length 1, removed spaces from function comments (RSienaTest was missed in revision 150). * R/effects.r: remove final few unused variables. 2011-05-27 R-forge revision 150 * cleanup.win, cleanup, src/Makevars, src/Makevars.win: changes for building and cleaning directories. * src/siena07utilities.cpp, src/sienaModels.cpp, src/models/ml/chain.cpp: remove compiler warning about set but unused variables * R/phase3.r, R/print01Report, R/siena08.r, R/sienaDataCreate.r, R/sienaDataCreateFromSession.r: remove partial argument matches * R/bayes.r, R/effects.r, R/initializeFRAN.r, R/maxlike.r, R/maxlikecalc.r, R/observationErrors.r, R/phase1.r, R/phase2.r, R/print01Report.r, R/printDataReport.r, R/printInitialDescription.r, R/robmon.r, R/RSienaRDocumentation.r, R/siena01.r, R/siena07.r, R/sienaDataCreate.r, R/sienaDataCrateFromSession.r, R/Sienatest.r, R/simstatsc.r: remove codetools warnings about variables set but unused * R/observationErrors.r: added various traps for vectors of length 1, removed spaces from function comments. 2011-05-26 R-forge revision 149 RSienaTest only * R/sienaGOF.R, NAMESPACE, doc/RSiena.bib, doc/s_man400.tex: Minor debugs for multi-wave data in sienaGOF, added summary.sienaGOF functionality, added a model selection script to the manual. 2011-05-25 R-forge revision 148 RSienaTest only * man/sienaGOF.Rd, man/sienaGOFsupplement.Rd, R/sienaGOF.R, NAMESPACE, src/initializeFRAN.r: overhaul of sienaGOF. 2011-05-19 R-forge revision 147 RSienaTest only * doc/s_man400.tex, doc/Siena_algorithms4.tex: updated documentation 2011-05-16 R-forge revision 146 * src/Makevars.win: alter linking to reduce command line length * doc/s_man400.tex: add tex code to reduce size of pdf, many updates * doc/RSiena.bib, doc/simstatsc.tex, doc/RSienaDeveloper.tex: updated documentation for symmetric networks and other minor changes. * R/siena08.r: formatting changes only * R/sienaDataCreate.r: set diagonals to NA for sparse matrices when calculating degree and setting attributes * R/sienaDataCreateFromSession.r: if using read.pajek to read a non-directed network duplicate the ties in the edgelist. 2011-04-20 R-forge revision 145 * src/model/effects/outTruncEffect.cpp: reformating 2011-04-19 R-forge revision 144 * data/allEffects.csv, src/model/effects/AllEffects.h, src/model/effects/EffectFactory.cpp, src/model/effects/OutTruncEffect.h, src/model/effects/OutTruncEffect.spp: new effect OutTruncEffect * R/siena08.r, R/observationsErrors.r, man/print.sienaMeta.Rd, man/siena08.Rd: added ML method to siena08, enhanced plots. * doc/RSiena.bib, doc/Siena_algorithms4.tex, doc/s_man400.tex, doc/RscriptDataFormat.R, doc/RscriptSienaBehaviour.R, doc/RscriptSienaRunModel.R, doc/RscripSienaVariableFormat.R: major edits, scripts now included in latex. * man/includeEffects.Rd: added another example * man/s50.Rd, man/s501.Rd, man/s502.Rd, man/s503.Rd, man/s50a.Rd: more helpful information. * R/initializeFRAN.r, R/maxlikec.r, man/summary.iwlsm.Rd: added eolstyle property. 2011-03-13 R-forge revision 143 RSienaTest only * data/allEffects.csv: Modified default parm for Gwesp effects * src/model/effects/GwespEffect.h added as superclass to all Gwesp effects * src/model/effects/GwespEffect.cpp Now implements GwespAbstract class * src/model/effects/GwespBFEffect.h Now implements GwespAbstract class * src/model/effects/GwespFBEffect.h Now implements GwespAbstract class * src/model/effects/GwespBBEffect.h Now implements GwespAbstract class * src/model/effects/GwespFFEffect.h Now implements GwespAbstract class * src/model/effects/GwespRREffect.h Now implements GwespAbstract class * src/model/effects/GwespBFEffect.cpp Now implements GwespAbstract class * src/model/effects/GwespFBEffect.cpp Now implements GwespAbstract class * src/model/effects/GwespBBEffect.cpp Now implements GwespAbstract class * src/model/effects/GwespFFEffect.cpp Now implements GwespAbstract class * src/model/effects/GwespRREffect.cpp Now implements GwespAbstract class * man/sienaGOF.Rd: Added primitive snow cluster support, option for robust covariance estimation * R/sienaGOF.r: Added primitive snow cluster support, option for robust covariance estimation 2011-03-06 R-forge revision 142 RSienaTest only * R/sienaGOF: fixed a plotting issue with missing data * src/model/effects/EffectFactory.cpp: added GWESP terms * src/model/effects/AllEffects.h: added GWESP terms * src/model/effects/EffectFactory.cpp: added GWESP terms * data/allEffects.csv: added GWESP terms * man/sienaGOF.Rd: Incorporated GWESP into the model * src/model/effects/GwespBFEffect.h added * src/model/effects/GwespFBEffect.h added * src/model/effects/GwespBBEffect.h added * src/model/effects/GwespFFEffect.h added * src/model/effects/GwespRREffect.h added * src/model/effects/GwespBFEffect.cpp added * src/model/effects/GwespFBEffect.cpp added * src/model/effects/GwespBBEffect.cpp added * src/model/effects/GwespFFEffect.cpp added * src/model/effects/GwespRREffect.cpp added * NOTE: the 'parm' column needs an integer, and I got around this by using it as a "hundredths" interpretation so that I x 100 when it reaches the effect object's constructor. It would be nice to have it imported in "createEffect" as a double. 2011-02-26 R-forge revision 141 * man/RSiena-package.Rd, DESCRIPTION: fix typos, one making check fail! 2011-02-24 R-forge revision 140 * R/sienaGOF.r: Added cumulative tests, simulated image function imageGOF, and cleaned up the code to reflect RSiena coding standards. Added image plot to plot.sienaGOF. * man/sienaGOF.Rd: Changes to reflect the above 2011-02-23 R-forge revision 139 * src/model/ml/MLsimulation.cpp, src/model/variables/NetworkVariable.cpp: ML for bipartite networks. 2011-02-22 R-forge revision 138 Change version number on RSiena to 137 2011-02-22 R-forge revision 137 * Changes to RSienaTest Only * DESCRIPTION: removed dependency on snopgof (for now!) and add -ed dependency for MASS, sna, vioplot for sienaGOF. * R/sienaTimeTest.r: added functionality for behavioral dummies but they will not work until behavioral interaction effects are supported. * R/sienaGOF.r: removed dependency on snopgof (runs standalone) and a number of smaller features like being able to run a joint test across all waves or break them out, having control over the centrality measure (mean, median, etc.), and not requiring that the auxiliary statistics are non-collinear (this is where MASS's ginv comes in). I also moved the relevant functionality from snopgof directly into the code. * man/sienaGOF.Rd: Changes to reflect the above 2011-02-21 R-forge revision 136 * R/initializeFRAN.r: fix bug in bipartite networks: diagonals were being zeroed. * R/siena01.r: correct test for maximum degree in display 2011-02-05 R-forge revision 135 * R/siena08.r: fix bug in summary method. Just layout, caused crash. 2011-02-05 R-forge revision 134 * R/phase2.r, R/siena08.r, man/siena08.Rd, man/print.sienaMeta.Rd: changes as in revision 133 copied to RSiena. * R/siena08.r, man/siena08.Rd, man/print.sienaMeta.Rd: changes to format of new code, reinstate object in summary method help page. * R/iwlsm.r, man/iwlsm.Rd: correct calculation of variance estimate * R/sienaDataCreate.r: minor amendments * R/sienaDataCreateFromSession.r: message from siena01Gui if changing dyadic covariates do not match number of observations. * R/sienaTimeTest.r: message that timedummies are not implemented for structural rate effects. * src/model/ml/MLSimulation.cpp, src/model/ml/NetworkChange.cpp, src/model/variables/NetworkVariable.cpp: changes for ML, should now run OK for bipartite networks. * src/model/variables/DependentVariable.cpp: added some error trapping. * tests/parallel.R, tests/parallel.Rout.save: removed multiple processes from tests as they were failing on R-forge. 2011-01-25 R-forge revision 133 (RSienaTest only) * R/phase2.r: comment out two test lines causing a crash of the ML estimation when model specifications get so large that subphases exceed 1000 iterations. * R/siena08.r: debugging and adding of functionalities to the meta- analysis. * man/siena08.Rd: explain new features in help function * man/print.sienaMeta.Rd: explain new features in help function 2011-01-17 R-forge revision 132 * Changing revision 131 to conform with coding standards 2011-01-17 R-forge revision 131 * Changes to RSienaTest Only * R/gof.r: Added. Contains the function sienaGof and other functions for performing basic goodness of fit tests from arbitrary functions. This function requires the snopgof package to perform the Monte Carlo test. There are also plotting facilities. * man/gof.rd: Added. Contains basics of how to use sienaGof * NAMESPACE: Added sienaGof functions to namespace for proper operation * DESCRIPTION: Added snopgof to the recommended packages. 2011-01-16 R-forge revision 130 * R/phase3.r: correct number of iterations in field Phase3nits * R/robmon.r, R/siena07.r, man/siena07.Rd: make initC=TRUE the default * src/model/variables/NetworkVariable.cpp: fix array bound error in initialisation for bipartite networks and reverse order of tests for symmetric model types to avoid problem with bipartite no change. * src/model/effects/generic/GenericNetworkEffect.cpp: edits to comments * src.model/tables/MixedConfigurationTable.cpp, MixedConfigurationTable.h: make size of table big enough for any of the senders or receivers. * doc/s_man400.tex, doc/RSiena.bib: various edits. * tests/parallel.R, test/parallel.Rout.save: added test with bipartite network and multiple processes. 2011-01-08 R-forge revision 129 * R/sienaTimeTest.r, doc/sienaTimeFix.tex: added interactions types for requested effect in call to includeInteraction. * R/siena07.r: suppress warning message when loading snow package. (Ineffective in sub processes) 2010-12-02 R-forge revision 128 * data/allEffects.csv: removed to effect from bipartite bipartite, added altDist2W and simDist2W to group covarNetNetObjective. * R/effects.r: fixed bug meaning covNetNet effect was not added for behavior variables. Altered code for covarNetNetEff to cope with new effects. * R/effectsMethods.r: now interaction names may be expanded even in the absence of time dummies. * R/initializeFRAN.r: make targets2 for maximum likelihood a matrix of the correct size, containing zeros. * R/initializeFRAN.r, R/sienaModelCreate, man/sienaModelCreate.Rd: Add multiplication factor, altered default ML probabiltities * R/sienaEffects.r: added period and group to setEffect so can set initial values on basic rates. * src/model/effects/CovariateDistance2AlterEffect.cpp: fixed a bug in calculation with parameter set to 2. * src/model/effects/EffectFactory.cpp, src/model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h src/model/effects/generic/CovariateDistance2NetworkFunction.cpp src/model/effects/generic/CovariateDistance2NetworkFunction.h src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction. cpp src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.h src/model/effects/generic/CovariateNetworkAlterFunction.cpp src/model/effects/generic/CovariateNetworkAlterFunction.h src/model/effects/generic/MixedNetworkAlterFunction.cpp src/model/effects/generic/MixedNetworkAlterFunction.h src/model/effects/generic/MixedTwoPathFunction.cpp src/model/effects/generic/MixedTwoPathFunction.h src/model/effects/generic/NetworkAlterFunction.h src/model/tables/MixedConfigurationTable.cpp src/model/tables/MixedConfigurationTable.h src/model/tables/MixedEgocentricConfigurationTable.cpp src/model/tables/MixedEgocentricConfigurationTable.h src/model/tables/MixedTwoPathTable.cpp src/model/tables/MixedTwoPathTable.h src/model/tables/TwoNetworkCache.cpp src/model/tables/TwoNetworkCache.h src/model/tables/Cache.cpp src/model/tables/Cache.h added new effects: to, altDist2W, simDist2W. Altered altDist2 and simDist2 to be generic effects which use same functions as altDist2W, simDist2W. New two-network cache with mixed-two-path table. * src/model/ml/MLSimulation.cpp: changes to ML routines * src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h: added calculation loop for rate effects depending on behavior variables, and stored the product term for the scores. Also stored product term for model type B scores. * src/model/variables/NetworkVariable.cpp: fixed bug in calculation of symmetric model type BFORCE scores. * R/sienaTimeTest.r: added code for finitedifferences and ML fits. * doc/sienaTimeFixDoc.tex: added to RSienaTest 2010-11-25 R-forge revision 127 * man/s_man400.tex: updated examples of sienaTimeTest. * R/initializeFRAN.r: (RSiena only): forgotten new file 2010-11-25 R-forge revision 126 * DESCRIPTION: new main version number for RSiena, 1.0.12 * R/sienaTimeTest.r, R/effects.r, R/sienaeffects.r, R/effectsMethods.r, man/sienaTimeTest.Rd, plot.sienaTimeTest.Rd, man/print.sienaEffects.Rd, man/includeInteraction.Rd: amendment and extension of sienaTimeTest and sienaTimeFix. includeInteraction now adds rows if necessary and has parameter to suppress printing. Time dummy rows can optionally be added to print and summary of sienaEffects object. * src/siena07internals.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h: return values for rates for multiple dependent variables. * doc/RSiena.bib: minor updates * man/sienaNet.Rd, getEffects.Rd, siena07.Rd, sienaDataCreate.Rd, doc/RSIENAspec.tex: documentation * tests/parallel.Rout.save: minor changes for compatibility * R/terminateFRAN.r, R/simstatsc.r, R/maxlikec.r: new function terminateFRAN in separate file. * R/Sienatest.r: added traps for matrix inversion failure * R/sienaDataCreate.r, R/initializeFRAN: minor amendments * R/phase1.r, R/phase3.r, R/maxlikec.c: return contributions to dfra for maximum likelihood and finite differences by wave 2010-11-06 R-forge revision 125 * data/allEffects.csv, src/model/effects/InStructuralEquivalenceEffect.cpp, src/model/effects/InStructuralEquivalenceEffect.h, src/model/effects/EffectFactory.cpp,src/model/effects/AllEffects.h, src/data/OneModeNetworkLongitudinalData.cpp, src/data/OneModeNetworkLongitudinalData.h, R/sienadataCreate.r, R/initializeFRAN.r, src/siena07internals.cpp: new in-structural equivalence effect (RSienaTest only) * data/allEffects.csv, R/sienaModelCreate.r, R/initializeFRAN.r, R/sienaprint.r, man/sienaModelCreate.Rd, R/printDataReport.r, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/model/variables/BehaviorVariable.cpp, src/model/EpochSimulation.cpp, src/model/Model.h, doc/simstats0c.tex: symmetric models (RSienaTest only) * R/robmon.r, man/siena01Gui.Rd : minor textual corrections * R/sienaDataCreate.r: sorted networks before behavior variables * doc/RSienaDeveloper.tex, doc/Siena_algorithms4.tex: documentation (RSienaTest only) * R/phase1.r: do finite difference calculations for fixed parameters during phase 3. * R/print07Report.r, R/phase3.r: fix typos in printing of report. * R/sienaTimeTest.r: fix bugs with missing interaction effects, multiple dependent networks and multiple groups. * src/model/effects/DenseTriadsEffect.cpp: add parentheses to remove a compiler warning. * src/model/ml/MLSimulation.cpp: commented a problem (RSienaTest only) * src/siena07models.cpp: return chains as dataframe not list. (RSienaTest only) * cleanup.win: remove siena01.exe part 2010-10-22 R-forge revision 124 * R/sienaTimeTest.r: fix bug causing error when only one effect (added multiple drop=FALSE) * src/win32/(all), configure.win, R/siena01.r: removed siena.exe, install function now gives a message. * doc/classdesign.tex (RSienaTest only) updated documentation 2010-10-13 R-forge revision 123 RSienaTest only * doc/RSienaDeveloper.tex: added details about change logs etc 2010-10-09 R-forge revision 122 * src/siena07models.cpp: corrected loop for return of MH acceptances and rejections. (RSienaTest only) * doc/RSienaDeveloper.tex, doc/RSiena.bib, doc/s_man400.tex, doc/siena_algorithms4.tex, doc/simstats0c.tex: documentation updates. (RSienaTest only) * R/effects.r: fixed bug in starting values for behavior variables when all changes were in one direction (in revision 120 for RSienaTest) * src/data/various, src/model/ml: ML code (RSienaTest only) * src/model/effects/AltersCovariateAverageEffect.cpp, CovariateDistance2AlterEffect.cpp: implemented new parameter. * data/allEffects.csv: removed effects added in error (revision 120) * data/allEffects.csv: added dyadic/ego to various effects to allow inclusion of interaction effects. 2010-10-08 R-forge revision 121 RSienaTest only * src/model/ml/chain.cpp: commented out a rogue "Rprintf" command 2010-09-20 R-forge revision 120 * data/allEffects.csv: added alter average distance 2 effects for behavior variables * R/sienaDataCreate.r: fixed bug in names of dyadic covariates when converted to varying covariates for groups * R/effects.r: fixed bug in starting values for behavior variables when all changes were in one direction (missed this in RSiena) * R/phase3.r: minor correction to text in siena07 report. * R/print01Report: minor correction to text. * R/simstatsc.r (RSiena only): make sure types are available to multiple processes. 2010-08-21 R-forge revision 119 * R/sienaDataCreate.r: fix function comments so documentation runs. * R/RSienaRDocumentation.r: minor source format changes. 2010-08-20 R-forge revision 118 RSienaTest only * src/siena07internals.cpp, src/siena07models.cpp, src/siena07setup.cpp, src/siena07utilities.cpp, src/siena07internals.h, src/siena07models.h, src/siena07setup.h, src/siena07utilities.h: set eol style * doc/config.dox: added doxygen configuration file 2010-08-20 R-forge revision 117 RSienaTest only * doc/RSiena.bib, s_man400.tex, Siena_algorithms4.tex, simstats0c.tex: documentation updates * inst/examples/algorithms.r: improvements! * R/initialiseFRAN.r, R/simstatsc.r: removed initialise function to separate source file * src/siena07.cpp deleted * src/siena07internals.cpp, src/siena07models.cpp, src/siena07setup.cpp, src/siena07utilities.cpp, src/siena07internals.h, src/siena07models.h, src/siena07setup.h, src/siena07utilities.h: replacements for siena07.cpp * R/bayes.r, R/maxlikec.r, R/phase1.r, R/robmon.r, R/siena07.r, src/many, man/siena07.Rd : ML changes (in progress) * src/model/variables/DependentVariable.cpp, src/model/variables/NetworkVariable.cpp, src/model/variables/DependentVariable.h, src/model/variables/NetworkVariable.h: symmetric networks (in progress) 2010-08-20 R-forge revision 116 RSiena only * R/simstatsc.r: forgotten part of previous change to print. 2010-08-20 R-forge revision 115 * R/siena08.r: correct p-values on report. * R/sienaprint.r: correct print layout in special cases * R/sienaDataCreate.r: changes for ML (in progress) 2010-07-19 R-forge revision 114 * R/print01Report.r: fix bug in names of multiple behavior variables on siena01 report. * R/print07Report.r, R/sienaprint.r: remove references to data in printing, as object gets too large. 2010-07-10 R-forge revision 113 * src/model/variables/NetworkVariable.cpp: bug fix for endowment effects, since a recent change * src/model/ml/NetworkChange: bug fix, could not return bipartite simulations. * src/siena07.cpp, src/model/Model.h, src/model/Model.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/MLSimulation.h, R/simstatsc.r, R/sienaDataCreate.r, R/sienaModelCreate.r: adaptive permutation length and probabilities for missings for ML (in progress still!) * src/model/ml/Chain.cpp: removed structural links from initial chain (ML) 2010-07-04 R-forge revision 112 * R/sienautils.r: fix bug with groups and constant dyadic covariates with only 2 periods. (Introduced in revision 109!) 2010-07-03 R-forge revision 111 * src/siena07.cpp, src/model/ml/Chain.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/Option.cpp, src/model/ml/MLSimulation.h, src/model/ml/Option.h, R/phase1.r, R/sienaModelCreate.r, R/simstatsc.r, R/maxlike.r, man/sienaModelCreate.Rd: ML changes * src/model/variables/NetworkVariable.cpp, doc/simstats0c.tex (RSienaTest only): added option of no change for bipartite networks. * doc/RSienaDeveloper.tex (RSienaTest only): added some details about C++ and Doxygen. 2010-06-25 R-forge revision 110 * man/coDyadCovar.Rd, man/varDyadCovar.Rd: added sparse parameter to documentation. 2010-06-25 R-forge revision 109 * data/allEffects.csv, R/effects.r: removed inappropriate dyadic covariate effects for bipartite networks. * src/model/variables/NetworkVariable.cpp: correct distance accumulation for symmetric networks with conditional estimation * R/sienaModelCreate.r: add default variable for cond=TRUE * R/sienaprint.r: add Score test results to summary.sienaFit * R/simstatsc.r: remove data object from stored f again (still on z) * src/data/ChangingDyadicCovariate.cpp, src/data/ChangingDyadicCovariate.h, src/model/effects/DyadicCovariateDependentNetworkEffect.cpp, src/model/effects/DyadicCovariateDependentNetworkEffect.h src/model/effects/DyadicCovariateMainEffect.cpp, src/model/effects/DyadicCovariateReciprocityEffect.cpp, src/model/effects/EffectFactory.cpp, src/model/effects/NetworkEffect.cpp, R/sienaDataCreate.r, R/sienaDataCreateFromSession, R/print01Report.r, R/sienautils.r, R/simstatsc.r, man/coDyadCovar.Rd, man/varDyadCovar.Rd: dyadic covariates now deal correctly with missing values and can be sparse matrices. 2010-06-21 R-forge revision 108 * doc/RSienaDeveloper.tex: added note about Rd2dvi. * data/allEffects.csv, R/effects.r, R/sienaDataCreate.r, src/data/BehaviorLongitudinalData.cpp, BehaviorLongitudinalData.h, src/data/Covariate.cpp, src/data/Covariate.h, src/model/effects/AllEffects.h, src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h, src/model/effects/CovariateAndNetworkBehaviorEffect.cpp, src/model/effects/CovariateAndNetworkBehaviorEffect.h, src/model/effects/CovariateDependentNetworkEffect.cpp, src/model/effects/CovariateDependentNetworkEffect.h, src/model/effects/CovariateDistance2AlterEffect.cpp, src/model/effects/CovariateDistance2AlterEffect.h, src/model/effects/CovariateDistance2NetworkEffect.cpp, src/model/effects/CovariateDistance2NetworkEffect.h, src/model/effects/CovariateDistance2SimilarityEffect.cpp, src/model/effects/CovariateDistance2SimilarityEffect.h, src/model/effects/EffectFactory.cpp, src/model/variables/BehaviorVariable.cpp, src/model/variables/BehaviorVariable.h, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/siena07.cpp, tests/parallel.R, tests/parallel.Rout.save : (RSiena only) covariate-at-distance-2 effects * man/coDyadCovar.Rd, man/siena01Gui.Rd, man/sienaDataCreate.Rd, man/sienaDataCreateFromSession.Rd, man/sienaNet.Rd, man/sienaNodeSet.Rd, man/sienaTimeTest.Rd, man/simstats0c.Rd, man/varDyadCovar.Rd: minor edits * R/effectsDocumentation.r: bug caused by insertion of timeDummy column * R/effectsMethods.r, man/print.sienaEffects.Rd: more fixes for empty cases, new argument to allow printing of all lines. * man/siena07.Rd, sienaModelCreate.Rd: major edits. * R/bayes.r: defer the plots till later * R/globals.r (RSiena only): allow use of Report with no file, suppress everything with silent. * R/maxlikec.r, R/phase1.r, phase2.r, phase3.r, src/model/EpochSimulation.cpp, src/model/EpochSimulation.h, src/model/ml/BehaviorChange.cpp, src/model/ml/BehaviorChange.h, src/model/ml/Chain.cpp, src/model/ml/Chain.h, src/model/ml/MiniStep.cpp, src/model/ml/MiniStep.h, src/model/MLSimulation.cpp, src/model/ml/NetworkChange.cpp, src/model/ml/NetworkChange.h, src/model/Model.cpp, src/model/Model.h, src/model/variables/BehaviorVariable.cpp, src/model/variables/BehaviorVariable.h, src/model/variables/DependentVariable.h, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h, src/siena07.cpp: (RSiena only): minor changes for ML or algorithms * src/model/EpochSimulation.cpp: (RSiena only) corrected error message if unlikely to terminate epoch. * inst/doc/effects.pdf: updated list, after correcting bug * R/print01Report.r: fix bug with more than 2 groups * R/printInitialDescription.r: fix bug with 8 waves * R/sienaDataCreate.r: make covariate-at-dist-2 effects work for groups and for bipartites, multiple networks, behavior variables with missing values... * R/simstatsc.r: fix bug in naming user defined dyadic interactions. * R/sienaTimeTest.r: (RSiena only) make RateX effects work with varying covariates too. 2010-06-21 R-forge revision 107 RSienaTest only * NAMESPACE, R/sienaTimeTest.r, man/includeTimeDummy.Rd, man/sienaTimeTest.Rd, man/plot.sienaTimeTest.Rd, man/setEffect.Rd, CHANGELOG, doc/s_man400.tex : Reinstated includeTimeDummy. 2010-06-18 R-forge revision 106 * DESCRIPTION: new version numbers: added 105 to end. 2010-06-18 R-forge revision 105 * R/siena01.r: bug fix: call edit.data.frame directly to avoid the edit method of sienaEffects objects. 2010-06-10 R-forge revision 104 RSiena * doc/s_man400.tex: Updated RSiena manual script as per Tom's request. 2010-06-08 R-forge revision 103 RSienaTest only * man/sienaTimeTest.Rd, man/setEffect.Rd, CHANGELOG, doc/s_man400.tex: get through checks 2010-06-08 R-forge revision 102 RSienaTest only * NAMESPACE, R/sienaTimeTest.r, man/includeTimeDummy.Rd, man/sienaTimeTest.Rd, man/plot.sienaTimeTest.Rd, man/setEffect.Rd, CHANGELOG, doc/s_man400.tex: Deleted includeTimeDummy. 2010-06-08 R-forge revision 101 RSienaTest only * R/sienaTimeTest.r: added changing covariate functionality to sienaTimeFix for RateX effects. 2010-06-08 R-forge revision 100 * Changelog, doc/s_man400.tex: fixed incorrect revision numbers. 2010-06-08 R-forge revision 99 * R/simstatsc.r: fixed bug that bipartite networks not allowed 'loops' 2010-06-08 R-forge revision 98 * R/simstatsc.r: constant dyadic covariates with missing values should now work correctly, varying ones do not fail, but the centering and filling in of missing values for these is still to be sorted out. Also treatment of bipartite nets with composition change has been corrected. (Previously missings were not processed correctly if a sparse-matrix format network (even after the previous change!) and composition change was ignored for all bipartite networks.) * doc/RSiena.bib: additions. 2010-06-04 R-forge revision 97 * NAMESPACE: added forgotten includeTimeDummy 2010-06-04 R-forge revision 96 (RSiena mainly) * R/sienaTimeTest.r, R/sienaeffects.r, man/sienaTimeTest.rd, man/includeTimeDummy.rd, man/includeEffects.Rd, man/setEffects.Rd, man/plot.sienaTimeTest.rd, man/inlcudeInteraction.Rd : as for revisions 85-89, 93 for RSienaTest * R/effects.r: bug fixes as in revision 92 * R/effectsMethods.r: bug fixes as in revision 93 * R/sienaPrint.r: bug fixes as in revision 93 * R/simstatsc.r: bug fixes as in revision 93 2010-06-04 R-forge revision 95 * .Rbuildignore: added Makefile.profile to suppress warning * R/phase2.r: removed stray RSiena::: * doc/s_man400.tex: updated changelog 2010-06-04 R-forge revision 94 * src/Makefile.win replaced by src/Makevars.win. Amended src/Makevars. 2010-06-04 R-forge revision 93 (RSienaTest only) * R/effectsMethods.r: fix to print.sienaEffects for empty object * R/globals.r: make silent parameter suppress all screen output * R/maxlikec.r, R/phase1.r, src/model/ml/many, doc/Siena_algorithms4.tex : maximum likelihood * inst/examples/algorithms.r, inst/examples/runalg.r, R/phase2.r, R/phase3.r, R/simstatsc.r, src/model/EpochSimulation.cpp, src/model/EpochSimulation.h, src/model/Model.cpp, src/model/Model.h, src/model/ml/many, doc/RSienaDeveloper.tex: algorithms * R/sienaDataCreate.r: calculate similarity mean for alters, reverted revision 88 * R/sienaeffects.r, man/includeEffects.Rd, man/includeInteraction.Rd, man/setEffect.Rd: reverted revision 88, added timedummy to setEffect, allow includeInteraction to set include to FALSE as well as TRUE. * R/sienaprint.r: fixed bug if interactions or time dummies present: use requested effects not effects object. Also fix for added lines in print.sienaFit, which were wrong if there were a large number of effects. * R/sienaTimeTest.r: added include parameter to includeTimeDummy, and print out changed lines. Changed header comment. * R/simstatsc.r: error message if use composition change with bipartite networks (temporary, till I fix this!). Added similarity mean for alters. Fix to treatment of missings in sparse bipartite networks. * src/model/EpochSimulation.cpp: fix to error message if unlikely to terminate the epoch. * tests/parallel.R, parallel.Rout.save: change in line number of effect * man/plot.sienaTimeTest.Rd, man/sienaTimeTest.Rd, man/includeTimeDummy.Rd: split the help file into three. 2010-06-04 R-forge revision 92 (RSienaTest only) * data/allEffects.csv, R/effects.r, src/siena07.cpp, src/model/effects/allEffects.h, src/model/effects/EffectFactory.cpp, src/model/effects/BehaviorEffect.cpp, src/model/effects/BehaviorEffect.h, src/model/effects/AltersCovariateAverageEffect.cpp, src/model/effects/AltersCovariateAverageEffect.h, src/model/effects/CovariateandNetworkBehaviorEffect.cpp, src/model/effects/CovariateandNetworkBehaviorEffect.h, src/model/effects/CovariateDependentNetworkEffect.cpp, src/model/effects/CovariateDependentNetworkEffect.h, src/model/effects/CovariateDistance2AlterEffect.h, src/model/effects/CovariateDistance2AlterEffect.cpp, src/model/effects/CovariateDistance2AlterEffect.h, src/model/effects/CovariateDistance2NetworkEffect.cpp, src/model/effects/CovariateDistance2NetworkEffect.h, src/model/effects/CovariateDistance2SimilarityEffect.cpp, src/model/effects/CovariateDistance2SimilarityEffect.h, src/data/Covariate.cpp, src/data/Covariate.h, src/data/BehaviorLongitudinalData.cpp, src/data/BehaviorLongitudinalData.h, src/model/variables/BehaviorVariable.cpp, src/model/variables/BehaviorVariable.h, src/model/variables/DependentVariable.h, src/model/variables/NetworkVariable.cpp, src/model/variables/NetworkVariable.h: new average alter effects * R/effects.r: fixed bugs for more than two groups and no effects 2010-05-30 R-forge revision 91 (RSienaTest only) * Changelog: Updated changelog! 2010-05-29 R-forge revision 90 (RSienaTest only) * man/s_man400.tex, RSiena.bib. Added Tom's changes to manual and sorted out corrupted characters from previous update. 2010-05-29 R-forge revision 89 (RSienaTest only) * R/sienaTimeTest.r, R/sienaeffects.r, man/sienaTimeTest.Rd, man/includeEffects.Rd, doc/s_man400.tex, RSiena.bib: new option to control orthogonalization in sienaTimeTest, add parameters to includeEffects, documentation update. 2010-05-28 R-forge revision 88 (RSienaTest only) * R/sienaTimeTest.r, sienaDataCreate.r, simstatsc.r, man/sienaTimeTest.Rd: TimeDummies for RateX effects (constant covariate only!). 2010-05-27 R-forge revision 87 (RSienaTest only) * R/sienaTimeTest.r: fix to plot.sienaTimeTest 2010-05-23 R-forge revision 86 (RSienaTest only) * R/sienaTimeTest.r, man/sienaTimeTest.Rd, NAMESPACE: new function: includeTimeDummy, fix naming in plot.sienaTimeTest 2010-05-22 R-forge revision 85 (RSienaTest only) * R/sienaTimeTest.r: fix for unconditional estimation 2010-04-28 R-forge revision 84 * src/many: removed and adjusted other header files * man/iwlms.Rd: (RSienaTest only) eol-style property set. * doc/RSienaDeveloper.tex: notes about headers and R/C interface. (RSienatest only) 2010-04-25 R-forge revision 83 * R/effectsMethods.r: fix bug introduced trying to pass checks 2010-04-24 R-forge revision 82 * R/effectsMethods.r, man/print.sienaEffects.Rd, man/edit.sienaEffects.Rd, NAMESPACE: print, summary and edit methods for sienaEffects objects. 2010-04-24 R-forge revision 81 * src/model/effects/structuralRateEffect.cpp: fix crash caused by size of effect table for bipartite networks. * R/bayes.r, src/siena07.cpp, src/model/ml/MLSimulation.cpp, src/model/ml/MLsimulation.h, src/model/model.cpp, src/model/model.h, src/model/variables/DependentVariable.cpp, src/model/variables/DependentVariable.h, src/utils/Random.cpp, src/utils/Random.h: New function bayes and supporting methods. * R/phase3.r, R/simstatsc.r: changes for ML * R/simstatscr, src/siena07.cpp, src/model/EpochSimulation.cpp, src/model/variables/BehaviorVariable.cpp, src/model/variables/NetworkVariable.cpp src/model/EpochSimulation.h: create and return chain after MOM simulation * src/model/EpochSimulation.cpp: added trap to stop conditional estimation after 1000000 steps. * src/model/ml/chains.cpp, src/model/ml/chains.h, src/model/ml/MiniStep.cpp, src/model/ml/MiniStep.h, src/siena07.cpp: print utilities for chains. create an R dataframe from a ministep. Print list of CCP's * src/model/ml/MLSimulation.cpp, src/model/model/cpp, src/model/model.h: changes for ML * src/model/variables/BehaviorVariable.cpp: fixed ambiguous call to abs: need cstdlib as well as cmath. Possibly to do with NO_C_HEADERS. 2010-04-14 R-forge revision 80 * R/sienaTimeTest.r, man/sienaTimeTest.Rd. corrected default plevels for plot * RSienaTest only NAMESPACE: corrected package name 2010-04-13 R-forge revision 79 * R/sienaTimeTest.r, man/sienaTimeTest.Rd, data/allEffects.csv, R/simstatsc.r, man/allEffects.Rd, man/getEffects.Rd: new function sienaTimeTest. 2010-04-12 R-forge revision 78 * R/sienaeffects.r, man/includeEffects.Rd, man/includeInteraction.Rd, man/setEffects.Rd: allow character or non character input of effect names. * R/siena01.r: include effectNumber, effect1, effect2, effect3 in display of included effects. * R/print01Report.r: ignore diagonal missing values in total count 2010-04-12 R-forge revision 77 (RSiena only) * inst/examples/many, man/coDyadCovar.Rd: added new line to end. * data/allEffects.csv: remove trailing blanks * man/includeEffects.Rd, man/siena07.Rd, R/siena07.r, R/sienaDataCreateFromSession.r: minor formatting * R/sienaModelCreate.R, man/sienaModelCreate.Rd: changes to storage of function to be used, additions of ML parameters. * R/globals.r: changed matrix print to stop using scientific notation * R/phase1.r: changed dfra to use for loops rather than apply's to save memory * R/maxlike.r, phase1.r, phase2.r, phase3.r, robmon.r: new function makeZsmall, minor changes for maxlike. * R/print01Report.r: fix bug which did not find whether symmetric correctly. * R/printInitialDescription.r: fix bug to printout of average degrees. * R/siena01.r: fix bug: the save function did not keep the model options * R/sienaDataCreate.r: changes to attributes concerning missing values. Remove warning in checkConstraints with bipartite networks. * R/sienaPrint.r: fix to text re rates for conditional simulation * R/simstatsc.r: changes for maxlike * tests/parallel.Rout.save: updated test output. 2010-04-12 R-forge revision 76 (RSienaTest only) * src/data/ActorSet.cpp, src/model/effects/AverageReciprocatedAlterEffect.cpp, src/model/effects/ReciprocalDegreeBehaviorEffect.cpp, src/model/variables/BehaviorVariable.cpp, src/model/variables/EffectValueTable.cpp, src/network/OneModeNetwork.cpp,src/utils/SqrtTable.cpp: changes for Solaris compiling. * inst/examples/many, man/coDyadCovar.Rd: added new line to end. * data/allEffects.csv: remove trailing blanks * doc/RSiena.bib, doc/s_man400.tex: changes to manual * man/includeEffects.Rd, man/siena07.Rd, R/siena07.r, R/sienaDataCreateFromSession.r: minor formatting * R/sienaModelCreate.R, man/sienaModelCreate.Rd: changes to storage of function to be used, additions of ML parameters. * R/globals.r: changed matrix print to stop using scientific notation * R/phase1.r: changed dfra to use for loops rather than apply's to save memory * R/maxlike.r, phase1.r, phase2.r, phase3.r, robmon.r: new function makeZsmall, minor changes for maxlike. * R/iwlsm.r, maxlikecalc.r, siena08.r: added eolstyle native * R/print01Report.r: fix bug which did not find whether symmetric correctly. * R/printInitialDescription.r: fix bug to printout of average degrees. * R/siena01.r: fix bug: the save function did not keep the model options * R/sienaDataCreate.r: changes to attributes concerning missing values. Remove warning in checkConstraints with bipartite networks. * R/sienaPrint.r: fix to text re rates for conditional simulation * R/simstatsc.r: changes for maxlike, also changes to use of previous values * R/maxlikec.r: new function for maximum likelihood, corresponding to simstatsc.r * src/model/Model.cpp, Model.h, ml/MLSimulation.cpp, ml/MLSimulation.h, ml/NetworkChange.cpp, ml/NetworkChange.h, variables/DependentVariable.cpp, variables/DependentVariable.h, variables/NetworkVariable.cpp, variables/NetworkVariable.h, siena07.cpp: changes for max like. * tests/parallel.Rout.save: updated test output. * R/phase2.r: fixed bug, could not use multiple processors with only one effect 2010-03-31 R-forge revision 75 * R/getEffects.r: fix bug causing crash with Dyadic covariates and bipartite networks 2010-03-30 R-forge revision 74 (RSiena only) * R/print01Report.r: change to text about missing values * inst/doc/s_man400.pdf: updated manual 2010-03-30 R-forge revision 73 (RSienaTest only) * R/print01Report.r: change to text about missing values * doc/s_man400.tex: updated manual source * doc/RSienaDeveloper.tex: updated documentation * inst/doc/s_man400.pdf: updated manual 2010-03-30 R-forge revision 72 (RSienaTest only) * doc/RSiena.bib: added bibliography file 2010-03-27 R-forge revision 71 (RSienaTest only) (cf revision 68, 69, 70 for RSiena) * data/allEffects.csv, src/model/effects/EffectFactory.cpp: renamed 4-cycle shortname to cycle4. Needs to be a permissible R name. * DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.12 * NAMESPACE: removed addAttributes.default as does not exist * R/maxlike.r, phase2.r: altered comments * R/phase1.r (FiniteDifferences) ensure z$npos update is always a vector (a dimension could be lost). * R/simstatsc.r, R/phase3.r: move definition of ntim to phase3 * R/print01Report.r: some percentages had not been multiplied by 100. * R/printInitialDescription.r: another fix re crashing with one mode and bipartite networks together. * R/siena01.r: fix to carrying forward theta if abnormal termination * R/siena07.r: remove tk variables from return object * R/sienaDataCreateFromSession.r: fix to allow more than one value indicating missing for covariates etc. * R/sienaDataCreateFromSession.r: allow periods to be numbered other than from 1 in siena net input. * R/simstatsc.r: sped up carry forward for NA arcs in sparse input. Also new function to initialise. Some changes relevant for ML. * R/simstatsc.r (unpackBehavior) carry forward and back or use mode for missings * src/many changes for ML 2010-03-27 R-forge revision 70 (RSiena only) * R/simstatsc.r, R/phase3.r: move definition of ntim to phase3 * R/simstatsc.r (unpackBehavior) carry forward and back or use mode for missings * R/siena07.r: remove tk variables from return object * R/phase1.r (FiniteDifferences) ensure z$npos update is always a vector (a dimension could be lost). 2010-03-24 R-forge revision 69 (RSiena only) (cf revision 63, 67 for RSienaTest) * src/many: mostly incomplete, changes for ML. * R/simstatsc.r: sped up carry forward for NA arcs in sparse input. Also new function to initialise. Some changes relevant for ML. * R/print01Report.r: some percentages had not been multiplied by 100. * R/sienaDataCreateFromSession.r: fix to allow more than one value indicating missing for covariates etc. * data/allEffects.csv, src/model/effects/EffectFactory.cpp: renamed 4-cycle shortname to cycle4. Needs to be a permissible R name. * inst/examples/baerveldt3.csv, baerveldt4.csv: changed the changing covariates to constant as only 2 periods. * R/siena08.r, R/iwlsm.r, man/siena08.Rd, man/print.sienameta.Rd, man/iwlsm.Rd, summary.iwlsm.Rd: siena08 Meta analysis * R/robmon.r, R/sienaModelCreate.r, man/sienaModelCreate.Rd: remove the function from the model object. Use name instead so no need to load package on R startup with model object in .RData. * R/siena01.r: now uses sienaModelCreate rather than creating object itself. * R/siena07.r, R/phase1.r, R/phase2.r, R/phase3.r, R/robmon.r, R/simstatsc.r, R.sienaDataCreate.r, src/siena07.cpp, man/siena07.Rd: fixed rlecuyer random numbers and added facility to use multiple processors by wave. * R/globals.r, R/print01Report.r, R/siena07.r: Report function can now be used with optional output file * R/print01Report.r, R/sienaDataCreate.r, src/siena07.cpp: missing values in dyadic covariates (incomplete!) * R/siena01.r: fix to creation of model for unconditional estimation, fix to carrying forward theta if abnormal termination * R/phase3.r: fix to timing of progress reports for multiple processors * R/printInitialDescription.r: fix, was crashing with one mode and bipartite networks together. 2010-03-21 R-forge revision 68 (RSiena only) new version number 1.0.11 for RSiena * R/sienaDataCreateFromSession.r: allow periods to be numbered other than from 1 in siena net input. 2010-03-17 R-forge revision 67 (RSienaTest only) * R/siena01.r: fix to creation of model for unconditional estimation * R/phase3.r: fix to timing of progress reports for multiple processors * R/printInitialDescription.r: fix, was crashing with one mode and bipartite networks together 2010-03-17 R-forge revision 66 * R/simstatsc.r: bug fix: user interaction effects did not work with multiple processors. 2010-03-17 R-forge revision 65 (RSienaTest only) * src/model/ml/MLsimulation.cpp, src/model/ml/MLsimulation.ch: forgotten files 2010-03-16 R-forge revision 64 * data/allEffects.csv: covarBipartite egoX should have been an ego effect not dyadic. 2010-03-15 R-forge revision 63 (RSienaTest only) * R/siena08.r, R/iwlsm.r, man/siena08.Rd, man/print.sienameta.Rd, man/iwlsm.Rd, summary.iwlsm.Rd: siena08 Meta analysis * R/robmon.r, R/sienaModelCreate.r, man/sienaModelCreate.Rd: remove the function from the model object. Use name instead so no need to load package on R startup with model object in .RData. * R/siena01.r: now uses sienaModelCreate rather than creating object itself. * R/siena07.r, R/phase1.r, R/phase2.r, R/phase3.r, R/robmon.r, R/simstatsc.r, R.sienaDataCreate.r, src/siena07.cpp, man/siena07.Rd: fixed rlecuyer random numbers and added facility to use multiple processors by wave. * R/globals.r, R/print01Report.r, R/siena07.r: Report function can now be used with optional output file * R/print01Report.r, R/sienaDataCreate.r, src/siena07.cpp: missing values in dyadic covariates (incomplete!) 2010-03-15 R-forge revision 62 (RSienaTest only) * doc/RSienaDeveloper.tex, doc/Siena_algorithms2.tex * inst/examples/baerveldt3.csv, inst/examples/baerveldt4.csv: altered changing covariate text to constant covariate as only 2 waves. * src/data/BehaviorLongitudinalData.cpp, .h: C++ support for structural variables. (Not yet in R) * src/model/many: more code for ML routine. * src/utils/Random.cpp: changes to commments 2010-02-27 R-forge revision 61 (Riena only) * R/robmon.r: generate rlecuyer random numbers from the siena01 seed. * R/phase3.r: bug in displaying information with few iterations. 2010-02-16 R-forge revision 60 (RSienaTest only) * R/printInitialDescription.r, R/sienaDataCreate.r, src/data/NetworkLongitudinalData.h, src/data/NetworkLongitudinalData.cpp, src/siena07.cpp: average indegrees and outdegrees added to data objects, reports and passed into to C++ * R/print01Report.r: report on constraints, reformat list of inactive actors. * R/simstatsc.r, R/phase2.r, R/maxlike.r: fixes for maxlike routine. 2010-02-12 R-forge revision 59 (RSienaTest only except for manual) * DESCRIPTION, man/RSiena-package.Rd: new version: 1.0.11 * R/siena07.r, R/zzz.R, R/siena01.r, R/sienaRDocumentation.r, R/robmon.r, R/print01Report.r, R/getTargets.r, R/simstatsc.r: bug fix: replace string "RSiena" or "RSienaTest" by variable containing package name * R/makelike.r, R/maxlikecalc.r, man/maxlikefn.Rd, man/sienaModelCreate.rd, R/phase2.r, R/phase3.r, R/sienaModelCreate.r, R/sienaprint.r, NAMESPACE: simple MCMC routine intended for algorithm testing only. 2010-02-11 R-forge revision 58 (RSiena only) * man/, src/: some files from revision 56 which got missed. 2010-02-11 R-forge revision 57 * R/siena01.r: fix bug which stopped Siena update of effects initial values after conditional estimation. 2010-02-11 R-forge revision 56 (RSiena only, cf revision 47) * DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.10 * src/model/effects/generic/*, src/model/effects/effectfactory.cpp: multiple networks * src/model/filters, src/model/EpochSimulation.cpp, src/model/variables/*, src/data/Data.cpp, R/sienaDataCreate.r, R/sienautils.r, R/simstatsc.r, NAMESPACE: constraints between pairs of networks. * src/Makefile, Makefile.win: add new directories * R/sienaDataCreate.r, R/print01Report.r: separate balance means etc. for groups * src/model/ml/*: functions for ML, work in progress. 2010-02-11 R-forge revision 55 (RSienaTest only, (cf revision 52) * R/globals.r, R/siena07.r, man/siena07.Rd: new silent option with no output. * tests/parallel.R, tests/parallel.Rout.save: suppress progress message output and include prints of results. 2010-02-11 R-forge revision 54 (RSienaTest only) * R/print07Report.r: source formatting * data/allEffects.csv: bug in covariate behavior effects * configure.win, src/Makefile.win, src/win32/Makefile: changes for Win64 2010-02-11 R-forge revision 53 * R/siena01.r: fixed bug in editing all effects 2010-02-07 R-forge revision 52 RSiena * R/globals.r, R/siena07.r, man/siena07.Rd: new silent option with no output. * tests/parallel.R, tests/parallel.Rout.save: suppress progress message output and include prints of results. 2010-02-04 R-forge revision 51 RSiena * data/allEffects/csv: Bug in covariate behavior effects * configure.win, src/Makefile.win, src/Makevars, src/win32/Makefile: changes for Win64 * r/effects.r: minor fixes to getEffects function (default effects for multiple dependent networks.) 2010-02-01 R-forge Revision 50 * doc/s_man400.tex 2010-02-01 R-forge Revision 49 RSienatest * R/simstatsc.r, src/siena07.cpp: fixes to constraint * src/model/effects/EffectFactory.cpp, src/model/effects/generic/ConstantFunction.cpp: fixes to multiple network effects 2010-01-28 R-forge revision 48 * R/simstatsc.r: fixed bug in sort order of effects 2010-01-26 R-forge revision 47 RSienaTest * DESCRIPTION, man/RSiena-package.Rd: new version number 1.0.10 * src/model/effects/generic/*, src/model/effects/effectfactory.cpp: multiple networks * src/model/filters, src/model/EpochSimulation.cpp, src/model/variables/*, src/data/Data.cpp, R/sienaDataCreate.r, R/sienautils.r, R/simstatsc.r, NAMESPACE: constraints between pairs of networks. * src/Makefile, Makefile.win: add new directories * R/sienaDataCreate.r, R/print01Report.r: separate balance means etc. for groups * src/model/ml/*: functions for ML, work in progress. * doc/Siena_algorithms.tex, doc/Siena_ChainStructures.tex: added 2010-01-19 R-forge revision 46 RSienaTest * R/effectsDocumentation.r, man/effectsDocumentation.Rd, inst/doc/effects.pdf: effects documentation system. 2010-01-19 R-forge revision 45 RSiena * NAMESPACE, R/effectsDocumentation.r, man/effectsDocumentation.Rd: new documentation function * inst/doc/effects.pdf: output from the documentation function/ 2010-01-18 R-forge revision 44 RSiena * src/model/effects/various.cpp, .h: removed superfluous files 2010-01-18 R-forge revision 43 Siena * DESCRIPTION: new version 1.0.9 * NAMESPACE: new utility functions * data/alleffects.csv : new behavior effects, user-specified interactions. * R/sienaeffects.r, man/includeEffects.Rd, man/includeInteractions.Rd, man/setEffect.Rd: utilities to update effects object. * R/effects.r, man/getEffects.Rd: new parameter for number of behavior interaction effects. * src/model/effects/many: new behavior effects, user-specified interactions. 2010-01-15 R-forge revision 42 RSienaTest * inst/doc/s_man400.pdf: new manual 2010-01-15 R-forge revision 41 RSienaTest * doc/*, .Rbuildignore, src/sienaProfile.cpp: added developer documentation * data/allEffects.csv: new effect, altered effect1-3 to integers to remove bug in fix(myeff) * inst/*.out, *.Rdata: removed stray files from examples directory * R/sienaeffects.r, NAMESPACE, man/includeEffects.Rd, man/includeInteraction.Rd, man/setEffect.Rd: utility functions to update effects object * R/siena01.r, R/simstatsc.r, R/printDataReport.r, R/print07Report.r, R/Sienatest.r: no longer necessary to include underlying effects for interactions. * R/effects.r, man/getEffects.Rd: user parameter for number of unspecified behavior interactions * R/print07report.r, R/sienaprint.r: remove extra sqrt roots in standard error of rates for conditional estimation (see revision 31) * R/zzz.r: minor typo * src/Makefile.win, src/win32/Makefile: Changes to makefile for 64 bit windows * src/model/effects/AllEffects.h, src/model/effects/EffectFactory.cpp, src/model/effects/PopularityAlterEffect.cpp: New effect * src/model/variables/BehaviorVariable.h, src/model/effects/BehaviorVariable.cpp: new method * tests/parallel.R, tests/parallel.R.save: reduce tests to save time in Check. * man/RSiena-package.Rd, man/siena07.Rd, man/simstats0c.Rd, man/sienaFit.Rd: made examples faster. 2010-01-15 R-forge revision 40 RSiena * R/print01report.r, R/sienaprint.r: remove extra sqrt roots in standard error of rates for conditional estimation (see revision 32) * src/Makefile.win, src/win32/Makefile: Changes to makefile for 64 bit windows * tests/parallel.R, tests/parallel.R.save: remove timers from tests to reduce differences with output. 2010-01-12 R-forge revision 39 RSiena * tests/parallel.r: fix bug: use library RSiena not RSienaTest 2010-01-12 R-forge revision 38 RSiena * man/RSiena-package.Rd, man/siena07.Rd, man/sienaFit.Rd, man/simstats0c.Rd: reduce time for examples * tests/parallel.r, tests/parallel.Rout.save: reduce time for tests 2010-01-12 R-forge revision 37: RSienaTest * inst/sienascript: reverted to LF eol-style 2010-01-12 R-forge revision 36: RSienaTest * all source files: eol-style: native 2010-01-11 R-forge revision 35 RSienaTest * inst: added manual and examples to RSienaTest 2010-01-02 R-forge revision 34 RSiena and RSienaTest * R/sienaprint.r: corrected layout of sienaFitThetaTable for models with both behavior and network variables 2010-01-01 R-forge revision 33 RSiena and RSienaTest * inst/doc: updated changes in manual * CHANGELOG: updated 2010-01-01 R-forge revision 32 (RSiena: copy of relevant changes from revisions 29-31 to RSienaTest) * R/simstatsc.r: bug fixes to interactions (not yet functional) and name in header block * R/print07report.r: took square root of standard errors of rate estimates for conditional estimation. 2009-31-12 R-forge revision 31 * R/simstatsc.r: name in header * R/effects.r: made covariate from effects all use the same short name. * R/print07report.r: standard errors for rate estimate for conditional estimation needed square roots. * src/*.cpp, src/*.h: many changes, additions and deletions for (new) behavior effects. * data/allEffects.csv: turned off endowment effects where not implemented. 2009-12-17 R-forge revision 30 * R/simstatsc.r: fixed typo in dyadic interactions 2009-12-17 R-forge revision 29 * R/simstatsc.r: fixed typo in 3-way interations 2009-12-14 R-forge revision 27 * R/simstatsc.r: fixed problem with multiple processors. 2009-12-01 R-forge revision 26 added RSienaTest version 1.0.9 * Added many files for user-specified interactions. * DESCRIPTION, NAMESPACE, R/simstatsc.r, tests/parallel.r, src/Makefile.win: changes necessary for the new package 2009-11-20 R-forge revision 25 new version 1.0.8 * R/simstatsc.r, R/siena01.r: default method for estimation is conditional if there is only one dependent variable. * R/simstatsc.r: fixed bug if only one missing value: missing drop=FALSE. * R/simstatsc.r: fixed bug in naming of returned simulations * inst/sienascript: set to LF only eol style. * R/effects.r: uponly, downonly: remove density effect and linear shape effect * R/sienaDataCreate.r: set the uponly, downonly flags correctly for behavior variables. * R/effects.r: corrected bug in creation of effects data frame for changing dyadic covariates. * R/effects.r: amend some matches for nodesets for bipartite nets * R/effects.r, R/printInitialDescription.r: remove structValid argument from getNetworkStartingVals as unused * R/effects.r: Named the rows and columns of matrix of changes in getNetworkStartingVals and getBipartiteStartingVals * R/phase3.r, R/sienaprint.r: added t-stat to print method for sienaFit objects, improved xtable method * R/print01Report.r: added warning about non-integer behavior variables * R/siena01.r: fixed a bug in deleting rows from table: format and object type were out of sync * R/sienaDataCreate.r: new methods for adding attributes to covariate objects * R/Sienatest.r: fix bug: change sign of one-sided tests * R/simstatsc.r: change to returndeps flag to avoid it in phase 2. * R/simstatsc.r: Create names for interaction effects in fixUpEffectNames * src/model/EpochSimulation.h, src/model/variables/BehaviorVariables.cpp, src/model/variables/NetworkVariable.h: removed outdated comments and unused variables. * R/siena01.r: fixed bug in editing all effects rather than a subset. * R/print01Report.r: added or corrected report of uponly and downonly processing. 2009-11-08 R-forge revision 24 * DESCRIPTION, man/RSiena.RD: version Number 1.0.7 2009-11-08 R-forge revision 23 * R/phase1.3, R/phase3.r: Created subroutine to calculate derivative matrix * R/effects.r: corrected possible bug in creation of effects data frame for multigroup projects. * R/effects.r: corrected bug in creation of effects data frame for changing covariates. * R/siena07.r: added effect numbers to the Estimation screen and rationalised the display routines. * R/sienaTest.r: altered function interface so can call the scoreTest function from outside siena07 context. Corrected a missing change of sign for onesided test values. * R/sienaPrint.r: print methods now return their argument invisibly * src/siena07.cpp: altered flag for return of simulated dependent variables. 2009-11-08 R-forge revision 22 * R/siena01.r new option to edit effects split by dependent variable. Only partially functioning... 2009-11-08 R-forge revision 21 * src/model/variables/BehaviorVariable.cpp, src/model/variables/BehaviorVariable.h: Uninitialised data in scores causing NaN's in derivative. 2009-11-05 R-forge revision 20 * man/siena07.Rd: added detail to return value description * src/siena07.cpp: added functionalilty for user-specified interactions 2009-11-04 R-forge revision 19 * R/phase1.r, R/phase2.r, R/phase3.r, R/simstatsc.r; corrected finDiff.method flag 2009-10-31 R-forge revision 18 * src/model/tables/NetWorkCache.cpp, etc: New files added 2009-10-31 R-forge revision 17 many minor bug-fix changes also * DESCRIPTION, man/RSiena.RD: version Number 1.0.6 * NAMESPACE, DESCRIPTION, R/sienaPrint.r : xtable method * R/phase1.r, R/phase2.r, R/phase3.r: stopped using ... in call to FRAN, which restored speed gain of multiple processors. * data/allEffects.R, data/alleffects.csv, R/effects.r: new R effects system * tests: directory added * R/sienaDataCreate.r, R/effects.r, R/printDataReport.r, R/simstatsc.r, R/sienaDataCreateFromSession.r, R/print01Report.r, R/printInitialDescription: bipartite nets * src/data, src/model, src/network, src/utils, src/siena07.cpp: new C++ effects system * src/model/statisticCalculator.cpp: structural zeros code corrected * src/model/EpochSimulation.cpp: revert to proper random number generator unless parallel running. 2009-10-31 R-forge revision 16 added eol-style properties to text files