Thu, 10 Apr 2014

Package MRCV updated to version 0.3-1 with previous version 0.3-0 dated 2014-03-26

Title: Methods for Analyzing Multiple Response Categorical Variables (MRCVs)
Description: The MRCV package provides functions for analyzing the association between one single response categorical variable (SRCV) and one multiple response categorical variable (MRCV), or between two or three MRCVs. A modified Pearson chi-square statistic can be used to test for marginal independence for the one or two MRCV case, or a more general loglinear modeling approach can be used to examine various other structures of association for the two or three MRCV case. Bootstrap- and asymptotic-based standardized residuals and model-predicted odds ratios are available, in addition to other descriptive information.
Author: Natalie Koziol and Chris Bilder
Maintainer: Natalie Koziol

Diff between MRCV versions 0.3-0 dated 2014-03-26 and 0.3-1 dated 2014-04-10

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Package tab updated to version 2.1.1 with previous version 1.0 dated 2014-01-18

Title: Functions for creating summary tables for statistical reports.
Description: This package contains functions for generating tables for statistical reports written in Microsoft Word or LaTeX. There are functions for I-by-J frequency tables, comparison of means across levels of a categorical variable, generalized linear models, generalized estimating equations, and Cox proportional hazards regression. The package is intended to make it easier for researchers to translate results from statistical analyses in R to their reports or manuscripts.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen

Diff between tab versions 1.0 dated 2014-01-18 and 2.1.1 dated 2014-04-10

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Package Rsomoclu updated to version 1.3.1 with previous version 1.3 dated 2014-04-07

Title: R package for somoclu
Description: Somoclu is a cluster-oriented implementation of self-organizing maps. It relies on MPI for distributing the workload, and it can be accelerated by CUDA on a GPU cluster. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes.
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao

Diff between Rsomoclu versions 1.3 dated 2014-04-07 and 1.3.1 dated 2014-04-10

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 11 files changed, 28 insertions(+), 65 deletions(-)

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Package RcppCNPy updated to version 0.2.3 with previous version 0.2.2 dated 2013-11-30

Title: Rcpp bindings for NumPy files
Description: This package use the cnpy library written by Carl Rogers to provide read and write facilities for files created with (or for) the NumPy extension for Python. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with -std=c++11 which is the default starting with release 0.2.3 following the release of R 3.1.0.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between RcppCNPy versions 0.2.2 dated 2013-11-30 and 0.2.3 dated 2014-04-10

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Package ora updated to version 2.0-1 with previous version 2.0-0 dated 2013-06-19

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 ora versions 2.0-0 dated 2013-06-19 and 2.0-1 dated 2014-04-10

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New package PSMix with initial version 1.1.1
Package: PSMix
Type: Package
Title: Population structure inference using mixture model
Version: 1.1.1
Encoding: UTF-8
Authors@R: c(person(given = "Baolin", family = "Wu", role = c("aut","cph"),email = "baolin@umn.edu"), person(given = "Nianjun", family = "Liu", role = c("aut","cph"),email = "nliu@ms.soph.uab.edu"), person(given = "Hongyu", family = "Zhao", role = c("aut","cph"),email = "hongyu.zhao@yale.edu"), person(given = "Jose", family = "Gama", role = "cre",email = "jgama@abo.fi"))
Description: population structure inference using likelihood-based approach
URL: http://bioinformatics.med.yale.edu/PSMIX
License: GPL (>= 2)
Depends: R (>= 2.10)
Author: Baolin Wu [aut, cph], Nianjun Liu [aut, cph], Hongyu Zhao [aut, cph], Jose Gama [cre]
Maintainer: Jose Gama
Repository: CRAN
Repository/R-Forge/Project: psmix
Repository/R-Forge/Revision: 3
Repository/R-Forge/DateTimeStamp: 2014-04-10 09:54:12
Date/Publication: 2014-04-10 15:16:20
Packaged: 2014-04-10 10:15:20 UTC; rforge
NeedsCompilation: yes

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Package mnlogit updated to version 1.1.1 with previous version 1.1.0 dated 2014-03-21

Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Wang Zhiyu, Asad Hasan
Maintainer: Asad Hasan

Diff between mnlogit versions 1.1.0 dated 2014-03-21 and 1.1.1 dated 2014-04-10

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 5 files changed, 20 insertions(+), 9 deletions(-)

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Package grt updated to version 0.2 with previous version 0.1-2 dated 2011-01-20

Title: General Recognition Theory
Description: Functions to generate and analyze data for psychology experiments based on the General Recognition Theory.
Author: Kazunaga Matsuki
Maintainer: Kazunaga Matsuki

Diff between grt versions 0.1-2 dated 2011-01-20 and 0.2 dated 2014-04-10

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Package dataview updated to version 2.0-9 with previous version 1.4-8 dated 2012-07-19

Title: Human readable data presentation
Description: This package provides clear, informative and colorful ways of presenting the contents of data.frame, list, environment etc. in the prompt. Ideally this package should be used in terminals supporting xterm 256 colour mode, e.g. the standard Ubuntu terminal. The Mac OS X terminal (as of Snow Leopard) only support ANSI colour, which still works but doesn't look as nice. On Windows systems no colouring is supported. If the output of functions like 'whos' is a mess or somehow doesn't look like it should check the help for the functions 'style' and 'style.mode' of the 'xtermStyle' package.
Author: Christofer Backlin
Maintainer: Christofer Backlin

Diff between dataview versions 1.4-8 dated 2012-07-19 and 2.0-9 dated 2014-04-10

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New package toaster with initial version 0.2.5
Package: toaster
Type: Package
Title: analytics and visualization with Aster Database
Version: 0.2.5
Author: Gregory Kanevsky
Maintainer: Gregory Kanevsky
Description: toaster (a.k.a 'to Aster') is a set of tools to perform in-database analytics with Teradata Aster Discovery Platform. toaster embraces simple approach by dividing tasks into 2 steps: compute in Aster - visualize and analyze in R. toaster `compute` functions use distributed, highly scalable, parallel SQL and map-reduce for processing of large data sets in Aster database. Then `create` functions visualize results with boxplots, scatterplots, histograms, heatmaps, word clouds, maps, or slope graphs. Advanced options such as faceting, coloring, labeling, and others are supported with most plots.
URL: https://grigory@bitbucket.org/grigory/toaster.git
SystemRequirements: Teradata Aster 5.1 or higher, Teradata Aster Analytical Foundation 5.10 or higher (5.11 or higher is recommended)
Depends: R (>= 2.14), RODBC (>= 1.3-9)
Suggests: testthat (>= 0.2), memoise
Imports: plyr (>= 1.8), reshape2 (>= 1.2.2), ggplot2 (>= 0.9.3.1), scales, RColorBrewer (>= 1.0-5), grid, wordcloud (>= 2.4), ggmap (>= 2.3)
License: GPL-2
Collate: 'toaster.R' 'misc.R' 'utils.R' 'computeCorrelations.R' 'computeHistogram.R' 'computeHeatmap.R' 'plotting.R' 'maps.R' 'showData.R' 'computeAggregates.R' 'computeBarchart.R' 'computeSample.R' 'computePercentiles.R' 'computeLm.R'
Packaged: 2014-04-09 23:04:29 UTC; gk186006
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-10 09:18:08

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Package stylo updated to version 0.5.5-1 with previous version 0.5.5 dated 2014-04-02

Title: Functions for a variety of stylometric analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder

Diff between stylo versions 0.5.5 dated 2014-04-02 and 0.5.5-1 dated 2014-04-10

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Package seqMeta updated to version 1.4 with previous version 1.3 dated 2013-12-03

Title: An R package for meta-analyzing region-based tests of rare DNA variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arend Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Arend Voorman

Diff between seqMeta versions 1.3 dated 2013-12-03 and 1.4 dated 2014-04-10

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Package lsmeans updated to version 2.00-5 with previous version 2.00-4 dated 2014-03-24

Title: Least-Squares Means
Description: This package provides methods for obtaining least-squares means for various linear models. It can also compute contrasts or linear combinations of these least-squares means, comparisons of slopes, interaction plots, and compact letter displays.
Author: Russell V. Lenth
Maintainer: Russ Lenth

Diff between lsmeans versions 2.00-4 dated 2014-03-24 and 2.00-5 dated 2014-04-10

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New package edmr with initial version 0.6.3
Package: edmr
Type: Package
Title: Empirical differentially methylated regions calculation
Description: Optimized DMR analysis based on bimodal normal distribution model and cost function for regional methylation analysis optimization. It captures the regional methylation modification by taking the spatial distribution of CpGs into account for the enrichment DNA methylation sequencing data so as to optimize the definition of the empirical regions. Combined with the dependent adjustment for regional p-value combination and DMR annotation.
Version: 0.6.3
Authors@R: c(person(given="Sheng", family="Li", role=c("aut","cre", "cph"), email = "shelly1436@gmail.com"), person(given="Francine", family="Garrett-Bakelman", role="ctb"), person(family="Akalin", given="Altuna", role="ctb"), person(family="Zumbo", given="Paul", role="ctb"), person(family="Melnick", given="Ari", role="ctb"), person(family="Mason", given="Chris", role=c("ctb","ths")))
Maintainer: Sheng Li
Depends: R (>= 3.0.2)
Imports: GenomicRanges, IRanges, data.table, mixtools
License: MIT + file LICENSE
URL: https://github.com/ShengLi/edmr
LazyData: true
Collate: 'ACF.R' 'edmr.R' 'eDMR.sub.R' 'get.dist.cutoff.R' 'getDMR.R' 'getPeaks.R' 'helpers.R' 'myDiff.to.mixmdl.R' 'myDiffToDMR.R' 'plotCost.R' 'plotMdl1.R' 'filter.dmr.R' 'annotation.R' 'document_data.R'
Packaged: 2014-04-07 15:24:10 UTC; shl2018
Author: Sheng Li [aut, cre, cph], Francine Garrett-Bakelman [ctb], Altuna Akalin [ctb], Paul Zumbo [ctb], Ari Melnick [ctb], Chris Mason [ctb, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-10 09:18:01

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New package CatDyn with initial version 1.0-5
Package: CatDyn
Type: Package
Title: Fishery Stock Assessment by Catch Dynamic Models
LazyLoad: yes
LazyData: yes
Version: 1.0-5
Date: 2014-04-07
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta
Depends: R (>= 3.0.0)
Imports: optimx (>= 2013.8.6), BB
Description: Using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean body mass by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 57 types of catch dynamics models of increasing complexity, and two distributions for the catch data.
License: GPL (>= 2)
Packaged: 2014-04-10 05:35:28 UTC; Rubin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-10 09:17:54

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Package archetypes updated to version 2.2-0 with previous version 2.1-2 dated 2013-12-16

Title: Archetypal Analysis
Description: The main function archetypes implements a framework for archetypal analysis supporting arbitrary problem solving mechanisms for the different conceptual parts of the algorithm.
Author: Manuel J. A. Eugster [aut, cre], Friedrich Leisch [aut], Sohan Seth [ctb]
Maintainer: Manuel J. A. Eugster

Diff between archetypes versions 2.1-2 dated 2013-12-16 and 2.2-0 dated 2014-04-10

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 MD5                              |   98 +++----
 NAMESPACE                        |   61 ++--
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 51 files changed, 1963 insertions(+), 1937 deletions(-)

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