Thu, 09 Jul 2015

Package topologyGSA updated to version 1.4.5 with previous version 1.4.4 dated 2014-08-02

Title: Gene Set Analysis Exploiting Pathway Topology
Description: Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques).
Author: Sofia Massa, Gabriele Sales
Maintainer: Gabriele Sales <gabriele.sales@unipd.it>

Diff between topologyGSA versions 1.4.4 dated 2014-08-02 and 1.4.5 dated 2015-07-09

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New package spduration with initial version 0.13.1
Package: spduration
Title: Split-Population Duration (Cure) Regression
Version: 0.13.1
Date: 2015-08-09
Authors@R: c( person("Andreas", "Beger", role = c("aut", "cre"), email = "adbeger@gmail.com"), person("Daina", "Chiba", role = c("aut"), email = "dchiba@essex.ac.uk"), person("Daniel", "Hill", role = c("aut"), email = "dwhill@uga.edu"), person("Nils", "Metternich", role = c("aut"), email = "n.metternich@ucl.ac.uk"), person("Shahryar", "Minhas", role = c("aut"), email = "hermes829@gmail.com"), person("Michael", "Ward", role = c("cph"), email = "michael.don.ward@gmail.com") )
Description: Functions for estimating split-duration regression models and \ various associated generic function methods.
Depends: R (>= 3.1.2)
License: GPL-3
LazyData: true
Imports: corpcor, graphics, plyr, MASS, separationplot, stats, Rcpp (>= 0.11.0), xtable
Suggests: testthat
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-07-09 15:27:45 UTC; andybega
Author: Andreas Beger [aut, cre], Daina Chiba [aut], Daniel Hill [aut], Nils Metternich [aut], Shahryar Minhas [aut], Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Repository: CRAN
Date/Publication: 2015-07-09 18:13:05

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Package rncl updated to version 0.4.0 with previous version 0.2.2 dated 2015-02-06

Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Author: Francois Michonneau [aut, cre], Ben Bolker [aut], Mark Holder [aut], Paul Lewis [aut], Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package plotKML updated to version 0.5-3 with previous version 0.5-2 dated 2015-05-06

Title: Visualization of Spatial and Spatio-Temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>

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Package phangorn updated to version 1.99.14 with previous version 1.99-13 dated 2015-04-07

Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

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Package penDvine updated to version 0.2.4 with previous version 0.2.2 dated 2013-03-12

Title: Flexible Pair-Copula Estimation in D-Vines using Bivariate Penalized Splines
Description: Flexible Pair-Copula Estimation in D-vines using Bivariate Penalized Splines.
Author: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>

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Package MXM updated to version 0.4.1 with previous version 0.4 dated 2015-07-01

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>

Diff between MXM versions 0.4 dated 2015-07-01 and 0.4.1 dated 2015-07-09

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Package mitml updated to version 0.2-3 with previous version 0.2-2 dated 2015-05-22

Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the 'pan' package, and several functions for visualization, data management and the analysis of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>

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Package kknn updated to version 1.3.0 with previous version 1.2-5 dated 2014-02-11

Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
Author: Klaus Schliep & Klaus Hechenbichler
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

Diff between kknn versions 1.2-5 dated 2014-02-11 and 1.3.0 dated 2015-07-09

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Package gamlss.spatial updated to version 1.3 with previous version 0.2 dated 2015-02-05

Title: Spatial Terms in GAMLSS Models
Description: It allows us to fit Markov Random Field (MRF) within the GAMLSS algorithms.
Author: Fernanda De Bastiani [aut, cre, cph], Mikis Stasinopoulos [aut], Bob Rigby [aut]
Maintainer: Fernanda De Bastiani <fernandadebastiani@gmail.com>

Diff between gamlss.spatial versions 0.2 dated 2015-02-05 and 1.3 dated 2015-07-09

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Package rlist updated to version 0.4.2.3 with previous version 0.4 dated 2015-01-24

Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>

Diff between rlist versions 0.4 dated 2015-01-24 and 0.4.2.3 dated 2015-07-09

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Package rebird updated to version 0.2 with previous version 0.1.1 dated 2014-03-05

Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
Author: Rafael Maia [aut], Scott Chamberlain [aut], Andy Teucher [aut], Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>

Diff between rebird versions 0.1.1 dated 2014-03-05 and 0.2 dated 2015-07-09

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Permanent link

New package PythonInR with initial version 0.1-0
Package: PythonInR
Title: Use Python from Within R
Version: 0.1-0
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Description: Interact with Python from within R.
Depends: R (>= 2.15)
Imports: pack, methods, R6, stats
SystemRequirements: Python (>= 2.7.0) with header files and shared library (UNIX) / static library (Windows)
Note: More information about the system requirements can be found in the README file.
URL: https://bitbucket.org/Floooo/pythoninr/
BugReports: https://bitbucket.org/Floooo/pythoninr/issues
License: GPL-3
NeedsCompilation: yes
Packaged: 2015-07-08 22:36:22 UTC; florian
Repository: CRAN
Date/Publication: 2015-07-09 14:47:38

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Package maps updated to version 2.3-10 with previous version 2.3-9 dated 2014-09-22

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>. Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>

Diff between maps versions 2.3-9 dated 2014-09-22 and 2.3-10 dated 2015-07-09

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Package mapproj updated to version 1.2-3 with previous version 1.2-2 dated 2014-01-16

Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>

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Package mapdata updated to version 2.2-4 with previous version 2.2-3 dated 2014-06-03

Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>

Diff between mapdata versions 2.2-3 dated 2014-06-03 and 2.2-4 dated 2015-07-09

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Package FactoMineR updated to version 1.31.3 with previous version 1.31.2 dated 2015-07-06

Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>

Diff between FactoMineR versions 1.31.2 dated 2015-07-06 and 1.31.3 dated 2015-07-09

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Package emil updated to version 2.1.1 with previous version 2.0.2 dated 2015-05-20

Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with resampling methods. The aim of this package is to provide a simple and efficient general framework for working with any type of prediction problem, be it classification, regression or survival analysis, that is easy to extend and adapt to your specific setting. Some commonly used methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre], Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>

Diff between emil versions 2.0.2 dated 2015-05-20 and 2.1.1 dated 2015-07-09

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New package edmr with initial version 0.6.3.1
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: 0.6.3.1
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 <shelly1436@gmail.com>
Depends: R (>= 3.2.1)
Imports: GenomicRanges, IRanges, data.table, mixtools, S4Vectors
License: Artistic-2.0
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: 2015-07-09 14:55:26

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Package downloader updated to version 0.4 with previous version 0.3 dated 2013-05-01

Title: Download Files over HTTP and HTTPS
Description: Provides a wrapper for the download.file function, making it possible to download files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. The 'RCurl' package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.
Author: Winston Chang <winston@stdout.org>
Maintainer: Winston Chang <winston@stdout.org>

Diff between downloader versions 0.3 dated 2013-05-01 and 0.4 dated 2015-07-09

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Package Biodem updated to version 0.4 with previous version 0.3 dated 2012-10-29

Title: Biodemography Functions
Description: The Biodem package provides a number of functions for Biodemographic analysis.
Author: Alessio Boattini and Federico C. F. Calboli; Vincente Canto Cassola together with Martin Maechler authored the function mtx.exp.
Maintainer: Federico Calboli <federico.calboli@helsinki.fi>

Diff between Biodem versions 0.3 dated 2012-10-29 and 0.4 dated 2015-07-09

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Package AcceptanceSampling updated to version 1.0-4 with previous version 1.0-3 dated 2014-01-14

Title: Creation and Evaluation of Acceptance Sampling Plans
Description: Provides functionality for creating and evaluating acceptance sampling plans. Sampling plans can be single, double or multiple.
Author: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>
Maintainer: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>

Diff between AcceptanceSampling versions 1.0-3 dated 2014-01-14 and 1.0-4 dated 2015-07-09

 DESCRIPTION        |   18 +++++++++---------
 MD5                |   12 ++++++------
 NAMESPACE          |    4 +++-
 R/code_generic.R   |    7 +++----
 R/code_twoclass.R  |    1 -
 R/code_var.R       |    1 -
 build/vignette.rds |binary
 7 files changed, 21 insertions(+), 22 deletions(-)

More information about AcceptanceSampling at CRAN
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Package weightedKmeans (with last version 1.2.0) was removed from CRAN

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

2012-04-27 1.2.0

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