Mon, 19 Oct 2009

Package spdep updated to version 0.4-50 with previous version 0.4-49 dated 2009-10-13

Author: Roger Bivand , with contributions by Luc Anselin, Renato Assunção, Olaf Berke, Andrew Bernat, Marilia Carvalho, Yongwan Chun, Bjarke Christensen, Carsten Dormann, Stéphane Dray, Rein Halbersma, Elias Krainski, Nicholas Lewin-Koh, Hongfei Li, Jielai Ma, Giovanni Millo, Werner Mueller, Hisaji Ono, Pedro Peres-Neto, Markus Reder, Michael Tiefelsdorf, and Danlin Yu.
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tesselations, for summarising these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.

Diff between spdep versions 0.4-49 dated 2009-10-13 and 0.4-50 dated 2009-10-19

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Package doBy updated to version 4.0.4 with previous version 4.0.3 dated 2009-10-18

Author: Søren Højsgaard with contributions from Kevin Wright and Alessandro A. Leidi.
Title: Groupwise computations of summary statistics, general linear contrasts and other utilities
Description: Facilities for groupwise computations of summary statistics and other facilities for working with grouped data.

Diff between doBy versions 4.0.3 dated 2009-10-18 and 4.0.4 dated 2009-10-19

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New package geneARMA with initial version 1.0
Package: geneARMA
Type: Package
Title: Simulate, model, and display data from a time-course microarray experiment with periodic gene expression
Version: 1.0
Date: 2009-10-06
Author: Timothy McMurry , Arthur Berg
Maintainer: Timothy McMurry
Depends: mvtnorm
Description: Fit models for periodic gene expression to time-course microarray data in a normal mixture model framework with mean approximated by a truncated Fourier series and covariance structure modeled by an ARMA(p,q) process. Estimation is performed with the EM algorithm.
License: GPL-3
LazyLoad: yes
Packaged: 2009-10-19 18:00:13 UTC; tmcmurry
Repository: CRAN
Date/Publication: 2009-10-19 19:43:48

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Package bestglm updated to version 0.14 with previous version 0.13 dated 2009-09-10

Author: A.I. McLeod and Changjiang Xu
Title: Best Subset GLM
Description: Best subset glm using AIC, BIC, EBIC, BICq or Cross-Validation. For the normal case, the 'leaps' is used. Otherwise, a slower exhaustive search. The 'xtable' package is needed for vignette 'SimExperimentBICq.Rnw' accompanying this package.

Diff between bestglm versions 0.13 dated 2009-09-10 and 0.14 dated 2009-10-19

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Package snp.plotter updated to version 0.3 with previous version 0.2 dated 2007-01-21

Author: Augustin Luna , Kristin K. Nicodemus ,
Title: snp.plotter
Description: Creates plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple datasets simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either PDF/EPS files.

Diff between snp.plotter versions 0.2 dated 2007-01-21 and 0.3 dated 2009-10-19

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Package relaimpo updated to version 2.1-4 with previous version 2.1-2 dated 2009-05-17

Author: Ulrike Groemping, with contributions from Matthias Lehrkamp
Title: Relative importance of regressors in linear models
Description: relaimpo provides several metrics for assessing relative importance in linear models. These can be printed, plotted and bootstrapped. The recommended metric is lmg, which provides a decomposition of the model explained variance into non-negative contributions. There is a version of this package available that additionally provides a new and also recommended metric called pmvd. If you are a non-US user, you can download this extended version from Ulrike Groempings web site.

Diff between relaimpo versions 2.1-2 dated 2009-05-17 and 2.1-4 dated 2009-10-19

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Package pastecs updated to version 1.3-10 with previous version 1.3-8 dated 2009-02-23

Author: Frederic Ibanez , Philippe Grosjean & Michele Etienne
Title: Package for Analysis of Space-Time Ecological Series
Description: Regulation, decomposition and analysis of space-time series. The pastecs library is a PNEC-Art4 and IFREMER (Benoit Beliaeff ) initiative to bring PASSTEC 2000 (http://www.obs-vlfr.fr/~enseigne/anado/passtec/passtec.htm) functionnalities to R.

Diff between pastecs versions 1.3-8 dated 2009-02-23 and 1.3-10 dated 2009-10-19

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Package irr updated to version 0.80 with previous version 0.70 dated 2007-06-16

Author: Matthias Gamer , Jim Lemon , Ian Fellows
Title: Various Coefficients of Interrater Reliability and Agreement
Description: Coefficients of Interrater Reliability and Agreement for quantitative, ordinal and nominal data: ICC, Finn-Coefficient, Robinson'A, Kendall's W, Cohen's Kappa, ...

Diff between irr versions 0.70 dated 2007-06-16 and 0.80 dated 2009-10-19

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Package e1071 updated to version 1.5-20 with previous version 1.5-19 dated 2009-01-06

Author: Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David Meyer, and Andreas Weingessel
Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...

Diff between e1071 versions 1.5-19 dated 2009-01-06 and 1.5-20 dated 2009-10-19

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Package dlnm updated to version 1.1.0 with previous version 1.0.2 dated 2009-10-13

Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and cross-basis matrices in order to run distributed lag models and their non-linear extension, then to predict and graph the results for a fitted model.

Diff between dlnm versions 1.0.2 dated 2009-10-13 and 1.1.0 dated 2009-10-19

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New package cudaBayesreg with initial version 0.1-1
Package: cudaBayesreg
Version: 0.1-1
Date: 2009-10-10
Title: CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
Depends: R (>= 2.9.2), AnalyzeFMRI
SystemRequirements: nvcc (release 2.3) NVIDIA Cuda Compiler driver, and g++ GNU compiler version 3.4 (version 4.4 is not yet compatible with nvcc).
Description: Compute Unified Device Architecture (CUDA) is a software platform for massively parallel high-performance computing on NVIDIA GPUs. This package provides a CUDA implementation of a Bayesian multilevel model for the analysis of brain fMRI data. A fMRI data set consists of time series of volume data in 4D space. Typically, volumes are collected as slices of 64 x 64 "voxels". Analysis of fMRI data often relies on fitting linear regression models at each voxel of the brain. The volume of the data to be processed, and the type of statistical analysis to perform in fMRI analysis, call for high-performance computing strategies. In this package, the CUDA programming model uses a separate thread for fitting a linear regression model at each voxel in parallel. The global statistical model implements a Gibbs Sampler for hierarchical linear models with a normal prior. This model has been proposed by Rossi, Allenby and McCulloch in "Bayesian Statistics and Marketing", Chapter 3, and is referred to as "rhierLinearModel" in the R-package "bayesm". A notebook equipped with a NVIDIA "GeForce 8400M GS" card having Compute Capability 1.1 has been used in the tests.
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2009-10-19 17:01:37
Packaged: 2009-10-19 12:55:10 UTC; afs

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Package R.oo updated to version 1.6.2 with previous version 1.5.0 dated 2009-09-10

Author: Henrik Bengtsson
Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.

Diff between R.oo versions 1.5.0 dated 2009-09-10 and 1.6.2 dated 2009-10-19

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Package KFAS updated to version 0.4.5 with previous version 0.4.4 dated 2009-10-01

Author: Jouni Helske
Title: Multivariate Kalman filter and smoother, simulation smoother and forecasting of gaussian state space models. Approximate likelihood of linear non-gaussian state space models.
Description: Package KFAS provides functions for fast Kalman filtering, state and disturbance smoothing, forecasting and simulation of multivariate time-variant state space models. All functions can use exact diffuse initialisation when distributions of some or all elements of initial state vector are unknown. Filtering, state smoothing and simulation functions use sequential processing algorithm, which is faster than standard approach, and it also allows singularity of prediction error variance matrix. KFAS also contains function which computes approximate likelihood of linear non-gaussian state space model.

Diff between KFAS versions 0.4.4 dated 2009-10-01 and 0.4.5 dated 2009-10-19

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Package FKF updated to version 0.1.0 with previous version 0.0.2 dated 2009-07-18

Author: David Luethi, Philipp Erb, Simon Otziger
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman filter, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.

Diff between FKF versions 0.0.2 dated 2009-07-18 and 0.1.0 dated 2009-10-19

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Package AnalyzeFMRI updated to version 1.1-11 with previous version 1.1-10 dated 2008-02-28

Author: J L Marchini , P Lafaye de Micheaux
Title: Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.

Diff between AnalyzeFMRI versions 1.1-10 dated 2008-02-28 and 1.1-11 dated 2009-10-19

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Package quantreg updated to version 4.43 with previous version 4.38 dated 2009-08-04

Author: Roger Koenker
Title: Quantile Regression
Description: Quantile regression and related methods.

Diff between quantreg versions 4.38 dated 2009-08-04 and 4.43 dated 2009-10-19

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 31 files changed, 1266 insertions(+), 909 deletions(-)

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Package contrast updated to version 0.12 with previous version 0.10 dated 2009-07-18

Author: Max Kuhn, contributions from Steve Weston, Jed Wing and James Forester
Title: A collection of contrast methods
Description: Contrast methods, in the style of the Design package, for fit objects produced by the lm, glm, gls, and geese functions.

Diff between contrast versions 0.10 dated 2009-07-18 and 0.12 dated 2009-10-19

 DESCRIPTION           |   10 +-
 R/contrast.lm.R       |  205 +++++++++++++++++++++++++-------------------------
 inst/CHANGES          |   12 ++
 inst/doc/contrast.Rnw |   88 +++++----------------
 inst/doc/contrast.pdf |binary
 man/contrast.Rd       |    2 
 6 files changed, 146 insertions(+), 171 deletions(-)

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Package aroma.apd updated to version 0.1.7 with previous version 0.1.6 dated 2009-06-14

Author: Henrik Bengtsson
Title: A probe-level data file format used by aroma.affymetrix [DEPRECATED]
Description: THIS PACKAGE HAS BEEN DEPRECATED. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensites. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speed up the read substantially. This package is supporting the aroma.affymetrix package and not intended to be used elsewhere.)

Diff between aroma.apd versions 0.1.6 dated 2009-06-14 and 0.1.7 dated 2009-10-19

 DESCRIPTION           |   13 ++++++++-----
 R/hide                |only
 R/readApd.R           |    2 +-
 R/readApdMap.R        |    2 +-
 R/updateApdUnits.R    |    2 +-
 inst/NEWS             |    4 ++++
 man/readApd.Rd        |    2 +-
 man/readApdMap.Rd     |    2 +-
 man/updateApdUnits.Rd |    2 +-
 9 files changed, 18 insertions(+), 11 deletions(-)

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Package RcmdrPlugin.DoE updated to version 0.6 with previous version 0.5-6 dated 2009-10-18

Author: Ulrike Groemping
Title: R Commander Plugin for (industrial) Design of Experiments
Description: WARNING: This package is currently in beta status! The package provides a platform-independent GUI for design of experiments. It is implemented as a plugin to the R-Commander, which is a more general graphical user interface for statistics in R based on tcl/tk. DoE functionality can be accessed through the menu Design that is added to the R-Commander menus.

Diff between RcmdrPlugin.DoE versions 0.5-6 dated 2009-10-18 and 0.6 dated 2009-10-19

 DESCRIPTION                |    8 ++++----
 R/Menu.FrF2level.R         |    7 ++++++-
 R/Menu.addcenter.R         |   11 +++++++----
 R/Menu.addresponse.R       |    3 ++-
 R/Menu.aggregate.R         |   15 +++++++++------
 R/Menu.augmentlhs.R        |   14 +++++++-------
 R/Menu.bbd.r               |   12 ++++++------
 R/Menu.ccd.r               |   14 +++++++-------
 R/Menu.export.R            |    1 +
 R/Menu.fac.R               |   12 ++++++------
 R/Menu.importrdacsv.R      |    9 ++++++---
 R/Menu.lhs.R               |   12 ++++++------
 R/Menu.linearModelDesign.R |   11 +++++++++--
 R/Menu.oa.R                |   12 ++++++------
 R/Menu.param.R             |    5 +++--
 R/Menu.pb2level.R          |   12 ++++++------
 R/Menu.summarize.R         |    6 +++++-
 R/Menu.wide.R              |    6 ++++--
 R/justDoItDoE.R            |    3 ++-
 inst/NEWS                  |   18 ++++++++++++++++++
 inst/etc/menus.txt         |    2 +-
 21 files changed, 121 insertions(+), 72 deletions(-)

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Package Mcomp updated to version 2.01 with previous version 2.00 dated 2009-09-07

Author: Rob J Hyndman
Title: Data from the M-competitions
Description: The 1001 time series from the M-competition (Makridakis et al. 1982) and the 3003 time series from the IJF-M3 competition (Makridakis and Hibon, 2000).

Diff between Mcomp versions 2.00 dated 2009-09-07 and 2.01 dated 2009-10-19

 ChangeLog            |    4 ++++
 DESCRIPTION          |    8 ++++----
 R/Mdata.R            |    9 ++++++++-
 R/x111.R             |only
 man/M1.Rd            |    4 ++--
 man/Mcomp-package.Rd |    4 ++--
 man/subset.Mcomp.Rd  |    3 +++
 7 files changed, 23 insertions(+), 9 deletions(-)

More information about Mcomp at CRAN
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