Mon, 15 Oct 2012

Package XLConnect updated to version 0.2-2 with previous version 0.2-1 dated 2012-08-17

Title: Excel Connector for R
Description: Manipulate Excel files from R
Author: Mirai Solutions GmbH
Maintainer: Martin Studer

Diff between XLConnect versions 0.2-1 dated 2012-08-17 and 0.2-2 dated 2012-10-15

 DESCRIPTION              |    8 ++++----
 MD5                      |   12 ++++++------
 NEWS                     |    3 +++
 inst/XLConnect.R         |    7 +++++--
 inst/doc/XLConnect.Rnw   |    6 ++++--
 inst/doc/XLConnect.pdf   |binary
 man/XLConnect-package.Rd |    4 ++--
 7 files changed, 24 insertions(+), 16 deletions(-)

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Package survPresmooth updated to version 1.1-3 with previous version 1.1-2 dated 2011-10-19

Title: Presmoothed Estimation in Survival Analysis
Description: Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data
Author: Ignacio Lopez-de-Ullibarri and Maria Amalia Jacome
Maintainer: Ignacio Lopez-de-Ullibarri

Diff between survPresmooth versions 1.1-2 dated 2011-10-19 and 1.1-3 dated 2012-10-15

 ChangeLog                  |   65 +++++++--
 DESCRIPTION                |    8 -
 MD5                        |   24 +--
 R/presmooth.R              |  325 +++++++++++++++++++++++++++++----------------
 man/control.presmooth.Rd   |   11 -
 man/presmooth.Rd           |  185 +++++++++++--------------
 man/print.survPresmooth.Rd |   14 +
 src/isevect.c              |  230 ++++++++++++++++++++-----------
 src/pilot2forhintegrand.c  |    2 
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 src/survPresmooth.h        |    4 
 src/termsmise.c            |   32 +---
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 14 files changed, 543 insertions(+), 365 deletions(-)

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New package Ridit with initial version 1.1
Package: Ridit
Type: Package
Title: Ridit Analysis (An extension of the Kruskal-Wallis Test.)
Version: 1.1
Date: 2012-10-15
Author: SeyedMahmood TaghaviShahri
Maintainer: SeyedMahmood TaghaviShahri
Description: An extension of the Kruskal-Wallis Test that allow selection of arbitrary reference group. Also provide Mean Ridit for each group. Mean Ridit of a group is an estimate of probability a random observation from that group will be greater than or equal to a random observation from reference group.
License: GPL-2 | GPL-3
Packaged: 2012-10-15 18:15:11 UTC; Taghavi
Repository: CRAN
Date/Publication: 2012-10-15 20:03:34

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Package RHRV updated to version 3.0.0 with previous version 2.6 dated 2012-04-17

Title: Heart rate variability analysis of ECG data
Description: This is a package for developing heart rate variability studies of ECG records
Author: M. Lado, A. Mendez, D. Olivieri, L. Rodriguez-Linares, X. Vila
Maintainer: L. Rodriguez-Linares

Diff between RHRV versions 2.6 dated 2012-04-17 and 3.0.0 dated 2012-10-15

 DESCRIPTION                      |   11 +--
 MD5                              |   60 ++++++++---------
 NAMESPACE                        |    1 
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 R/CalculateApEn.R                |    6 -
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 R/CalculateRfromCorrelation.R    |   25 +------
 R/CreateTimeAnalysis.R           |    2 
 R/getC.r                         |   63 +++++++++++++++--
 R/getNodes.r                     |   79 +++++++++++++++++-----
 R/getPower.r                     |   25 +++----
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 man/CalculateApEn.Rd             |    9 +-
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 man/CalculateRfromCorrelation.Rd |    2 
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 man/CreateTimeAnalysis.Rd        |    3 
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 man/LoadEpisodesAscii.Rd         |    3 
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 man/PlotSpectrogram.Rd           |   22 ++++--
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 man/SplitPowerBandByEpisodes.Rd  |    3 
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 32 files changed, 413 insertions(+), 239 deletions(-)

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New package rentrez with initial version 0.1.1
Package: rentrez
Version: 0.1.1
Date: 2011-11-22
Title: Entrez in R
Author: David Winter
Maintainer: David Winter
Depends: R (>= 2.6.0), RCurl, XML
Description: NA
License: MIT
Collate: 'entrez_fetch.r' 'entrez_link.r' 'entrez_search.r' 'set_globals.r' 'parse_pubmed_xml.r' 'entrez_global_query.r' 'entrez_summary.r' 'help.r' 'entrez_post.r'
Packaged: 2012-10-15 19:45:31 UTC; david
Repository: CRAN
Date/Publication: 2012-10-15 20:21:24

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Package phonTools updated to version 0.1-3 with previous version 0.1-2 dated 2012-09-14

Title: Functions for phonetics in R.
Description: The functions contained in this package are intended to facilitate the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation.
Author: Santiago Barreda
Maintainer: Santiago Barreda

Diff between phonTools versions 0.1-2 dated 2012-09-14 and 0.1-3 dated 2012-10-15

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 phonTools-0.1-3/phonTools/man/interpolate.Rd    |   16 ++-
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 37 files changed, 176 insertions(+), 132 deletions(-)

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New package pbdDMAT with initial version 0.1-0
Package: pbdDMAT
Title: Programming with Big Data -- Distributed Matrix Computation
Version: 0.1-0
Date: 2012-10-02
Depends: R (>= 2.15.0), methods, rlecuyer, pbdMPI (>= 0.1-1), pbdSLAP, Rcpp (>= 0.9.10), pbdBASE
Authors@R: c(person("Drew", "Schmidt", role = c("aut", "cre"), email = "schmidt@math.utk.edu"), person("Wei-Chen", "Chen", role = "aut"), person("George", "Ostrouchov", role = "aut"), person("Pragneshkumar", "Patel", role = "aut"))
Description: pbdDMAT is a package for distributed matrix algebra computations over MPI to BLACS, PBLAS, and ScaLAPACK via pbdMPI, pbdSLAP, and pbdBASE.
SystemRequirements: OpenMPI (>= 1.5.4) on Solaris, Linux and Mac, MPICH2 (>= 1.4.1p1) on Windows
License: GPL (>= 2)
URL: http://r-pbd.org/
Packaged: 2012-10-15 04:17:17 UTC; mschmid3
Author: Drew Schmidt [aut, cre], Wei-Chen Chen [aut], George Ostrouchov [aut], Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt
Repository: CRAN
Date/Publication: 2012-10-15 20:01:11

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Package clinfun updated to version 1.0.3 with previous version 1.0.2 dated 2012-09-25

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

Diff between clinfun versions 1.0.2 dated 2012-09-25 and 1.0.3 dated 2012-10-15

 CHANGES              |    5 +++++
 DESCRIPTION          |    6 +++---
 MD5                  |   20 ++++++++++----------
 R/jonkheere.R        |    6 +++---
 man/calogrank.Rd     |    3 ++-
 man/coxphERR.Rd      |   11 +++++++----
 man/coxphQuantile.Rd |   16 ++++++++--------
 man/gsdesign.Rd      |   26 +++++++++++++-------------
 man/pselect.Rd       |   12 ++++++++----
 man/roc.perm.test.Rd |    3 ++-
 man/toxbdry.Rd       |    6 ++++--
 11 files changed, 65 insertions(+), 49 deletions(-)

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New package xoi with initial version 0.59-2
Package: xoi
Version: 0.59-2
Date: 10/15/2012
Depends: R (>= 2.10.1), qtl, stats
Title: Tools for analyzing crossover interference
Author: Karl W Broman , Il youp Kwak
Maintainer: Karl W Broman
Description: Analysis of crossover interference in experimental crosses, particularly regarding the gamma model.
License: GPL-3
URL: http://www.biostat.wisc.edu/~kbroman/software.html
Packaged: 2012-10-15 15:20:59 UTC; kbroman
Repository: CRAN
Date/Publication: 2012-10-15 15:30:05

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New package SAM with initial version 1.0.2
Package: SAM
Type: Package
Title: Sparse Additive Machine
Version: 1.0.2
Date: 2012-08-19
Author: Tuo Zhao, Xingguo Li, Han Liu, Lie Wang, Kathryn Roeder
Maintainer: Tuo Zhao
Depends: R (>= 2.10), splines
Description: The package SAM targets at high dimensional classification problem for complex data analysis. SAM is short for sparse additive machine, which is a explicit combination of high dimensional sparse additive modeling and support vector machine. Different from existing non-linear classification methods, which usually use, SAM adopts the computationally efficient basis spline technique. The optimization is solved by the Linearized Alternative Direction Method of Multipliers (L-ADMM). The computation is further accelerated by warm-start and active-set tricks. For users who are interested in large-scale problems, we also provide an implementation of L1 norm SVM for computational convenience.
License: GPL-2
Packaged: 2012-10-15 16:08:58 UTC; tourzhao
Repository: CRAN
Date/Publication: 2012-10-15 16:25:19

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Package npde updated to version 2.0 with previous version 1.2.1 dated 2010-08-31

Title: Normalised prediction distribution errors for nonlinear mixed-effect models
Description: Routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics
Author: Emmanuelle Comets, Karl Brendel, Thi Huyen Tram Nguyen, France Mentre.
Maintainer: Emmanuelle Comets

Diff between npde versions 1.2.1 dated 2010-08-31 and 2.0 dated 2012-10-15

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 74 files changed, 76 insertions(+), 58 deletions(-)

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New package muscle with initial version 3.8.31-0
Package: muscle
Type: Package
Title: Multiple Sequence Alignment
Version: 3.8.31-0
Date: 2012-10-05
Author: Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.
Maintainer: Alex T. Kalinka
Description: MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
License: Unlimited
URL: http://www.drive5.com/muscle/
LazyLoad: yes
LazyData: yes
Packaged: 2012-10-15 10:25:12 UTC; alexk
Repository: CRAN
Date/Publication: 2012-10-15 13:57:16

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Package minerva updated to version 1.1 with previous version 1.0 dated 2012-08-22

Title: minerva: Maximal Information-Based Nonparametric Exploration R package for Variable Analysis
Description: R wrapper for cmine implementation of Maximal Information-based Nonparametric Exploration statistics (MIC and MINE family)
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman [ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi

Diff between minerva versions 1.0 dated 2012-08-22 and 1.1 dated 2012-10-15

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 8 files changed, 334 insertions(+), 142 deletions(-)

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New package lineup with initial version 0.34-1
Package: lineup
Version: 0.34-1
Date: 10/15/2012
Title: Lining up two sets of measurements
Author: Karl W Broman
Maintainer: Karl W Broman
Depends: R (>= 2.10.1), qtl (>= 1.20-15), class, graphics
Description: Tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues.
License: GPL-3
URL: http://www.biostat.wisc.edu/~kbroman/software
Packaged: 2012-10-15 14:13:15 UTC; kbroman
Repository: CRAN
Date/Publication: 2012-10-15 14:26:11

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New package broman with initial version 0.38-2
Package: broman
Version: 0.38-2
Date: 10/4/2012
Title: Karl Broman's R code
Author: Karl W Broman
Maintainer: Karl W Broman
Depends: R (>= 2.0), utils, graphics, stats
Description: Miscellaneous R functions
License: GPL-3
URL: http://www.biostat.wisc.edu/~kbroman/software
Packaged: 2012-10-04 18:52:27 UTC; kbroman
Repository: CRAN
Date/Publication: 2012-10-15 14:29:06

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Package sybilSBML updated to version 1.1.15 with previous version 1.1.14 dated 2012-07-06

Title: SBML Integration in Package sybil
Description: SBML (Systems Biology Markup Language) integration in sybil
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between sybilSBML versions 1.1.14 dated 2012-07-06 and 1.1.15 dated 2012-10-15

 DESCRIPTION             |   20 ++++++++++----------
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 8 files changed, 35 insertions(+), 25 deletions(-)

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Package nonrandom updated to version 1.3 with previous version 1.2 dated 2012-10-02

Title: Stratification and matching by the propensity score
Description: This package offers a comprehensive data analysis if stratification and matching by the propensity score is done. Several functions are implemented, starting from the selection of the propensity score model up to estimating propensity score based treatment or exposure effects. All functions can be applied separately as well as combined.
Author: Susanne Stampf
Maintainer: Susanne Stampf

Diff between nonrandom versions 1.2 dated 2012-10-02 and 1.3 dated 2012-10-15

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Package modeest updated to version 2.1 with previous version 1.14 dated 2010-08-29

Title: Mode Estimation
Description: This package provides estimators of the mode of univariate unimodal data or univariate unimodal distributions
Author: P. PONCET
Maintainer: P. PONCET

Diff between modeest versions 1.14 dated 2010-08-29 and 2.1 dated 2012-10-15

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Package mgcv updated to version 1.7-22 with previous version 1.7-21 dated 2012-09-18

Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood

Diff between mgcv versions 1.7-21 dated 2012-09-18 and 1.7-22 dated 2012-10-15

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New package pbdBASE with initial version 0.1-0
Package: pbdBASE
Title: Programming with Big Data -- Core pbd Classes and Methods
Version: 0.1-0
Date: 2012-10-02
Depends: R (>= 2.13.0), methods, rlecuyer, pbdMPI (>= 0.1-1), pbdSLAP, Rcpp
LazyLoad: yes
LazyData: yes
Authors@R: c(person("Drew", "Schmidt", role = c("aut", "cre"), email = "schmidt@math.utk.edu"), person("Wei-Chen", "Chen", role = "aut"), person("George", "Ostrouchov", role = "aut"), person("Pragneshkumar", "Patel", role = "aut"))
Description: pbdBASE contains the basic methods for dealing with distributed data types, as well as the data types themselves.
SystemRequirements: OpenMPI (>= 1.5.4) on Solaris, Linux and Mac, MPICH2 (>= 1.4.1p1) on Windows
License: GPL (>= 2)
URL: http://r-pbd.org/
Packaged: 2012-10-15 04:04:03 UTC; mschmid3
Author: Drew Schmidt [aut, cre], Wei-Chen Chen [aut], George Ostrouchov [aut], Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt
Repository: CRAN
Date/Publication: 2012-10-15 06:15:10

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Package orcutt updated to version 1.1 with previous version 1.0 dated 2012-09-15

Title: Estimate procedure in case of first order autocorrelation
Description: This package has been implemented to solve first order autocorrelation problems using an iterative method. This procedure estimates both autocorrelation and beta coefficients recursively until we reach the convergence (8th decimal). The residuals are computed after estimating Beta using EGLS approach and Rho is estimated using the previous residuals.
Author: Stefano Spada, Matteo Quartagno, Marco Tamburini
Maintainer: Spada Stefano

Diff between orcutt versions 1.0 dated 2012-09-15 and 1.1 dated 2012-10-15

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Package logcondens updated to version 2.0.9 with previous version 2.0.8 dated 2012-10-11

Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), this package allows to compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach and Lutz Duembgen
Maintainer: Kaspar Rufibach

Diff between logcondens versions 2.0.8 dated 2012-10-11 and 2.0.9 dated 2012-10-15

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Package imguR updated to version 0.1.5 with previous version 0.1.4 dated 2010-12-20

Title: Share plots using the imgur.com image hosting service
Description: A package to share plots using the image hosting service imgur.com
Author: Aaron Statham
Maintainer: Aaron Statham

Diff between imguR versions 0.1.4 dated 2010-12-20 and 0.1.5 dated 2012-10-15

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