Sat, 19 Feb 2011

Package rattle updated to version 2.6.4 with previous version 2.6.3 dated 2011-02-14

Title: Graphical user interface for data mining in R
Description: Rattle (the R Analytic Tool To Learn Easily) provides a Gnome (RGtk2) based interface to R functionality for data mining. The aim is to provide a simple and intuitive interface that allows a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, build and evaluate models, and export models as PMML (predictive modelling markup language) or as scores. All of this with knowing little about R. All R commands are logged and commented through the log tab. Thus they are available to the user as a script file or as an aide for the user to learn R or to copy-and-paste directly into R itself. Rattle also exports a number of utility functions and the graphical user interface, invoked as rattle(), does not need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams

Diff between rattle versions 2.6.3 dated 2011-02-14 and 2.6.4 dated 2011-02-19

 DESCRIPTION                        |    8 +++----
 R/evaluate.R                       |   39 ++++++++++++++++++++-----------------
 R/explore.R                        |   16 +++++++++------
 R/rattle.R                         |   12 ++++++-----
 data/weatherAUS.RData              |binary
 inst/ChangeLog                     |   13 ++++++++++++
 inst/doc/rattle.pdf                |binary
 inst/po/de/LC_MESSAGES/ |binary
 inst/po/es/LC_MESSAGES/ |binary
 inst/po/fr/LC_MESSAGES/ |binary
 inst/po/ja/LC_MESSAGES/ |binary
 11 files changed, 56 insertions(+), 32 deletions(-)

More information about rattle at CRAN
Permanent link

Package bayespack updated to version 1.0-2 with previous version 1.0-1 dated 2011-02-17

Title: Numerical Integration for Bayesian Inference
Description: The bayespack package provides an R interface to the Fortran BAYESPACK integration routines written by Alan Genz. Given an unnormalized posterior distribution, the BAYESPACK routines approximate the normalization constant and the mean and covariance of the posterior. Posterior means of additional functions of the parameters can be calculated as well.
Author: Alan Genz (BAYESPACK Fortran source code) and Bjoern Bornkamp (R interface and minor adaptions in Fortran source code)
Maintainer: Bjoern Bornkamp

Diff between bayespack versions 1.0-1 dated 2011-02-17 and 1.0-2 dated 2011-02-19

 ChangeLog                |only
 DESCRIPTION              |    8 ++++----
 R/tools.R                |    2 +-
 man/bayespack-package.Rd |    4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

More information about bayespack at CRAN
Permanent link

New package copBasic with initial version 1.4
Package: copBasic
Title: Basic Copula Functions
Version: 1.4
Date: 2008-10-30
Author: William H. Asquith
Description: This package implements basic functions for copula computations and is used by several other packages by the author. This particular package provides the lower (W), upper (M), and product (P) copulas as well as the product-summation-product copula (PSP). Wrapper functions for the copula (COP), survival copula (surCOP), dual of a copula (duCOP), and co-copula (coCOP) are provided. The package has (level.curvesCOP) for drawing level curves of a given copula, and this function uses the inverse of a copula (COPinv and a COPinv2 is provided for completeness). The numerical derivative for the derivative of a copula is provided by (derCOP and derCOP2) and the inversion of these functions are by (derCOPinv and derCOPinv2). The diagonal sections of a copula are supported by (diagCOP), and sections and derivatives of sections are supported by (sectionCOP). The inverses of copula derivatives are important for random variate generation. Random variate generation for a copula using the conditional distribution method and the deriviative of a copula is provided by (simCOP and the reduced capability simCOPmicro). For slightly broader application for purposes of education and experimentation with copulas, this package also supports the Plackett copula (PLACKETTcop) because of the general applicability of this copula. The Plackett copula is comprehensive, which means that it can attain complete negative association, independence, and positive association. Plackett parameter estimation is straightforward with (PLACKETTpar). A Plackett-specific, random-variate algorithm is by (PLACKETTsim). Composition of two copulas is provided by (composite2COP), and composition of one copula is provided by function (composite1COP). Composite copula random variates are generated by (simcompositeCOP). These compositions generally yield asymmetric copulas. A data set is provided that contains darts thrown at the L-comoment space of a Plackett-Plackett composited compula; these data might be used for experimental copula estimation by the method of L-comoments. The package also provides a full suite of functions to numerically compute measures of association through concordance for a given copula such as Kendall's Tau (tauCOP), Spearman's Rho (rhoCOP), Gini's Gamma (giniCOP), and Blomqvist's Beta (blomCOP). The Schweizer and Wolff's Sigma (wolfCOP) is implemented as a measure of dependency as opposed the the concordance measures just listed. Upper and lower tail dependence is computed by numerical limit convergence by (taildepCOP). A numerical computation of the logical whether a copula is left-tail decreasing or right-tail increasing is provided by (isCOP.LTD and isCOP.RTI). The package supports quantile and median regression through (qua.regressCOP, qua.regress2COP, med.regressCOP, med.regress2COP) for a given copula where "2" represents V with respect to U instead of U with respect to V. The regressions can be plotted by (qua.regressCOP.draw).
Maintainer: William H. Asquith
Depends: lmomco
License: GPL
Packaged: 2011-02-18 19:19:05 UTC; wasquith
Repository: CRAN
Date/Publication: 2011-02-19 09:06:54

More information about copBasic at CRAN
Permanent link

Package RcppArmadillo updated to version 0.2.13 with previous version 0.2.12 dated 2011-02-16

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 1.1.4). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the GNU LGPL version 3 or later, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licenses under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates

Diff between RcppArmadillo versions 0.2.12 dated 2011-02-16 and 0.2.13 dated 2011-02-19

 ChangeLog                                               |    6 
 DESCRIPTION                                             |   14 
 inst/NEWS                                               |    8 
 inst/doc/RcppArmadillo-unitTests.pdf                    |binary
 inst/doc/unitTests-results/RcppArmadillo-unitTests.html |    6 
 inst/doc/unitTests-results/RcppArmadillo-unitTests.txt  |   36 
 inst/include/armadillo_bits/Col_meat.hpp                |   64 +
 inst/include/armadillo_bits/Col_proto.hpp               |    3 
 inst/include/armadillo_bits/Cube_meat.hpp               |  124 ++
 inst/include/armadillo_bits/Cube_proto.hpp              |    7 
 inst/include/armadillo_bits/Mat_meat.hpp                |  696 +++++++++++---
 inst/include/armadillo_bits/Mat_proto.hpp               |   36 
 inst/include/armadillo_bits/Row_meat.hpp                |   62 +
 inst/include/armadillo_bits/Row_proto.hpp               |    3 
 inst/include/armadillo_bits/arma_version.hpp            |    4 
 inst/include/armadillo_bits/arrayops_meat.hpp           |   76 -
 inst/include/armadillo_bits/debug.hpp                   |  254 ++++-
 inst/include/armadillo_bits/field_meat.hpp              |   44 
 inst/include/armadillo_bits/field_proto.hpp             |    2 
 inst/include/armadillo_bits/fn_accu.hpp                 |   15 
 inst/include/armadillo_bits/fn_prod.hpp                 |   10 
 inst/include/armadillo_bits/forward_proto.hpp           |    8 
 inst/include/armadillo_bits/injector_meat.hpp           |   70 +
 inst/include/armadillo_bits/injector_proto.hpp          |    4 
 inst/include/armadillo_bits/op_sort_meat.hpp            |  242 ++---
 inst/include/armadillo_bits/op_sort_proto.hpp           |   15 
 inst/include/armadillo_bits/span.hpp                    |   72 +
 inst/include/armadillo_bits/subview_cube_meat.hpp       |  759 +++++++++++++---
 inst/include/armadillo_bits/subview_cube_proto.hpp      |   19 
 inst/include/armadillo_bits/subview_field_meat.hpp      |   83 +
 inst/include/armadillo_bits/subview_field_proto.hpp     |   11 
 inst/include/armadillo_bits/subview_meat.hpp            |  118 +-
 inst/include/armadillo_bits/subview_proto.hpp           |   21 
 33 files changed, 2113 insertions(+), 779 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

Package ROracleUI updated to version 1.3-1 with previous version 1.3-0 dated 2010-11-19

Title: Convenient Tools for Working with Oracle Databases
Description: Easy-to-use functions to explore Oracle databases and import data into R. User interface for the ROracle package.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between ROracleUI versions 1.3-0 dated 2010-11-19 and 1.3-1 dated 2011-02-19

 DESCRIPTION |    8 ++++----
 NEWS        |    8 ++++++++
 R/sql.R     |    6 ++----
 3 files changed, 14 insertions(+), 8 deletions(-)

More information about ROracleUI at CRAN
Permanent link

Package MISA updated to version 2.11.1-1.0.1 with previous version 2.11.1-1.0 dated 2011-02-17

Title: Bayesian Model Search and Multilevel Inference for SNP Association Studies
Description: The functions in this package focus on intermediate throughput case-control association studies, where the outcome of interest is often a binary disease state and where the genetic markers have been chosen to capture variation in a set of related genes, such as those involved in a specific biochemical pathway. Given this data, we are interested in addressing two questions: "To what extent does the data support an overall association between the pathway and outcome of interest?" and "Which markers or genes are most likely to be driving this association?" To address both of these questions,this package performs a Bayesian model search technique that utilizes Evolutionary Monte Carlo and searches over models including main effects of all genetic markers and marker-specific genetic effects in a computationally efficient manner. The package incorporates functions that perform a marginal screen on the genetic markers, summarize the output of the model search algorithm, including image plots of the models with the highest posterior probability, marginal summaries of SNP and gene inclusion probabilities and Bayes Factors, and global summaries of the posterior probability and Bayes Factor giving evidence of an association in the set of SNPs of interest.
Author: Melanie Wilson
Maintainer: Gary Lipton

Diff between MISA versions 2.11.1-1.0 dated 2011-02-17 and 2.11.1-1.0.1 dated 2011-02-19

 ChangeLog               |    7 +++++--
 DESCRIPTION             |    6 +++---
 inst/doc/MISA.pdf       |binary
 src/Makevars            |    2 +-
 src/        |    2 +-
 src/ |    3 +--
 src/ |    1 +
 src/bayesglm.c          |    2 +-
 src/family.c            |   18 +++++++++++-------
 src/ |    1 +
 src/mconf.h             |    4 ++++
 src/sampling.h          |    5 ++++-
 12 files changed, 33 insertions(+), 18 deletions(-)

More information about MISA at CRAN
Permanent link

New package DAGGER with initial version 1.1
Package: DAGGER
Title: Consensus genetic maps
Version: 1.1
Date: 2011-02-18
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman
Description: Integrates the information from multiple linkage maps to create a consensus directed graph, which is then linearized to produce a consensus map.
Depends: Rglpk
License: GPL-3
LazyLoad: yes
Packaged: 2011-02-18 23:19:20 UTC; Jeffrey
Repository: CRAN
Date/Publication: 2011-02-19 09:11:12

More information about DAGGER at CRAN
Permanent link

Package BAMD updated to version 3.4 with previous version 3.3.1 dated 2010-04-25

Title: Bayesian Association Model for Genomic Data with Missing Covariates
Description: This package fits a linear mixed model where the covariates for the random effects have missing values.
Author: Gopal, V. and Li, Z. and Casella, G.
Maintainer: Gopal, V.

Diff between BAMD versions 3.3.1 dated 2010-04-25 and 3.4 dated 2011-02-19

 DESCRIPTION             |    8 ++++----
 NAMESPACE               |    2 +-
 R/imputedGenotypes.R    |only
 README                  |only
 man/imputedGenotypes.Rd |only
 5 files changed, 5 insertions(+), 5 deletions(-)

More information about BAMD at CRAN
Permanent link

Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.