CRANberries

Mon, 26 Nov 2007

Package MasterBayes updated to version 2.1 with previous version 2.0 dated 2006-12-15
Diff between MasterBayes versions 2.0 dated 2006-12-15 and 2.1 dated 2007-11-26 
 DESCRIPTION                       |   10 +++---
 NAMESPACE                         |    2 -
 R/MCMCped.R                       |   47 ++++++++++++++++---------------
 R/MLE.popsize.R                   |   36 +++++++++++++++++-------
 R/extractA.R                      |   13 ++++++++
 R/fillX.G.R                       |    4 --
 R/genotypeD.R                     |   14 ++++-----
 R/getPost.R                       |    9 +++---
 R/getXlist.R                      |    2 -
 R/getsPandtP.R                    |   12 +++++---
 R/legalG.R                        |    2 -
 R/modeP.R                         |   31 ++++++++++++++-------
 R/popsize.loglik.R                |   12 ++++----
 R/varPed.R                        |   56 ++++++++++++++++++++++++++------------
 inst/doc/MasterBayes.Tutorial.Rnw |   26 ++++++++++++-----
 inst/doc/MasterBayes.Tutorial.tex |   26 ++++++++++++-----
 man/GdataPed.Rd                   |    4 +-
 man/MCMCped.Rd                    |    7 ++--
 man/MLE.beta.Rd                   |    2 -
 man/MLE.ped.Rd                    |    2 -
 man/MLE.popsize.Rd                |    4 +-
 man/PdataPed.Rd                   |    2 -
 man/beta.loglik.Rd                |    2 -
 man/extractA.Rd                   |    2 -
 man/fillX.G.Rd                    |    2 -
 man/genotypeD.Rd                  |    4 +-
 man/getXlist.Rd                   |    2 -
 man/legalG.Rd                     |    2 -
 man/mismatches.Rd                 |    2 -
 man/modeG.Rd                      |    2 -
 man/modeP.Rd                      |    6 ++--
 man/order.ped.Rd                  |    4 +-
 man/popsize.loglik.Rd             |    6 ++--
 man/priorPed.Rd                   |    6 ++--
 man/reordXlist.Rd                 |    2 -
 man/simgenotypes.Rd               |    4 +-
 man/simpedigree.Rd                |    2 -
 man/startPed.Rd                   |   10 +++---
 man/summary.genotypeD.Rd          |    5 ++-
 man/tunePed.Rd                    |    6 ++--
 man/varPed.Rd                     |   27 ++++++++++++------
 src/LikFunctions.cc               |    9 ------
 src/MCMCped.cc                    |   11 +++++--
 src/SampDomG.cc                   |    4 --
 src/SampG.cc                      |    5 ---
 src/SampP.cc                      |   24 ++++------------
 src/fillXG.cc                     |    2 -
 src/legalG.cc                     |   17 +++++------
 src/mismatches.cc                 |    2 -
 49 files changed, 280 insertions(+), 213 deletions(-)
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New package CellularAutomaton with initial version 1.0 
Package: CellularAutomaton
Type: Package
Title: One-Dimensional Cellular Automata
Version: 1.0
Date: 2007-11-16
Author: John Hughes
Maintainer: John Hughes 
Depends: R.oo
Description: This package is an object-oriented implementation of one-dimensional cellular automata. It supports many of the features offered by Mathematica, including elementary rules, user-defined rules, radii, user-defined seeding, and plotting.
License: GPL
Packaged: Mon Nov 26 13:44:49 2007; jhughes
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New package glasso with initial version 1.0 
Package: glasso 
Title:  Graphical lasso
Version: 1.0
Author: Jerome Friedman and R. Tibshirani
Description:  Graphical lasso
Maintainer: Rob Tibshirani 
License: GPL-2
URL: http://www-stat.stanford.edu/~tibs/glasso
Packaged: Mon Nov 26 07:25:41 2007; tibs
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Package depmix updated to version 0.9.3 with previous version 0.9.2 dated 2007-10-21
Diff between depmix versions 0.9.2 dated 2007-10-21 and 0.9.3 dated 2007-11-26 
 depmix-0.9.2/depmix/changes.R                 |only
 depmix-0.9.2/depmix/man/balance.Rd            |only
 depmix-0.9.2/depmix/man/mbd.Rd                |only
 depmix-0.9.3/depmix/CHANGES                   |only
 depmix-0.9.3/depmix/DESCRIPTION               |   17 
 depmix-0.9.3/depmix/R/depmix-internal.R       |    2 
 depmix-0.9.3/depmix/R/depmix.R                |  841 +
 depmix-0.9.3/depmix/R/dmm.R                   |    2 
 depmix-0.9.3/depmix/R/lca.R                   |    2 
 depmix-0.9.3/depmix/R/markovdata.R            |    2 
 depmix-0.9.3/depmix/README                    |   36 
 depmix-0.9.3/depmix/inst/CITATION             |   10 
 depmix-0.9.3/depmix/inst/doc/depmix-intro.pdf |17981 +++-----------------------
 depmix-0.9.3/depmix/man/discrimination.Rd     |    6 
 depmix-0.9.3/depmix/man/dmm.Rd                |   85 
 depmix-0.9.3/depmix/man/fitdmm.Rd             |   84 
 depmix-0.9.3/depmix/man/generate.Rd           |   22 
 depmix-0.9.3/depmix/man/markovdata.Rd         |   40 
 depmix-0.9.3/depmix/man/mgdmm.Rd              |    1 
 depmix-0.9.3/depmix/src/globals.h             |    2 
 depmix-0.9.3/depmix/src/hessdist.h            |    2 
 depmix-0.9.3/depmix/src/logl.cc               |    6 
 depmix-0.9.3/depmix/src/logl.h                |    2 
 depmix-0.9.3/depmix/src/mdmm.cc               |   56 
 24 files changed, 3408 insertions(+), 15791 deletions(-)
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Package sde updated to version 2.0.0 with previous version 1.9.33 dated 2007-10-17
Diff between sde versions 1.9.33 dated 2007-10-17 and 2.0.0 dated 2007-11-26 
 DESCRIPTION           |   11 +--
 R/sde.sim.R           |    4 -
 R/simple.ef.R         |    2 
 R/simple.ef2.R        |    2 
 inst/book/ch3.R       |    9 ++
 inst/book/ex1.10.R    |    2 
 inst/book/ex1.11.R    |    2 
 inst/book/ex3.07.R    |  115 +++++++----------------------------
 inst/book/ex3.08.R    |  131 ++++++----------------------------------
 inst/book/ex3.09.R    |  163 ++++++++++++++++++++++++++------------------------
 inst/book/ex3.10.R    |  124 +++++++++++++++++++++++++++++++++-----
 inst/book/ex3.11.R    |  132 +++++++++++++++++++---------------------
 inst/book/ex3.12.R    |  115 +++++++++++++++++++++++++++++++----
 inst/book/ex3.13.R    |   37 ++++-------
 inst/book/ex3.14.R    |   56 +++++------------
 inst/book/ex3.15.R    |   83 +++++++++++--------------
 inst/book/ex3.16.R    |only
 inst/doc/changes.txt  |    7 ++
 man/BM.Rd             |   31 ++++-----
 man/DBridge.Rd        |   21 +++---
 man/DWJ.Rd            |    8 +-
 man/EULERloglik.Rd    |   14 ++--
 man/HPloglik.Rd       |   30 ++++-----
 man/SIMloglik.Rd      |   13 ++-
 man/cpoint.Rd         |   23 +++----
 man/dcElerian.Rd      |   25 +++----
 man/dcEuler.Rd        |   20 +++---
 man/dcKessler.Rd      |   37 +++++------
 man/dcOzaki.Rd        |   22 +++---
 man/dcShoji.Rd        |   34 +++++-----
 man/dcSim.Rd          |   38 ++++++-----
 man/gmm.Rd            |   49 ++++++++-------
 man/ksmooth.Rd        |   21 +++---
 man/linear.mart.ef.Rd |   30 ++++-----
 man/rcBS.Rd           |   21 +++---
 man/rcCIR.Rd          |   18 ++---
 man/rcOU.Rd           |   22 +++---
 man/rsCIR.Rd          |   16 ++--
 man/rsOU.Rd           |   18 ++---
 man/sde.sim.Rd        |   81 +++++++++++++-----------
 man/sdeAIC.Rd         |   40 ++++++------
 man/simple.ef.Rd      |   14 ++--
 man/simple.ef2.Rd     |   33 +++++-----
 43 files changed, 859 insertions(+), 815 deletions(-)
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Package mimR updated to version 2.1.0 with previous version 2.0.5 dated 2007-05-01
Diff between mimR versions 2.0.5 dated 2007-05-01 and 2.1.0 dated 2007-11-26 
 mimR-2.0.5/mimR/R/Afootest.R         |only
 mimR-2.0.5/mimR/R/MIM-gmData.R       |only
 mimR-2.0.5/mimR/R/fit-mim-model.R    |only
 mimR-2.0.5/mimR/R/gmData-access.R    |only
 mimR-2.0.5/mimR/R/gmData-basics.R    |only
 mimR-2.0.5/mimR/R/gmData-nameTable.R |only
 mimR-2.0.5/mimR/R/setop.R            |only
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 mimR-2.0.5/mimR/man/rats.Rd          |only
 mimR-2.1.0/mimR/DESCRIPTION          |    7 
 mimR-2.1.0/mimR/INDEX                |   18 -
 mimR-2.1.0/mimR/NAMESPACE            |  191 ++++++++++---------
 mimR-2.1.0/mimR/R/AllMethods.R       |   30 +--
 mimR-2.1.0/mimR/R/PrintSummaryEtc.R  |   84 +-------
 mimR-2.1.0/mimR/R/RScommands.R       |    8 
 mimR-2.1.0/mimR/R/SetOp.R            |only
 mimR-2.1.0/mimR/R/display.R          |  174 +++++++++++------
 mimR-2.1.0/mimR/R/editModels.R       |   28 +-
 mimR-2.1.0/mimR/R/fittedValues.R     |    8 
 mimR-2.1.0/mimR/R/internal-2006.R    |    4 
 mimR-2.1.0/mimR/R/mim-model-access.R |   15 +
 mimR-2.1.0/mimR/R/mim-model-fit.R    |only
 mimR-2.1.0/mimR/R/mim-model.R        |    4 
 mimR-2.1.0/mimR/R/misc-MIM.R         |   13 -
 mimR-2.1.0/mimR/R/momentStats.R      |  108 ++++++++--
 mimR-2.1.0/mimR/R/retrieveData.R     |    3 
 mimR-2.1.0/mimR/R/setopOLD.R         |only
 mimR-2.1.0/mimR/R/stepwise.R         |   36 +--
 mimR-2.1.0/mimR/R/testdelete.R       |   45 ++--
 mimR-2.1.0/mimR/R/toMIM-data.R       |  345 ++++++++++++++++++-----------------
 mimR-2.1.0/mimR/R/toMIM-misc.R       |   20 +-
 mimR-2.1.0/mimR/R/with-gRbase.R      |only
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 mimR-2.1.0/mimR/man/MIMfit.Rd        |    6 
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 mimR-2.1.0/mimR/man/editMIM.Rd       |   16 +
 mimR-2.1.0/mimR/man/internal-mimR.Rd |    6 
 mimR-2.1.0/mimR/man/mim-class.Rd     |    7 
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 49 files changed, 654 insertions(+), 593 deletions(-)
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Package gRbase updated to version 0.2.3 with previous version 0.2.2 dated 2007-11-07
Diff between gRbase versions 0.2.2 dated 2007-11-07 and 0.2.3 dated 2007-11-26 
 ChangeLog           |    9 +++++++++
 DESCRIPTION         |    6 +++---
 R/formulae.R        |    1 +
 R/gmData.R          |   10 +++++-----
 TODO                |   12 +++++++++---
 inst/doc/gRbase.log |    4 ++--
 inst/doc/gRbase.pdf |binary
 7 files changed, 29 insertions(+), 13 deletions(-)
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Package LoopAnalyst updated to version 1.2-0 with previous version 1.1-4 dated 2007-09-28
Diff between LoopAnalyst versions 1.1-4 dated 2007-09-28 and 1.2-0 dated 2007-11-26 
 DESCRIPTION                 |    8 ++++----
 R/._make.adjoint.R          |only
 R/._make.cem.R              |only
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 man/weighted.predictions.Rd |    4 +++-
 12 files changed, 10 insertions(+), 8 deletions(-)
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Package CPGchron updated to version 1.0 with previous version 0.1 dated 2007-08-04
Diff between CPGchron versions 0.1 dated 2007-08-04 and 1.0 dated 2007-11-26 
 CPGchron-0.1/CPGchron/src/Predict.c           |only
 CPGchron-1.0/CPGchron/DESCRIPTION             |    6 
 CPGchron-1.0/CPGchron/R/CPG.R                 |    1 
 CPGchron-1.0/CPGchron/R/CPGmenu.R             |   25 ++-
 CPGchron-1.0/CPGchron/R/PlotCPG.R             |    4 
 CPGchron-1.0/CPGchron/R/PlotDens.R            |    1 
 CPGchron-1.0/CPGchron/R/pause.R               |    4 
 CPGchron-1.0/CPGchron/data/Glendalough.dat    |   14 -
 CPGchron-1.0/CPGchron/man/CPGchron-package.Rd |   12 -
 CPGchron-1.0/CPGchron/src/CPG.c               |  190 ++++++++++++++++++--------
 CPGchron-1.0/CPGchron/src/calibrate.c         |   33 ++++
 CPGchron-1.0/CPGchron/src/predict.c           |only
 12 files changed, 204 insertions(+), 86 deletions(-)
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Package CompetingRiskFrailty updated to version 2.0 with previous version 1.0 dated 2006-08-11
Diff between CompetingRiskFrailty versions 1.0 dated 2006-08-11 and 2.0 dated 2007-11-26 
 DESCRIPTION                                                            |   22 +--
 R/CompetingRiskFrailtyOptim.function.R                                 |   64 ++++-----
 R/CompetingRiskFrailtySurvfitCreate.function.R                         |    2 
 inst/doc/R.functions.Code/CompetingRiskFrailtyOptim.function.R         |   66 +++++-----
 inst/doc/R.functions.Code/CompetingRiskFrailtySurvfitCreate.function.R |    2 
 man/plot.CompetingRiskFrailtySurvfit.Rd                                |    3 
 man/print.CompetingRiskFrailtySurvfit.Rd                               |    3 
 man/unemployed.comp.risk.Rd                                            |    2 
 8 files changed, 83 insertions(+), 81 deletions(-)
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