Thu, 15 Jan 2015

Package WGCNA updated to version 1.43 with previous version 1.42 dated 2014-12-04

Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder and Steve Horvath with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder

Diff between WGCNA versions 1.42 dated 2014-12-04 and 1.43 dated 2015-01-15

 Changelog                |   15 +++
 DESCRIPTION              |   13 +-
 MD5                      |   18 ++--
 NAMESPACE                |    2 
 R/Functions.R            |  206 ++++++++++++++++++++++++++++++++++++++++-------
 R/GOenrichmentAnalysis.R |   12 +-
 R/heatmapWithLegend.R    |   26 -----
 man/WGCNA-package.Rd     |    4 
 man/blueWhiteRed.Rd      |    8 +
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 10 files changed, 262 insertions(+), 82 deletions(-)

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Package mixer updated to version 1.8 with previous version 1.7 dated 2013-07-25

Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of networks using MIXtures of Erdos-Renyi random graphs
Author: Christophe Ambroise [aut], Gilles Grasseau [aut], Mark Hoebeke [aut], Pierre Latouche [aut, cre], Vincent Miele [aut], Franck Picard [aut], LAPACK authors [aut] (copyrights apply to src/*.f)
Maintainer: Pierre Latouche

Diff between mixer versions 1.7 dated 2013-07-25 and 1.8 dated 2015-01-15

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 mixer-1.8/mixer/inst/CITATION              |   72 ++++++++++++++---------------
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 mixer-1.8/mixer/src/ModelDesigner.cc       |    6 ++
 mixer-1.8/mixer/src/ModelImprover.cc       |    7 ++
 mixer-1.8/mixer/src/SOCEm.cc               |    8 ++-
 mixer-1.8/mixer/src/VEstep_R.cc            |    5 +-
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 mixer-1.8/mixer/src/ermgo_R.cc             |    8 +++
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 mixer-1.8/mixer/src/matrix.h               |    6 +-
 24 files changed, 199 insertions(+), 123 deletions(-)

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Package EMP updated to version 2.0.1 with previous version 2.0.0 dated 2015-01-08

Title: Expected Maximum Profit Classification Performance Measure
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014).
Author: Cristian Bravo, Seppe vanden Broucke and Thomas Verbraken
Maintainer: Cristian Bravo

Diff between EMP versions 2.0.0 dated 2015-01-08 and 2.0.1 dated 2015-01-15

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 EMP-2.0.1/EMP/R/empChurn.R            |   14 +++++++++-----
 EMP-2.0.1/EMP/R/empCreditScoring.R    |   12 +++++++-----
 EMP-2.0.1/EMP/R/empRocInfo.R          |   21 +++++++++++++--------
 EMP-2.0.1/EMP/man/EMP-package.Rd      |   17 +++++------------
 EMP-2.0.1/EMP/man/empChurn.Rd         |   14 ++++++--------
 EMP-2.0.1/EMP/man/empCreditScoring.Rd |   12 +++++-------
 11 files changed, 69 insertions(+), 62 deletions(-)

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Package spacetime updated to version 1.1-2 with previous version 1.1-1 dated 2014-08-22

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma

Diff between spacetime versions 1.1-1 dated 2014-08-22 and 1.1-2 dated 2015-01-15

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New package lfl with initial version 1.0
Package: lfl
Type: Package
Title: Linguistic Fuzzy Logic
Version: 1.0
Date: 2015-01-14
Author: Michal Burda
Maintainer: Michal Burda
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE).
License: GPL (>= 3.0)
Suggests: testthat
Depends: R (>= 3.1.1)
Imports: Rcpp (>= 0.11.0), foreach, forecast (>= 5.5), plyr, tseries, e1071, zoo, utils
LinkingTo: Rcpp
NeedsCompilation: yes
SystemRequirements: C++11
Packaged: 2015-01-15 13:27:44 UTC; michal
Repository: CRAN
Date/Publication: 2015-01-15 17:04:00

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Package diseasemapping updated to version 1.1.5 with previous version 1.1.4 dated 2015-01-05

Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formating of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown

Diff between diseasemapping versions 1.1.4 dated 2015-01-05 and 1.1.5 dated 2015-01-15

 DESCRIPTION |   12 ++++++------
 MD5         |    3 ++-
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 3 files changed, 8 insertions(+), 7 deletions(-)

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Package bmrm updated to version 3.0 with previous version 1.8 dated 2014-02-10

Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk under L1 or L2 regularization. Implements the algorithm proposed by Teo et al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR 2012). The package comes with lot of loss functions for machine learning which make it powerful for big data analysis. The applications includes: structured prediction, linear SVM, multi-class SVM, f-beta optimization, ROC optimization, ordinal regression, quantile regression, epsilon insensitive regression, least mean square, logistic regression, least absolute deviation regression (see package examples), etc... all with L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados

Diff between bmrm versions 1.8 dated 2014-02-10 and 3.0 dated 2015-01-15

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Package bgeva updated to version 0.3 with previous version 0.2 dated 2013-07-05

Title: Binary Generalized Extreme Value Additive Models
Description: Routine for fitting regression models for binary rare events with linear and nonlinear covariate effects when using the quantile function of the Generalized Extreme Value random variable.
Author: Giampiero Marra, Raffaella Calabrese and Silvia Angela Osmetti
Maintainer: Giampiero Marra

Diff between bgeva versions 0.2 dated 2013-07-05 and 0.3 dated 2015-01-15

 ChangeLog     |    3 +++
 DESCRIPTION   |   13 +++++--------
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 6 files changed, 26 insertions(+), 26 deletions(-)

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Package SemiParBIVProbit updated to version 3.2-13.2 with previous version 3.2-13.1 dated 2015-01-08

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-13.1 dated 2015-01-08 and 3.2-13.2 dated 2015-01-15

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Package rPref updated to version 0.4 with previous version 0.3 dated 2014-11-18

Title: Database preferences and Skyline computation
Description: Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator, and some generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks

Diff between rPref versions 0.3 dated 2014-11-18 and 0.4 dated 2015-01-15

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 31 files changed, 893 insertions(+), 677 deletions(-)

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Package RecordLinkage updated to version 0.4-7 with previous version 0.4-6 dated 2014-12-11

Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain.
Author: Andreas Borg , Murat Sariyar
Maintainer: Andreas Borg

Diff between RecordLinkage versions 0.4-6 dated 2014-12-11 and 0.4-7 dated 2015-01-15

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New package MultiMeta with initial version 0.1
Package: MultiMeta
Type: Package
Title: Meta-analysis of Multivariate Genome Wide Association Studies
Version: 0.1
Date: 2014-08-21
Author: Dragana Vuckovic
Maintainer: Dragana Vuckovic
Description: Allows running a meta-analysis of multivariate Genome Wide Association Studies (GWAS) and easily visualizing results through custom plotting functions. The multivariate setting implies that results for each single nucleotide polymorphism (SNP) include several effect sizes (also known as "beta coefficients", one for each trait), as well as related variance values, but also covariance between the betas. The main goal of the package is to provide combined beta coefficients across different cohorts, together with the combined variance/covariance matrix. The method is inverse-variance based, thus each beta is weighted by the inverse of its variance-covariance matrix, before taking the average across all betas. The default options of the main function \code{multi_meta} will work with files obtained from GEMMA multivariate option for GWAS (Zhou & Stephens, 2014). It will work with any other output, as soon as columns are formatted to have the according names. The package also provides several plotting functions for QQ-plots, Manhattan Plots and custom summary plots.
License: GPL (>= 2)
Imports: mvtnorm,expm,ggplot2,reshape2
Depends: gtable,grid
Collate: 'betas_plot.R' 'mhplot.R' 'multi_meta.R' 'qqplotter.R' 'Example_file_1.R' 'Example_file_2.R' 'Example_output_file.R'
Packaged: 2015-01-15 08:57:26 UTC; genetica
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-15 11:44:10

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Package Evapotranspiration updated to version 1.5 with previous version 1.4 dated 2014-06-12

Title: Estimating Potential and Actual Evapotranspiration with Multiple Models
Description: Allows the use of user-defined data and constants to calculate potential evapotranspiration (PET i.e. the amount of evaporation from a surface if sufficient water is available) and actual evapotranspiration (AET i.e. the actual amount of water evaporated from a surface) from 17 different formulations including the Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo , Seth Westra
Maintainer: Danlu Guo

Diff between Evapotranspiration versions 1.4 dated 2014-06-12 and 1.5 dated 2015-01-15

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Package RMySQL updated to version 0.10.1 with previous version 0.10 dated 2015-01-05

Title: Database Interface and MySQL Driver for R
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre], David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms

Diff between RMySQL versions 0.10 dated 2015-01-05 and 0.10.1 dated 2015-01-15

 DESCRIPTION |   22 ++++++++++------------
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Package cmm updated to version 0.8 with previous version 0.7 dated 2013-02-23

Title: Categorical Marginal Models
Description: Quite extensive package for the estimation of marginal models for categorical data.
Author: Wicher Bergsma and Andries van der Ark
Maintainer: L. A. van der Ark

Diff between cmm versions 0.7 dated 2013-02-23 and 0.8 dated 2015-01-15

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Package remMap (with last version 0.1-0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2009-01-17 0.1-0

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Package bark (with last version 0.1-0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2008-07-16 0.1-0

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Package convexHaz (with last version 0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2009-01-29 0.2
2008-10-29 0.1
2008-09-10 0.0

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Package UScensus2000blkgrp (with last version 0.03) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2010-02-24 0.03

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Package PenLNM (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-11-28 1.0

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Package gemmR (with last version 1.3-2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-12-13 1.3-2

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Package PoMoS (with last version 1.1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2011-02-11 1.1.1
2010-10-23 1.1
2010-10-13 1.0

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Package NAM updated to version 1.0.2 with previous version 1.0.1 dated 2015-01-05

Title: Nested Association Mapping
Description: NAM, biparental and random populations toolbox
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu
Maintainer: Alencar Xavier

Diff between NAM versions 1.0.1 dated 2015-01-05 and 1.0.2 dated 2015-01-15

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Package COPASutils updated to version 0.1.6 with previous version 0.1.5 dated 2014-12-10

Title: Tools for processing COPAS large-particle flow cytometer data
Description: A logical workflow for the reading, processing, and visualization of data obtained from the Union Biometrica Complex Object Parametric Analyzer and Sorter (COPAS) platform large-particle flow cytometers and a powerful suite of functions for the rapid processing and analysis of large high-throughput screening data sets. It combines the speed of dplyr with the elegance of ggplot2 to make analysis of COPAS data fast and painless.
Author: Tyler Shimko , Erik Andersen
Maintainer: Erik Andersen

Diff between COPASutils versions 0.1.5 dated 2014-12-10 and 0.1.6 dated 2015-01-15

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Package CompRandFld updated to version 1.0.3-3 with previous version 1.0.3-1 dated 2014-08-23

Title: Composite-likelihood based Analysis of Random Fields
Description: The aim of this package is to collect a set of procedures for the analysis of Random Fields by Composite Likelihood methods. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood based methods are emerging as useful tools for mitigating such computational problems and show satisfactory results when compared with other techniques such as, for example the tapering method. Moreover, composite likelihood (and related quantities) have some good properties similar to those of the standard likelihood.
Author: Simone Padoan , Moreno Bevilacqua
Maintainer: Simone Padoan

Diff between CompRandFld versions 1.0.3-1 dated 2014-08-23 and 1.0.3-3 dated 2015-01-15

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