CRANberries

CRANberries aggregates information about new and and updated packages from the
CRAN network for R available as this html version and a corresponding RSS feed.
Created and provided by Dirk Eddelbuettel.

Thu, 04 Dec 2008

Package timeSeries updated to version 290.79 with previous version 280.78 dated 2008-10-27

Author: Diethelm Wuertz and Yohan Chalabi
Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching "Financial Engineering and Computational Finance"

Diff between timeSeries versions 280.78 dated 2008-10-27 and 290.79 dated 2008-12-04

 DESCRIPTION |   16 +++++++++-------
 R/time.R    |    5 +++--
 2 files changed, 12 insertions(+), 9 deletions(-)

More information about timeSeries at CRAN
Path: /cran/updated | permanent link

Package gRbase updated to version 0.6.4 with previous version 0.6.0 dated 2008-10-13

Author: Søren Højsgaard , Claus Dethlefsen
Title: A package for graphical modelling in R
Description: This package defines S3-classes gmData (graphical meta data), gModel (graphical model). Several other graphical modelling packages rely on these fundamental constructs. gRbase illustrates how hierarchical log-linear models (hllm) may be implemented.

Diff between gRbase versions 0.6.0 dated 2008-10-13 and 0.6.4 dated 2008-12-04

 gRbase-0.6.0/gRbase/man/DATA-cad1.Rd          |only
 gRbase-0.6.0/gRbase/man/graph-operations.Rd   |only
 gRbase-0.6.4/gRbase/ChangeLog                 |   22 +++
 gRbase-0.6.4/gRbase/DESCRIPTION               |    6 
 gRbase-0.6.4/gRbase/INDEX                     |    8 -
 gRbase-0.6.4/gRbase/R/GraphSH2.R              |   31 ----
 gRbase-0.6.4/gRbase/R/Graphsh-mcs-moral-rip.R |   18 +-
 gRbase-0.6.4/gRbase/R/Graphsh-querygSH2.R     |  178 +++++++++++++++-----------
 gRbase-0.6.4/gRbase/R/formulae.R              |   58 --------
 gRbase-0.6.4/gRbase/R/hllm.R                  |   34 ++++
 gRbase-0.6.4/gRbase/R/processFormula.R        |only
 gRbase-0.6.4/gRbase/R/processFormula2.R       |only
 gRbase-0.6.4/gRbase/R/setopsR.R               |    7 +
 gRbase-0.6.4/gRbase/R/utilities.R             |only
 gRbase-0.6.4/gRbase/R/utility.R               |    3 
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 gRbase-0.6.4/gRbase/man/gRbase-internal.Rd    |    3 
 gRbase-0.6.4/gRbase/man/gRbase-utilities.Rd   |    2 
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 28 files changed, 279 insertions(+), 209 deletions(-)

More information about gRbase at CRAN
Path: /cran/updated | permanent link

Package gRain updated to version 0.4.1 with previous version 0.4.0 dated 2008-10-28

Author: Søren Højsgaard
Title: Graphical Independence Networks
Description: A package for probability propagation in graphical independence networks, also known as probabilistic expert systems (which includes Bayesian networks as a special case).

Diff between gRain versions 0.4.0 dated 2008-10-28 and 0.4.1 dated 2008-12-04

 ChangeLog                |    7 +++++++
 DESCRIPTION              |    4 ++--
 R/gmInstance.R           |    2 +-
 inst/doc/gRain-intro.pdf |binary
 4 files changed, 10 insertions(+), 3 deletions(-)

More information about gRain at CRAN
Path: /cran/updated | permanent link

Package dti updated to version 0.6-0 with previous version 0.5-4 dated 2008-05-21

Author: Karsten Tabelow Joerg Polzehl
Title: DTI Analysis
Description: Diffusion Weighted Imaging is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data in the context of the diffusion tensor model (DTI). This includes the calculation of anisotropy measures and, most important, the implementation of our structural adaptive smoothing algorithm as described in K. Tabelow, J. Polzehl, V. Spokoiny, and H.U. Voss, Diffusion Tensor Imaging: Structural Adaptive Smoothing, Neuroimage 39(4), 1763-1773 (2008).

Diff between dti versions 0.5-4 dated 2008-05-21 and 0.6-0 dated 2008-12-04

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 dti-0.6-0/dti/DESCRIPTION               |    8 
 dti-0.6-0/dti/HISTORY                   |   10 
 dti-0.6-0/dti/NAMESPACE                 |    7 
 dti-0.6-0/dti/R/Classes.r               |   25 
 dti-0.6-0/dti/R/aws.r                   |  256 +------
 dti-0.6-0/dti/R/aws2.r                  |  188 +++--
 dti-0.6-0/dti/R/dti.r                   | 1039 +++++++++++++++++++++++++++++---
 dti-0.6-0/dti/R/misc.r                  |   69 +-
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 dti-0.6-0/dti/README                    |   59 +
 dti-0.6-0/dti/demo/dti_art.r            |  254 ++-----
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 dti-0.6-0/dti/src/aniso.f               |  381 ++++++-----
 dti-0.6-0/dti/src/awsvar.f              |  233 +++++--
 dti-0.6-0/dti/src/dtinraw2.f            |  588 ++++++------------
 dti-0.6-0/dti/src/misc.f                |  124 +++
 dti-0.6-0/dti/src/nlrdtirg.f            |  129 +--
 dti-0.6-0/dti/src/rice.f                |only
 49 files changed, 2148 insertions(+), 1335 deletions(-)

More information about dti at CRAN
Path: /cran/updated | permanent link

Package deal updated to version 1.2-31 with previous version 1.2-30 dated 2007-04-20

Author: Susanne Gammelgaard Bottcher , Claus Dethlefsen .
Title: Learning Bayesian Networks with Mixed Variables
Description: Bayesian networks with continuous and/or discrete variables can be learned and compared from data.

Diff between deal versions 1.2-30 dated 2007-04-20 and 1.2-31 dated 2008-12-04

 deal-1.2-30/deal/CHANGES.txt          |only
 deal-1.2-31/deal/CHANGELOG            |only
 deal-1.2-31/deal/DESCRIPTION          |    8 ++++----
 deal-1.2-31/deal/R/autosearch.R       |    6 +++---
 deal-1.2-31/deal/R/heuristic.R        |    6 +++---
 deal-1.2-31/deal/R/jointdisc.R        |    9 ++++++---
 deal-1.2-31/deal/man/autosearch.Rd    |    8 +++++---
 deal-1.2-31/deal/man/deal-internal.Rd |    6 +++---
 deal-1.2-31/deal/man/drawnetwork.Rd   |    8 +++++---
 deal-1.2-31/deal/man/genlatex.Rd      |   30 +++++++++++++++---------------
 deal-1.2-31/deal/man/insert.Rd        |    8 ++++----
 deal-1.2-31/deal/man/jointprior.Rd    |   12 ++++++------
 deal-1.2-31/deal/man/learn.Rd         |   12 ++++++------
 deal-1.2-31/deal/man/makesimprob.Rd   |    8 ++++----
 deal-1.2-31/deal/man/maketrylist.Rd   |    8 ++++----
 deal-1.2-31/deal/man/network.Rd       |    8 ++++----
 deal-1.2-31/deal/man/networkfamily.Rd |    8 ++++----
 deal-1.2-31/deal/man/node.Rd          |    8 ++++----
 deal-1.2-31/deal/man/numbermixed.Rd   |   12 ++++++------
 deal-1.2-31/deal/man/nwfsort.Rd       |    7 ++++---
 deal-1.2-31/deal/man/nwfunique.Rd     |    8 ++++----
 deal-1.2-31/deal/man/perturb.Rd       |    8 ++++----
 deal-1.2-31/deal/man/prob.Rd          |    8 ++++----
 deal-1.2-31/deal/man/readnet.Rd       |    3 ++-
 deal-1.2-31/deal/man/rnetwork.Rd      |    8 ++++----
 deal-1.2-31/deal/man/score.Rd         |   11 +++++++----
 26 files changed, 115 insertions(+), 103 deletions(-)

More information about deal at CRAN
Path: /cran/updated | permanent link

Package RQuantLib updated to version 0.2.10 with previous version 0.2.9 dated 2008-08-11

Author: Dirk Eddelbuettel with contributions from Dominick Samperi
Title: R interface to the QuantLib library
Description: The RQuantLib package makes selected parts of QuantLib visible to the R user. Currently some basic option pricing functions are included, as well as fixed-income functions that can be used for interest rate curve construction and Bermuda swaption pricing. Further software contributions are welcome. The QuantLib project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets. The Windows binary version is self-contained and does not require a QuantLib (or Boost) installation. RQuantLib use the Rcpp R/C++ interface class library. See the Rcpp package on CRAN (or R-Forge) for more information on Rcpp. Note that while RQuantLib's code is licensed under the GPL (v2 or later), QuantLib itself is released under a somewhat less restrictive Open Source license (see QuantLib-License.txt).

Diff between RQuantLib versions 0.2.9 dated 2008-08-11 and 0.2.10 dated 2008-12-04

 RQuantLib-0.2.10/RQuantLib/DESCRIPTION       |   53 +-
 RQuantLib-0.2.10/RQuantLib/INDEX             |    1 
 RQuantLib-0.2.10/RQuantLib/configure         |  676 +++++++++++----------------
 RQuantLib-0.2.10/RQuantLib/configure.in      |   93 ++-
 RQuantLib-0.2.10/RQuantLib/configure.win     |   13 
 RQuantLib-0.2.10/RQuantLib/inst/ChangeLog    |   22 
 RQuantLib-0.2.10/RQuantLib/src/Makefile.win  |   23 
 RQuantLib-0.2.10/RQuantLib/src/bermudan.cpp  |   14 
 RQuantLib-0.2.10/RQuantLib/src/discount.cpp  |   10 
 RQuantLib-0.2.10/RQuantLib/src/rquantlib.hpp |   13 
 RQuantLib-0.2.10/RQuantLib/src/utils.cpp     |    6 
 RQuantLib-0.2.9/RQuantLib/R/RcppVersion.R    |only
 RQuantLib-0.2.9/RQuantLib/RcppSrc            |only
 RQuantLib-0.2.9/RQuantLib/man/RcppVersion.Rd |only
 14 files changed, 442 insertions(+), 482 deletions(-)

More information about RQuantLib at CRAN
Path: /cran/updated | permanent link

New package SDaA with initial version 0.1
Package: SDaA
Type: Package
Title: Sampling: Design and Analysis
Version: 0.1
Date: 2008-09-15
Author: Tobias Verbeke
Maintainer: Tobias Verbeke
Description: Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, Duxbury.
Depends: survey, ggplot2, roxygen
License: GPL-3
LazyData: Yes
Collate: 'agpop.R' 'agsrs.R' 'agstrat.R' 'anthrop.R' 'anthsrs.R' 'anthuneq.R' 'audit.R' 'books.R' 'certify.R' 'coots.R' 'counties.R' 'divorce.R' 'golfsrs.R' 'htpop.R' 'htsrs.R' 'htstrat.R' 'journal.R' 'lahiri.design.R' 'measles.R' 'ncvs.R' 'nybight.R' 'otters.R' 'ozone.R' 'samples.R' 'seals.R' 'selectrs.R' 'statepop.R' 'statepps.R' 'syc.R' 'teachers.R' 'teachmi.R' 'teachnr.R' 'winter.R'
Packaged: Thu Dec 4 11:06:41 2008; tobias

More information about SDaA at CRAN
Path: /cran/new | permanent link

New package GridR with initial version 0.8.4
Package: GridR
Type: Package
Title: Executes functions on remote hosts, clusters or grids.
Version: 0.8.4
Date: 2008-12-04
Author: Dennis Wegener, Malte Lohmeyer, Stefan Rueping
Maintainer: Dennis Wegener
Description: GridR is an R-Package that can be used to submit R functions for execution on remote computers, clusters or grids. In addition, users are provided with an interface to share variables and functions with other users.
License: GPL-2
Depends: codetools
Packaged: Thu Dec 4 13:23:16 2008; root

More information about GridR at CRAN
Path: /cran/new | permanent link

Package sda updated to version 1.0.2 with previous version 1.0.1 dated 2008-11-22

Author: Korbinian Strimmer
Title: Shrinkage Discriminant Analysis
Description: This package performs linear and diagonal discriminant analysis where the classifier is trained using Stein-type shrinkage estimators. This approach is particularly suited for high-dimensional classification.

Diff between sda versions 1.0.1 dated 2008-11-22 and 1.0.2 dated 2008-12-04

 DESCRIPTION        |    8 ++---
 NEWS               |   15 ++++++++-
 R/centroids.R      |   57 +++++++++++++++++++++++------------
 R/predict.sda.R    |   51 +++++++++++++-------------------
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 10 files changed, 194 insertions(+), 138 deletions(-)

More information about sda at CRAN
Path: /cran/updated | permanent link

Package nsRFA updated to version 0.6-4 with previous version 0.6-2 dated 2008-09-19

Author: Alberto Viglione
Title: Non-supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology. The package refers to the index-value method and, more precisely, helps the hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions with similar growth curves; (3) fit distribution functions to the empirical regional growth curves.

Diff between nsRFA versions 0.6-2 dated 2008-09-19 and 0.6-4 dated 2008-12-04

 nsRFA-0.6-2/nsRFA/inst/doc/.build.timestamp      |only
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 nsRFA-0.6-4/nsRFA/inst/doc/Fig1ElamirSeheult.pdf |binary
 nsRFA-0.6-4/nsRFA/inst/doc/MSClaio2008.pdf       |binary
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 nsRFA-0.6-4/nsRFA/man/BayesianMCMC.Rd            |    4 
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 9 files changed, 321 insertions(+), 14 deletions(-)

More information about nsRFA at CRAN
Path: /cran/updated | permanent link

Package monomvn updated to version 1.6 with previous version 1.5 dated 2008-11-13

Author: Robert B. Gramacy
Title: Estimation for multivariate normal data with monotone missingness
Description: Estimation of multivariate normal data of arbitrary dimension where the pattern of missing data is monotone. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle an (almost) arbitrary amount of missing data. The current version supports maximum likelihood inference and implementation of a Bayesian version employing a Bayesian lasso. A fully functional standalone interface to the Bayesian lasso (from Park & Casella) and ridge regression with model selection via Reversible Jump is also provided

Diff between monomvn versions 1.5 dated 2008-11-13 and 1.6 dated 2008-12-04

 monomvn-1.5/monomvn/INDEX                   |only
 monomvn-1.6/monomvn/ChangeLog               |   32 +
 monomvn-1.6/monomvn/DESCRIPTION             |    6 
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 monomvn-1.6/monomvn/R/regress.fact.R        |    1 
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 monomvn-1.6/monomvn/src/bmonomvn.cc         |  526 +++++++-------------------
 monomvn-1.6/monomvn/src/bmonomvn.h          |   77 ---
 monomvn-1.6/monomvn/src/matrix.c            |   66 +++
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 29 files changed, 1233 insertions(+), 869 deletions(-)

More information about monomvn at CRAN
Path: /cran/updated | permanent link

Package clinfun updated to version 0.8.4 with previous version 0.8.3 dated 2008-11-18

Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.

Diff between clinfun versions 0.8.3 dated 2008-11-18 and 0.8.4 dated 2008-12-04

 CHANGES        |    7 ++++++
 DESCRIPTION    |    4 +--
 R/pselect.R    |   64 ++++++++++++++++++++++++++++++++++++++++++++++-----------
 man/pselect.Rd |   30 ++++++++++++++++----------
 4 files changed, 79 insertions(+), 26 deletions(-)

More information about clinfun at CRAN
Path: /cran/updated | permanent link

New package hexbin with initial version 1.17.0
Package: hexbin
Version: 1.17.0
Date: 2008-05-21
Title: Hexagonal Binning Routines
Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler
Maintainer: Nicholas Lewin-Koh
Depends: R (>= 2.0.1), methods, stats, grid, lattice
Suggests: marray, cluster, affy, Biobase
Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
Collate: BTC.R BTY.R grid.hexagons.R grid.hexlegend.R hbox.R hdiffplot.R hexbinList.R hexbinplot.R hexbin.s4.R hexpanel.R hexplom.R hexPlotMA.R hexutil.R hexViewport.R HO.R LINGRAY.R LOCS.R MAG.R RB.R smoothHexbin.R
License: GPL 2
Packaged: Tue Dec 2 22:38:34 2008; nikko

More information about hexbin at CRAN
Path: /cran/new | permanent link

Package bayesGARCH updated to version 1-00.02 with previous version 1-00.01 dated 2008-06-03

Author: David Ardia
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
Description: This package provides the bayesGARCH function which performs the Bayesian estimation of the GARCH(1,1) model with Student's t innovations.

Diff between bayesGARCH versions 1-00.01 dated 2008-06-03 and 1-00.02 dated 2008-12-04

 DESCRIPTION               |    8 ++++----
 R/onload.R                |    4 ++--
 README                    |    1 +
 man/addPriorConditions.Rd |    5 ++++-
 man/bayesGARCH.Rd         |   12 +++++++-----
 man/formSmpl.Rd           |    5 ++++-
 6 files changed, 22 insertions(+), 13 deletions(-)

More information about bayesGARCH at CRAN
Path: /cran/updated | permanent link

Package ZIGP updated to version 3.0 with previous version 2.7 dated 2008-11-14

Author: Vinzenz Erhardt
Title: Zero Inflated Generalized Poisson (ZIGP) regression models
Description: Adapt and analyze and compare GP, ZIP and ZIGP regression models

Diff between ZIGP versions 2.7 dated 2008-11-14 and 3.0 dated 2008-12-04

 ZIGP-2.7/ZIGP/R/wald.test.r                |only
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 ZIGP-3.0/ZIGP/DESCRIPTION                  |    6 +-
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 ZIGP-3.0/ZIGP/R/gradient.r                 |   12 ++---
 ZIGP-3.0/ZIGP/R/gradient1.r                |   14 +++---
 ZIGP-3.0/ZIGP/R/loglikelihood.zigp.full.r  |   26 ++++++------
 ZIGP-3.0/ZIGP/R/loglikelihood.zigp.r       |   14 +++---
 ZIGP-3.0/ZIGP/R/loglikelihood.zigp.vuong.r |   14 +++---
 ZIGP-3.0/ZIGP/R/mle.zigp.full.like.r       |   50 ++++++++++++------------
 ZIGP-3.0/ZIGP/R/mle.zigp.r                 |   27 +++++++++----
 ZIGP-3.0/ZIGP/R/optimized.run.r            |   16 +++----
 ZIGP-3.0/ZIGP/man/ZIGP-package.rd          |    9 ++--
 ZIGP-3.0/ZIGP/man/clarke.rd                |   39 ++++++++++---------
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 ZIGP-3.0/ZIGP/man/mle.zigp.rd              |   45 +++++++++-------------
 ZIGP-3.0/ZIGP/man/vuong.rd                 |   59 +++++++++++++++--------------
 25 files changed, 179 insertions(+), 162 deletions(-)

More information about ZIGP at CRAN
Path: /cran/updated | permanent link

Package Rcpp updated to version 0.6.2 with previous version 0.6.1 dated 2008-11-30

Author: Dominick Samperi and Dirk Eddelbuettel
Title: Rcpp R/C++ interface library and package template
Description: R/C++ interface class library and package template. The Rcpp library maps data types betweeen R and C++, and includes support for R types real, integer, character, vector, matrix, Date, datetime (i.e. POSIXct) data frame, and function. It supports calling R functions from C++. See the package documentation file doc/RcppAPI.pdf for more information, including details on building binary R packages for Windows.

Diff between Rcpp versions 0.6.1 dated 2008-11-30 and 0.6.2 dated 2008-12-04

 DESCRIPTION          |    6 +++---
 R/RcppLdpath.R       |    2 +-
 inst/ChangeLog       |   12 +++++++++---
 inst/doc/RcppAPI.pdf |binary
 4 files changed, 13 insertions(+), 7 deletions(-)

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Package PtProcess updated to version 3.1-2 with previous version 3.1-1 dated 2008-11-18

Author: David Harte
Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Changes".

Diff between PtProcess versions 3.1-1 dated 2008-11-18 and 3.1-2 dated 2008-12-04

 DESCRIPTION     |    6 +++---
 data/Phuket.R   |only
 data/Phuket.txt |only
 man/Changes.Rd  |    4 ++++
 man/Phuket.Rd   |only
 man/mpp.Rd      |    4 ++--
 6 files changed, 9 insertions(+), 5 deletions(-)

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Package MasterBayes updated to version 2.41 with previous version 2.4 dated 2008-09-05

Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficency.

Diff between MasterBayes versions 2.4 dated 2008-09-05 and 2.41 dated 2008-12-04

 DESCRIPTION           |    6 
 R/ErrorCheck.R        |    4 
 R/MCMCped.R           |    2 
 R/getXlist.R          |   96 ++--
 R/getsPandtP.R        |    9 
 inst/doc/Tutorial.pdf | 1065 ++++++++++++++++++++++++--------------------------
 src/SampP.cc          |   12 
 7 files changed, 602 insertions(+), 592 deletions(-)

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Package GOSim updated to version 1.1.5.4 with previous version 1.1.5.3 dated 2008-12-01

Author: Holger Froehlich , contributions by Tim Beissbarth
Title: Computation of functional similarities between GO terms and gene products; GO enrichement analysis
Description: This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis

Diff between GOSim versions 1.1.5.3 dated 2008-12-01 and 1.1.5.4 dated 2008-12-04

 DESCRIPTION         |    6 
 R/GOenrichment.R    |   36 +
 inst/doc/GOSim.pdf  | 1254 +++++++++++++++++++++++++---------------------------
 man/GOenrichment.Rd |   12 
 man/internal.Rd     |    2 
 5 files changed, 663 insertions(+), 647 deletions(-)

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Package DEoptim updated to version 1.3-0 with previous version 1.2-1 dated 2007-09-12

Author: David Ardia
Title: Differential Evolution Optimization
Description: This package provides the DEoptim function which performs Differential Evolution Optimization (evolutionary algorithm).

Diff between DEoptim versions 1.2-1 dated 2007-09-12 and 1.3-0 dated 2008-12-04

 CHANGES            |    5 ++++
 DESCRIPTION        |    6 ++---
 R/DEoptim.R        |   57 +++++++++++++++++++++++++++++++++++++++--------------
 XEmacs-21.4.20.lnk |only
 man/DEoptim.Rd     |   10 ++++++++-
 5 files changed, 60 insertions(+), 18 deletions(-)

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