[Rsiena-commits] r84 - in pkg: RSiena RSiena/src RSiena/src/model RSiena/src/model/effects RSiena/src/model/ml RSiena/src/model/variables RSiena/src/utils RSienaTest RSienaTest/doc RSienaTest/man RSienaTest/src RSienaTest/src/model RSienaTest/src/model/effects RSienaTest/src/model/ml RSienaTest/src/model/variables RSienaTest/src/utils
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 28 13:15:27 CEST 2010
Author: ripleyrm
Date: 2010-04-28 13:15:27 +0200 (Wed, 28 Apr 2010)
New Revision: 84
Modified:
pkg/RSiena/changeLog
pkg/RSiena/src/model/EpochSimulation.cpp
pkg/RSiena/src/model/StatisticCalculator.cpp
pkg/RSiena/src/model/effects/AverageAlterEffect.cpp
pkg/RSiena/src/model/effects/BehaviorEffect.cpp
pkg/RSiena/src/model/effects/CovariateDependentNetworkEffect.cpp
pkg/RSiena/src/model/effects/CovariateIndirectTiesEffect.cpp
pkg/RSiena/src/model/effects/DyadicCovariateMainEffect.cpp
pkg/RSiena/src/model/effects/IndegreeEffect.cpp
pkg/RSiena/src/model/effects/IsolateEffect.cpp
pkg/RSiena/src/model/effects/LinearShapeEffect.cpp
pkg/RSiena/src/model/effects/OutOutDegreeAssortativityEffect.cpp
pkg/RSiena/src/model/effects/OutdegreeEffect.cpp
pkg/RSiena/src/model/effects/ReciprocatedSimilarityEffect.cpp
pkg/RSiena/src/model/effects/SimilarityEffect.cpp
pkg/RSiena/src/model/ml/Chain.cpp
pkg/RSiena/src/model/ml/MLSimulation.cpp
pkg/RSiena/src/model/ml/NetworkChange.cpp
pkg/RSiena/src/model/variables/BehaviorVariable.cpp
pkg/RSiena/src/model/variables/DependentVariable.cpp
pkg/RSiena/src/model/variables/NetworkVariable.cpp
pkg/RSiena/src/siena07.cpp
pkg/RSiena/src/utils/Random.cpp
pkg/RSiena/src/utils/Random.h
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/RSienaDeveloper.tex
pkg/RSienaTest/man/iwlsm.Rd
pkg/RSienaTest/src/model/EpochSimulation.cpp
pkg/RSienaTest/src/model/StatisticCalculator.cpp
pkg/RSienaTest/src/model/effects/AverageAlterEffect.cpp
pkg/RSienaTest/src/model/effects/BehaviorEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/CovariateIndirectTiesEffect.cpp
pkg/RSienaTest/src/model/effects/DyadicCovariateMainEffect.cpp
pkg/RSienaTest/src/model/effects/IndegreeEffect.cpp
pkg/RSienaTest/src/model/effects/IsolateEffect.cpp
pkg/RSienaTest/src/model/effects/LinearShapeEffect.cpp
pkg/RSienaTest/src/model/effects/OutOutDegreeAssortativityEffect.cpp
pkg/RSienaTest/src/model/effects/OutdegreeEffect.cpp
pkg/RSienaTest/src/model/effects/ReciprocatedSimilarityEffect.cpp
pkg/RSienaTest/src/model/effects/SimilarityEffect.cpp
pkg/RSienaTest/src/model/ml/Chain.cpp
pkg/RSienaTest/src/model/ml/MLSimulation.cpp
pkg/RSienaTest/src/model/ml/NetworkChange.cpp
pkg/RSienaTest/src/model/variables/BehaviorVariable.cpp
pkg/RSienaTest/src/model/variables/DependentVariable.cpp
pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
pkg/RSienaTest/src/siena07.cpp
pkg/RSienaTest/src/utils/Random.cpp
pkg/RSienaTest/src/utils/Random.h
Log:
Header file changes again. And eol_style
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2010-04-25 01:57:02 UTC (rev 83)
+++ pkg/RSiena/changeLog 2010-04-28 11:15:27 UTC (rev 84)
@@ -1,649 +1,656 @@
-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
+2020-04-28 R-forge revision 84
+
+ * src/many: removed <R.h> 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
+
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 84
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