Tue, 04 Nov 2014

Package RPPanalyzer updated to version 1.4 with previous version 1.3 dated 2014-06-29

Title: Reads, annotates, and normalizes reverse phase protein array data
Description: Reads in sample description and slide description files and annotates the expression values taken from gpr files. After normalization data can be visualized as boxplot, heatmap or dotplot.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Christian Bender

Diff between RPPanalyzer versions 1.3 dated 2014-06-29 and 1.4 dated 2014-11-04

 DESCRIPTION        |   10 +++++-----
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 R/dataPreproc.R    |   23 ++++++++++++++++++-----
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 5 files changed, 30 insertions(+), 15 deletions(-)

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Package Quandl updated to version 2.4.0 with previous version 2.3.2 dated 2014-04-09

Title: Quandl Data Connection
Description: This package interacts directly with the Quandl API to offer data in a number of formats usable in R, as well as the ability to upload and search.
Author: Raymond McTaggart, Gergely Daroczi
Maintainer: Raymond McTaggart

Diff between Quandl versions 2.3.2 dated 2014-04-09 and 2.4.0 dated 2014-11-04

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 17 files changed, 227 insertions(+), 218 deletions(-)

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New package prc with initial version 2014.11-4
Package: prc
LazyLoad: yes
LazyData: yes
Version: 2014.11-4
Title: Paired Response Curve
Author: Youyi Fong
Maintainer: Youyi Fong
Depends: R (>= 3.0.0), kyotil, nlme
Suggests: RUnit, Rmosek, Matrix
Imports:
Additional_repositories: http://download.mosek.com/R/7
Description: Estimation, prediction and testing for analyzing serial dilution assay data using paired response curve.
License: GPL (>= 2)
Packaged: 2014-11-04 22:17:50 UTC; yfong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-05 01:16:53

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New package dfmta with initial version 1.0
Package: dfmta
Type: Package
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Version: 1.0
Date: 2014-11-03
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
Copyright: All files in src/CppBugs are copyright Whit Armstrong. All other files are copyright Institut de Recherches Internationales Servier and Institut national de la sante et de la recherche medicale.
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization", Statistics in Medicine, 2014.
License: GPL-3
Depends: R (>= 3.1.0)
LinkingTo: RcppArmadillo (>= 0.3.910), BH (>= 1.54), RcppProgress (>= 0.1), Rcpp
Packaged: 2014-11-04 23:30:49 UTC; jjourdan
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-05 01:20:37

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Package WARN updated to version 1.1 with previous version 1.0 dated 2013-04-12

Title: Weaning Age Reconstruction with Nitrogen isotope analysis
Description: This estimates precise weaning ages for a given skeletal population by analyzing the stable nitrogen isotope ratios of them. Bone collagen turnover rates estimated anew and the approximate Bayesian computation (ABC) were adopted in this package.
Author: Takumi Tsutaya
Maintainer: Takumi Tsutaya

Diff between WARN versions 1.0 dated 2013-04-12 and 1.1 dated 2014-11-04

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Package vardpoor updated to version 0.2.0.14 with previous version 0.2.0.13 dated 2014-10-06

Title: Variance estimation for surveys by the ultimate cluster method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks

Diff between vardpoor versions 0.2.0.13 dated 2014-10-06 and 0.2.0.14 dated 2014-11-04

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Package usl updated to version 1.4.0 with previous version 1.3.1 dated 2014-06-20

Title: Analyze system scalability with the Universal Scalability Law
Description: The Universal Scalability Law is a model to predict hardware and software scalability. It uses system capacity as a function of load to forecast the scalability for the system.
Author: Neil J. Gunther [aut], Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding

Diff between usl versions 1.3.1 dated 2014-06-20 and 1.4.0 dated 2014-11-04

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Package readBrukerFlexData updated to version 1.8.1 with previous version 1.8 dated 2014-09-27

Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb

Diff between readBrukerFlexData versions 1.8 dated 2014-09-27 and 1.8.1 dated 2014-11-04

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Package pca3d updated to version 0.3 with previous version 0.2 dated 2013-03-21

Title: Three dimensional PCA plots
Description: This package provides a function simplifying presentation of PCA models in a 3D interactive representation using rgl
Author: January Weiner
Maintainer: January Weiner

Diff between pca3d versions 0.2 dated 2013-03-21 and 0.3 dated 2014-11-04

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Package ordinalgmifs updated to version 1.0.2 with previous version 1.0.1 dated 2014-10-05

Title: Ordinal Regression for High-dimensional Data
Description: This package provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne, Amanda Gentry
Maintainer: Kellie J. Archer

Diff between ordinalgmifs versions 1.0.1 dated 2014-10-05 and 1.0.2 dated 2014-11-04

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Package lpSolveAPI updated to version 5.5.2.0-12 with previous version 5.5.2.0-11 dated 2014-06-27

Title: R Interface for lp_solve version 5.5.2.0
Description: The lpSolveAPI package provides an R interface for lp_solve, a Mixed Integer Linear Programming (MILP) solver with support for pure linear, (mixed) integer/binary, semi-continuous and special ordered sets (SOS) models.
Author: lp_solve , Kjell Konis .
Maintainer: Kjell Konis

Diff between lpSolveAPI versions 5.5.2.0-11 dated 2014-06-27 and 5.5.2.0-12 dated 2014-11-04

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 lpSolveAPI-5.5.2.0-12/lpSolveAPI/src/lp_solve/lusol.c    |    6 +-
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 13 files changed, 62 insertions(+), 58 deletions(-)

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Package descr updated to version 1.0.4 with previous version 1.0.3 dated 2014-08-01

Title: Descriptive statistics
Description: This package contains functions to describe weighted categorical variables and functions to facilitate the character encoding conversion of objects.
Author: Jakson Aquino. Includes R source code and/or documentation written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan Kraft
Maintainer: Jakson Aquino

Diff between descr versions 1.0.3 dated 2014-08-01 and 1.0.4 dated 2014-11-04

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New package geesmv with initial version 1.0
Package: geesmv
Type: Package
Title: Modified Variance Estimators for Generalized Estimating Equations
Version: 1.0
Date: 2014-10-29
Author: Ming Wang
Maintainer: Zheng Li
Depends: R (>= 3.0.2)
Imports: nlme, gee, matrixcalc, MASS
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
License: GPL (>= 3)
Packaged: 2014-11-04 16:49:42 UTC; Joe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 00:28:48

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Package biwavelet updated to version 0.17.4 with previous version 0.17.3 dated 2014-03-27

Title: Conduct Univariate and Bivariate Wavelet Analyses
Description: This is a port of the WTC MATLAB package written by Aslak Grinsted and the wavelet program written by Christopher Torrence and Gibert P. Compo. This package can be used to perform univariate and bivariate (cross-wavelet, wavelet coherence, wavelet clustering) analyses.
Author: Tarik C. Gouhier, Aslak Grinsted
Maintainer: Tarik C. Gouhier

Diff between biwavelet versions 0.17.3 dated 2014-03-27 and 0.17.4 dated 2014-11-04

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New package aoos with initial version 0.0.1
Package: aoos
Type: Package
Title: Another Object Orientation System
Version: 0.0.1
Date: 2014-11-03
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz
BugReports: https://github.com/wahani/aoos/issues
Description: Another implementation of object-orientation in R. Private and public methods are part of the class-definition. Allows to write a lot of small methods as part of the class definition without cluttering the object.
Depends: methods
License: GPL-3 | file LICENSE
Suggests: testthat
Packaged: 2014-11-04 16:35:49 UTC; sebastian
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-05 00:23:26

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Package snpEnrichment updated to version 1.6.0 with previous version 1.5-0 dated 2014-09-26

Title: SNPs Enrichment Analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal)
Author: Mickael Canouil [aut, cre], Loic Yengo [ctb]
Maintainer: Mickael Canouil

Diff between snpEnrichment versions 1.5-0 dated 2014-09-26 and 1.6.0 dated 2014-11-04

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New package WhiteStripe with initial version 1.0
Package: WhiteStripe
Type: Package
Title: Whitestripe White Matter Normalization for Magnetic Resonance Images
Version: 1.0
Date: 2014-04-28
Author: Taki Shinohara, John Muschelli
Maintainer: John Muschelli
Description: Whitestripe normalization from Shinohara et. al does For intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the MNI template and uses histogram-based methods.
License: GPL-2
Depends: R (>= 2.10)
Imports: oro.nifti, mgcv, fslr
BugReports: https://github.com/muschellij2/WhiteStripe/issues
Packaged: 2014-11-04 02:13:59 UTC; johnmuschelli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-04 22:31:43

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Package prim updated to version 1.0.15 with previous version 1.0.14 dated 2014-06-13

Title: Patient Rule Induction Method (PRIM)
Description: PRIM for bump hunting in high-dimensional data
Author: Tarn Duong
Maintainer: Tarn Duong

Diff between prim versions 1.0.14 dated 2014-06-13 and 1.0.15 dated 2014-11-04

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Package marelac updated to version 2.1.4 with previous version 2.1.3 dated 2014-01-07

Title: Tools for Aquatic Sciences
Description: Datasets, constants, conversion factors, utilities for MArine, Riverine, Estuarine, LAcustrine and Coastal science. The package contains among others: (1) chemical and physical constants and datasets, e.g. atomic weights, gas constants, the earths bathymetry; (2) conversion factors (e.g. gram to mol to liter, barometric units, temperature, salinity); (3) physical functions, e.g. to estimate concentrations of conservative substances, gas transfer and diffusion coefficients, the Coriolis force and gravity; (4) thermophysical properties of the seawater, as from the UNESCO polynomial or from the more recent derivation based on a Gibbs function.
Author: Karline Soetaert , Thomas Petzoldt , Filip Meysman
Maintainer: Karline Soetaert

Diff between marelac versions 2.1.3 dated 2014-01-07 and 2.1.4 dated 2014-11-04

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New package FAMILY with initial version 0.1.18
Package: FAMILY
Type: Package
Title: A Convex Formulation for Modeling Interactions with Strong Heredity
Version: 0.1.18
Date: 2014-09-23
Author: Asad Haris
Maintainer: Asad Haris
Description: Fits penalized linear and logistic regression models with pairwise interaction terms.
License: GPL (>= 2)
Imports: pheatmap, pROC
Packaged: 2014-11-04 02:43:22 UTC; Asad
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-04 22:29:52

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Package VGAMdata updated to version 0.9-5 with previous version 0.9-4 dated 2014-05-28

Title: Data supporting the VGAM package
Description: Data sets to accompany the VGAM package. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology.
Author: Thomas W. Yee
Maintainer: Thomas Yee

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Package SKAT updated to version 1.0.1 with previous version 1.0 dated 2014-10-31

Title: SNP-set (Sequence) Kernel Association Test
Description: SKAT is a kernel regression based association test between a set of single nucleotide polymorphism (SNP) and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates, such as principal components to account for population stratification.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee

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Package sglOptim updated to version 1.0.122.1 with previous version 1.0.122.0 dated 2014-03-24

Title: Sparse group lasso generic optimizer
Description: Fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. This package apply template metaprogramming techniques, therefore -- when compiling the package from source -- a high level of optimization is needed to gain full speed (e.g. for the GCC compiler use -O3). Use of multiple processors for cross validation and subsampling is supported through OpenMP. The Armadillo C++ library is used as the primary linear algebra engine. (The sglOptim package version a.b.c.d is interpreted as follows: a - primary version, b - major updates and fixes, c - source revision as corresponding to R-Forge, d - minor fixes made only to the CRAN branch of the source)
Author: Martin Vincent
Maintainer: Martin Vincent

Diff between sglOptim versions 1.0.122.0 dated 2014-03-24 and 1.0.122.1 dated 2014-11-04

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Package RPushbullet updated to version 0.1.1 with previous version 0.1.0 dated 2014-10-10

Title: R Interface to the Pushbullet Messaging Service
Description: This package provides an easy-to-use interface for the Pushbullet messaging service which provides fast and efficient notifications (and file transfer) between computers, phones and tablets. An account has to be registered at the site http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

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Package pvar updated to version 2.0 with previous version 1.0.9 dated 2013-12-11

Title: the Calculation and Application of p-variation
Description: The calculation of p-variation of the finite sample data
Author: Vygantas Butkus
Maintainer: Vygantas Butkus

Diff between pvar versions 1.0.9 dated 2013-12-11 and 2.0 dated 2014-11-04

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Package ONETr updated to version 1.0.1 with previous version 1.0 dated 2014-09-13

Title: Efficient authenticated interaction with the O*NET API.
Description: This package provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API . The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Author: Eric Knudsen
Maintainer: Eric Knudsen

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Package geomorph updated to version 2.1.2 with previous version 2.1.1 dated 2014-07-19

Title: geometric morphometric analyses of 2d/3d landmark data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams

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Package feature updated to version 1.2.11 with previous version 1.2.10 dated 2013-11-18

Title: Feature significance for multivariate kernel density estimation
Description: Feature significance for multivariate kernel density estimation
Author: Tarn Duong & Matt Wand
Maintainer: Tarn Duong

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Package cvAUC updated to version 1.0.1 with previous version 1.0-0 dated 2013-01-15

Title: Cross-Validated Area Under the ROC Curve Confidence Intervals
Description: This package contains various tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators. The primary functions of the package are ci.cvAUC and ci.pooled.cvAUC, which report cross-validated AUC and compute confidence intervals for cross-validated AUC estimates based on influence curves for i.i.d. and pooled repeated measures data, respectively. One benefit to using influence curve based confidence intervals is that they require much less computation time than bootstrapping methods. The utility functions, AUC and cvAUC, are simple wrappers for functions from the ROCR package.
Author: Erin LeDell, Maya Petersen, Mark van der Laan
Maintainer: Erin LeDell

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Package CorReg updated to version 0.15.8 with previous version 0.15.7 dated 2014-10-02

Title: Linear regression based on linear structure between covariates
Description: Linear regression based on a recursive structural equation model (explicit correlations) found by a MCMC algorithm. It permits to face highly correlated covariates. Variable selection is included (by lasso, elasticnet, etc.). It also provides some graphical tools for basic statistics.
Author: Clement THERY [aut, cre], Christophe BIERNACKI [ctb], Gaetan LORIDANT [ctb], Florian WATRIN [ctb], Quentin GRIMONPREZ [ctb], Vincent KUBICKI [ctb], Samuel BLANCK [ctb], Jeremie KELLNER [ctb]
Maintainer: Clement THERY

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