CRANberries

Wed, 19 Jun 2013

New package ora with initial version 2.0-0
Package: ora
Version: 2.0-0
Date: 2013-06-17
Title: Convenient Tools for Working with Oracle Databases
Author: Arni Magnusson
Maintainer: Arni Magnusson
Depends: DBI, ROracle
SystemRequirements: Oracle client
Description: Easy-to-use functions to explore Oracle databases and import data into R. User interface for the ROracle package.
License: GPL (>= 2)
Packaged: 2013-06-18 11:10:45 UTC; arnima
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-19 09:06:20

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New package MConjoint with initial version 0.1
Package: MConjoint
Type: Package
Title: Conjoint Analysis through Averaging of Multiple Analyses
Version: 0.1
Date: 2013-05-14
Author: William Hughes
Maintainer: William Hughes
Description: The package aids in creating a Conjoint Analysis design with extra cards. Unlike traditional "holdout" cards these cards are used to create a set of "good" (balanced and low correlation) designs. Each of these designs is analyzed and the average calculated.
License: GPL-3
Packaged: 2013-06-19 06:38:26 UTC; william
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-19 09:01:22

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Tue, 18 Jun 2013

New package ZIM with initial version 1.0
Package: ZIM
Type: Package
Title: Statistical Models for Count Time Series with Excess Zeros
Version: 1.0
Date: 2013-06-15
Author: Ming Yang, Gideon K. D. Zamba, and Joseph E. Cavanaugh
Maintainer: Ming Yang
Depends: MASS
Description: Fits observation-driven and parameter-driven models for count time series with excess zeros.
License: GPL-2
Packaged: 2013-06-15 18:07:55 UTC; myang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-19 00:41:33

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New package MethComp with initial version 1.22
Package: MethComp
Version: 1.22
Date: 2013-05-08
Title: Functions for analysis of agreement in method comparison studies.
Author: Bendix Carstensen, Lyle Gurrin, Claus Ekstrom, Michal Figurski
Maintainer: Bendix Carstensen
Depends: R (>= 3.0.0), nlme
Suggests: R2WinBUGS, BRugs, rjags, coda, lattice, lme4
Description: Methods (standard and advanced) for analysis of agreement between measurement methods.
License: GPL (>= 2)
URL: http://BendixCarstensen.com/MethComp/
Packaged: 2013-06-18 18:24:13 UTC; bxc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-19 00:50:51

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New package mlDNA with initial version 1.0
Package: mlDNA
Type: Package
Title: Machine Learning-based Differential Network Analysis of Transcriptome Data
Version: 1.0
Date: 2013-06-16
Author: Chuang Ma and Xiangfeng Wang
Maintainer: Chuang Ma
URL: http://www.cmbb.arizona.edu/?page_id=36
Depends: R (>= 2.15.1), biwt, cairoDevice, e1071, fBasics, GeneSelector, grDevices, gplots, gWidgets, gWidgetsRGtk2, hash, igraph, nnet, parmigene, pROC, qvalue, ROCR, rsgcc, stringr, snowfall
Suggests: bigmemory
Description: Functions necessary to perform the machine learning-based differential network analysis of transcriptome data.
LazyLoad: yes
License: GPL (>= 2)
Packaged: 2013-06-17 17:05:23 UTC; wanglab
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-18 16:24:38

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New package glmlep with initial version 0.1
Package: glmlep
Type: Package
Title: Fit GLM with LEP-based penalized maximum likelihood
Version: 0.1
Date: 2013-06-18
Author: Canhong Wen, Hao Lin
Maintainer: Canhong Wen
Suggests: mvtnorm
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by LEP.
License: GPL-2
Packaged: 2013-06-18 03:42:57 UTC; linhao
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-18 07:40:42

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Mon, 17 Jun 2013

New package nhlscrapr with initial version 1.0
Package: nhlscrapr
Type: Package
Title: Compiling the NHL Real Time Scoring System Database for easy use in R
Version: 1.0
Date: 2013-06-16
Author: A.C. Thomas, Samuel L. Ventura
Maintainer: A.C. Thomas
Depends: R (>= 2.15.0), RCurl, rjson
Description: Compiling the NHL Real Time Scoring System Database for easy use in R
License: GPL (>= 3)
Packaged: 2013-06-17 15:40:27 UTC; acthomas
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-17 18:18:49

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Sun, 16 Jun 2013

New package nsga2R with initial version 1.0
Package: nsga2R
Type: Package
Title: Elitist Non-dominated Sorting Genetic Algorithm based on R
Version: 1.0
Date: 2013-06-12
Author: Ching-Shih (Vince) Tsou
Maintainer: Ming-Chang (Alan) Lee
Description: This package provide functions for box-constrained multiobjective optimization using the elitist non-dominated sorting genetic algorithm - NSGA-II. Fast non-dominated sorting, crowding distance, tournament selection, simulated binary crossover, and polynomial mutation are called in the main program, nsga2R, to complete the search.
Depends: mco
License: LGPL-3
Packaged: 2013-06-16 05:29:35 UTC; vince
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-16 18:26:19

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New package JointRegBC with initial version 0.1.1
Package: JointRegBC
Version: 0.1.1
Date: 2013-06-13
Title: Joint Modelling of Mixed Correlated Binary and Continuous Responses : A Latent Variable Approach
Author: Ehsan Bahrami Samani and Zhale Tahmasebinejad
Maintainer: Ehsan Bahrami Samani
Description: A joint regression model for mixed correlated binary and continuous responses is presented. In this model binary response can be dependent on the continuous response. With this model, the dependence between responses can be taken into account by the correlation between errors in the models for binary and continuous responses.
Depends: R (>= 2.14.0),nlme,MASS,survival
License: GPL (>= 2)
Contact: +982129902910
Packaged: 2013-06-16 03:32:10 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-16 08:27:19

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Sat, 15 Jun 2013

New package TInPosition with initial version 0.10.4
Package: TInPosition
Type: Package
Title: Inference tests for TExPosition
Version: 0.10.4
Date: 2013-06-04
Author: Derek Beaton, Jenny Rieck, Herve Abdi
Maintainer: Derek Beaton
Description: Non-parametric resampling-based inference tests for TExPosition.
License: GPL-2
Depends: prettyGraphs (>= 2.0.0), TExPosition (>= 2.0.0), ExPosition (>= 2.0.0), InPosition
Packaged: 2013-06-14 03:44:45 UTC; dbeaton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-15 19:07:47

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New package InPosition with initial version 0.10.4
Package: InPosition
Type: Package
Title: Inference Tests for ExPosition
Version: 0.10.4
Date: 2013-06-09
Author: Derek Beaton, Joseph Dunlop, Herve Abdi
Maintainer: Derek Beaton
Description: Non-parametric resampling-based inference tests for ExPosition.
License: GPL-2
Depends: prettyGraphs (>= 2.0.0), ExPosition (>= 2.0.0)
Packaged: 2013-06-14 03:44:41 UTC; dbeaton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-15 18:37:31

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New package dcemriS4 with initial version 0.50
Package: dcemriS4
Version: 0.50
Date: 2013-06-14
Title: A Package for Medical Image Analysis (S4 implementation)
Author: Brandon Whitcher and Volker Schmid, with contributions from Andrew Thornton
Maintainer: Brandon Whitcher
Depends: R (>= 2.14.0), grDevices, graphics, methods, oro.nifti (>= 0.3.0), parallel, utils
Suggests: bitops, minpack.lm, splines, XML, oro.dicom
Description: A collection of routines and documentation that allows one to perform voxel-wise quantitative analysis of dynamic contrast-enhanced or diffusion-weighted MRI data, with emphasis on oncology applications.
License: BSD
URL: http://www.dcemri.org/, http://dcemri.sourceforge.net/, http://dcemri.blogspot.com/
LazyData: yes
ZipData: yes
Packaged: 2013-06-15 12:18:12 UTC; brandon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-15 15:37:28

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Fri, 14 Jun 2013

New package clogitL1 with initial version 1.0
Package: clogitL1
Type: Package
Title: Fitting exact conditional logistic regression with lasso and elastic net penalties.
Version: 1.0
Date: 2013-05-06
Author: Stephen Reid and Robert Tibshirani
Maintainer: Stephen Reid
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
License: GPL-2
Depends: Rcpp (>= 0.10.2)
LinkingTo: Rcpp
Packaged: 2013-06-14 17:59:41 UTC; sreid
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-14 21:44:33

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New package attfad with initial version 1.1
Package: attfad
Type: Package
Title: Evaluation and comparison of expression data and GRNs
Version: 1.1
Date: 2012-09-12
Author: Robert Maier
Maintainer: Robert Maier
Description: This package facilitates evaluation of expression data sets compendia. They can either be based on real data or be the result of a simulation. Some statics make use of a gene regulatory network, on which the expression data is based, and some require the presence of replicates of microarray experiments.
Depends:
License: GPL-2
Packaged: 2013-06-14 16:04:01 UTC; maierr
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-14 21:43:58

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New package wpp2012 with initial version 1.0-0
Package: wpp2012
Version: 1.0-0
Date: 2013-6-13
Title: World Population Prospects 2012
Author: Hana Sevcikova , Patrick Gerland , Kirill Andreev (andreev@un.org), Nan Li (li32@un.org), Danan Gu (gud@un.org), Thomas Spoorenberg (spoorenberg@un.org)
Maintainer: Hana Sevcikova
Depends: R (>= 2.14.2)
Description: Data from the United Nation's World Population Prospects 2012
License: GPL (>= 2)
URL: http://esa.un.org/wpp
Packaged: 2013-06-14 00:59:20 UTC; hana
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-14 17:42:29

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New package gitter with initial version 1.0
Package: gitter
Type: Package
Title: Robust gridding and quantifying of pinned genetic screens
Version: 1.0
Date: 2013-04-18
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih
Description: gitter is a image analysis package for R. Its primary goal is to allow users to robustly and quickly grid and quantify biological images of pinned colonies. It includes several image pre-processing techniques, such as autorotation of plates, noise removal, contrast adjustment and image resizing.
License: LGPL
Depends: jpeg, logging, parallel, EBImage
Packaged: 2013-06-13 18:36:03 UTC; omarwagih
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-14 07:00:25

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Thu, 13 Jun 2013

New package SynchWave with initial version 1.1.0
Package: SynchWave
Version: 1.1.0
Date: 2013-06-12
Title: Synchrosqueezed Wavelet Transform
Author: Matlab original by Eugene Brevdo; R port by Dongik Jang, Hee-Seok Oh and Donghoh Kim
Maintainer: Donghoh Kim
Depends: R (>= 2.13), fields (>= 6.7.6)
Description: This package carries out synchrosqueezed wavelet transform. The package is a translation of MATLAB Synchrosqueezing Toolbox, version 1.1 originally developed by Eugene Brevdo (2012). The C code for curve_ext was authored by Jianfeng Lu, and translated to Fortran by Dongik Jang. Synchrosqueezing is based on the papers: [1] Daubechies, I., Lu, J. and Wu, H. T. (2011) Synchrosqueezed wavelet transforms: An empirical mode decomposition-like tool. Applied and Computational Harmonic Analysis, 30. 243-261. [2] Thakur, G., Brevdo, E., Fukar, N. S. and Wu, H-T. (2013) The Synchrosqueezing algorithm for time-varying spectral analysis: Robustness properties and new paleoclimate applications. Signal Processing, 93, 1079-1094.
License: LGPL (>= 2)
Packaged: 2013-06-13 11:52:11 UTC; donghohkim
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-13 16:06:35

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New package mixer with initial version 1.6
Package: mixer
Type: Package
Title: Random graph clustering
Version: 1.6
Date: 2013-06-07
Author: Christophe Ambroise, Gilles Grasseau, Mark Hoebeke, Pierre Latouche, Vincent Miele, Franck Picard
Maintainer: Pierre Latouche
Description: Routines for the analysis (unsupervised clustering) of networks using MIXtures of Erdos-Renyi random graphs
URL: http://ssbgroup.fr/mixnet/mixer.html, http://ssbgroup.fr
License: GPL (>= 2)
Depends: R (>= 2.5.0), methods
Encoding: UTF-8
Packaged: 2013-06-13 08:02:42 UTC; pierrelatouche
Repository: CRAN
Date/Publication: 2013-06-13 16:11:24
NeedsCompilation: yes

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New package fscaret with initial version 0.8.4
Package: fscaret
Type: Package
Title: Automated caret feature selection
Version: 0.8.4
Date: 2013-06-13
Depends: R (>= 3.0.0), caret, gsubfn, utils, parallel, multicore
Suggests: ada, affy, arm, Boruta, bst, C50, car, caTools, class, Cubist, e1071, earth (>= 2.2-3), elasticnet, ellipse, evtree, extraTrees, fastICA, foba, gam, gbm (>= 2.1), glmnet (>= 1.8), gpls, grid, hda, HDclassif, HiDimDA, Hmisc, ipred, kernlab, kknn, klaR, kohonen, KRLS, lars, leaps, LogicForest, logicFS, LogicReg, MASS, mboost, mda, mgcv, mlbench, neuralnet, nnet, nodeHarvest, obliqueRF, pamr, partDSA, party (>= 0.9-99992), penalized, penalizedLDA, pls, pROC, proxy, qrnn, quantregForest, randomForest, RANN, relaxo, rFerns, rocc, rpart, rrcov, RRF, rrlda, RSNNS, RWeka (>= 0.4-1), sda, SDDA, sparseLDA (>= 0.1-1), spls, stepPlr,superpc, vbmp
Author: Jakub Szlek , acknowledgments to Aleksander Mendyk, contribution to stackoverflow and r-help@r-project.org mailing list community.
Maintainer: Jakub Szlek
License: GPL-2 | GPL-3
Description: Automated feature selection using variety of models provided by caret package
Packaged: 2013-06-13 11:56:13 UTC; kuba
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-13 16:11:47

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New package govStatJPN with initial version 0.1
Package: govStatJPN
Type: Package
Title: functions to get public survey data in Japan
Version: 0.1
Date: 2013-06-11
Author: Yuichiro Otani
Maintainer: Yuichiro Otani
Description: This package purposes to deal with public survey data of Japanese government via their Application Programming Interface (http://statdb.nstac.go.jp/)
License: GPL
LazyLoad: yes
Packaged: 2013-06-13 07:07:52 UTC; yuichiro
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-13 09:40:18

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Wed, 12 Jun 2013

New package SciencePo with initial version 0.3.6.12
Package: SciencePo
Type: Package
Title: A Tool for Analyzing Political Behaviour
Version: 0.3.6.12
Date: 2013-06-12
Author: Daniel Marcelino
Maintainer: Daniel Marcelino
Description: SciencePo is a facility package to make using R even more intuitive for political scientists. The very objective of the package is covering standard analyses for random and nonrandom data. Later updates will focus on implement analytical procedures published in the relevant journals of the field.
URL: http://sciencepo.r-forge.r-project.org/
License: LGPL (>= 2.0, < 3)
Depends: R (>= 3.0), stats, utils, graphics, grDevices
Imports: maptools
Suggests: MASS, methods, Zelig, descr, xtable, foreign, MCMCpack, sandwich, data.table, plyr, ggplot2, maptools
LazyData: yes
Repository: CRAN
BugReports: https://r-forge.r-project.org/forum/?group_id=1560
ByteCompile: TRUE
Packaged: 2013-06-12 19:27:26 UTC; dmarcelino
NeedsCompilation: no
Date/Publication: 2013-06-12 21:52:37

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New package DTR with initial version 1.1-1
Package: DTR
Version: 1.1-1
Date: 2013-06-11
Title: Estimation and comparison of dynamic treatment regimes
Authors@R: c(person("Xinyu", "Tang", role = c("aut", "cre"), email = "xtang@uams.edu"), person("Maria", "Melguizo", role = "aut"))
Author: Xinyu Tang and Maria Melguizo
Maintainer: Xinyu Tang
Depends: survival, R (>= 2.13.0)
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials
License: GPL (>= 2)
URL: http://www.arpediatrics.org/index.php?option=com_uams&view=faculty&sap=00035081
Packaged: 2013-06-12 13:28:53 UTC; TangXinyu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-12 17:36:37

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New package HEAT with initial version 1.0
Package: HEAT
Type: Package
Title: Health Effects of Air Pollution and Temperature (HEAT)
Version: 1.0
Date: 2013-06-11
Author: Youn-Hee Lim and Ho Kim
Maintainer: Il-Sang Ohn
Description: Timeseries analysis is conducted using Korean mortality and environment variables
Depends: R (>= 2.10), splines
License: GPL-2
LazyLoad: yes
Packaged: 2013-06-12 02:50:54 UTC; ilsang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-12 14:02:58

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New package migration.indices with initial version 0.2
Package: migration.indices
Maintainer: Gergely Daróczi
License: AGPL-3
BugReports: https://github.com/daroczig/migration.indices/issues
Title: Migration indices
LazyData: no
Type: Package
Author: Lajos Bálint and Gergely Daróczi
Description: This package provides various indices, like Crude Migration Rate, different Gini indices or the Coefficient of Variation among others, to show the (un)equality of migration.
Version: 0.2
URL: http://github.com/daroczig/migration.indices
Date: 2013-05-27
Encoding: UTF-8
Collate: 'gini.R' 'migration.indices.R' 'crude.R' 'others.R' 'acv.R'
Packaged: 2013-06-11 21:56:24 UTC; daroczig
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-12 08:34:20

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Tue, 11 Jun 2013

New package RTConnect with initial version 0.1
Package: RTConnect
Type: Package
Title: Tools for analyzing sales report files of iTunes Connect.
Version: 0.1
Date: 2013-06-12
Author: Yusuke Miyazaki
Maintainer: Yusuke Miyazaki
Description: Tools for analyzing sales report files of iTunes Connect.
License: BSD_3_clause + file LICENSE
Depends: R (>= 2.14), graphics
Packaged: 2013-06-11 16:58:59 UTC; yusuke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-11 19:11:00

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New package SIMMS with initial version 0.0.1
Package: SIMMS
Version: 0.0.1
Type: Package
Title: Subnetwork Integration for Multi-Modal Signatures
Date: 2013-06-11
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider
Depends: R (>= 2.14.0), survival (>= 2.36-2), MASS (>= 7.3-12)
Description: Algorithms to create prognostic biomarkers using biological networks
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-11 18:09:24

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New package tbdiag with initial version 0.1
Package: tbdiag
Type: Package
Title: Functions for tuberculosis diagnostics research
Version: 0.1
Date: 2013-06-10
Author: Matt Parker
Maintainer: Matt Parker
Description: This package provides functions to assist researchers working in the field of tuberculosis diagnostics. Functions for the interpretation of two popular interferon-gamma release assays are provided, and additional functionality is planned.
License: MIT
URL: https://github.com/mmparker/tbdiag
LazyLoad: yes
LazyData: true
Suggests: testthat
Collate: 'equal.lengths.r' 'is.wholenumber.r' 'qft.cens.r' 'qft.criteria.070.r' 'qft.criteria.cellestis.nomito.r' 'qft.criteria.cellestis.usa.r' 'trim.output.r' 'tbdiag-package.r' 'tspot.cens.r' 'tspot.criteria.10spot.r' 'tspot.criteria.oxford.global.r' 'tspot.criteria.oxford.usa.r' 'qft.interp.R' 'tspot.interp.R'
Packaged: 2013-06-10 21:47:58 UTC; mparker
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-11 07:12:47

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Mon, 10 Jun 2013

New package ISLR with initial version 1.0
Package: ISLR
Type: Package
Title: Data for An Introduction to Statistical Learning with Applications in R
Version: 1.0
Date: 2013-06-10
Author: Gareth James, Daniela Witten, Trevor Hastie and Rob Tibshirani
Maintainer: Trevor Hastie
Suggests: MASS
Description: The collection of datasets used in the book "An Introduction to Statistical Learning with Applications in R"
License: GPL-2
LazyLoad: yes
LazyData: yes
URL: http://www.StatLearning.com
Packaged: 2013-06-10 19:32:17 UTC; hastie
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-11 00:17:23

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New package cabootcrs with initial version 1.0
Package: cabootcrs
Type: Package
Title: Bootstrap Confidence Regions for Correspondence Analysis.
Version: 1.0
Date: 2013-04-23
Author: T.J. Ringrose
Maintainer: T.J. Ringrose
Description: Performs correspondence analysis on a two-way contingency table and produces bootstrap-based elliptical confidence regions around the projected coordinates for the category points. Includes routines to plot the results in a variety of styles. Also reports the standard numerical output for correspondence analysis.
License: GPL-2
Imports: methods, utils
LazyData: TRUE
Packaged: 2013-06-10 13:00:57 UTC; ringroset
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-10 18:23:46

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New package covLCA with initial version 1.0
Package: covLCA
Type: Package
Title: Latent Class Models with Covariate Effects on Underlying and Measured Variables
Version: 1.0
Date: 2013-05-03
Author: Aurelie Bertrand and Christian M. Hafner
Maintainer: Aurelie Bertrand
Description: Estimation of latent class models with covariate effects on underlying and measured variables. The measured variables are dichotomous or polytomous, all with the same number of categories.
License: GPL-2
Depends: Matrix, mlogit, poLCA
Repository: CRAN
Packaged: 2013-06-10 07:53:54 UTC; aurbertrand
NeedsCompilation: no
Date/Publication: 2013-06-10 11:06:36

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New package sparktex with initial version 0.1
Package: sparktex
Version: 0.1
Date: 2013-06-06
Title: Generate LaTeX sparklines in R
Authors@R: c(person("Thomas", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"), person("Andy", "Barbour", role = "ctb"))
Depends: R (>= 3.0.0)
Description: Generate syntax for use with the sparklines package for LaTeX.
License: GPL-2
URL: http://thomasleeper.com/software.html
Packaged: 2013-06-09 20:58:58 UTC; Thomas
Author: Thomas Leeper [aut, cre], Andy Barbour [ctb]
Maintainer: Thomas Leeper
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-10 07:54:02

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Sun, 09 Jun 2013

New package TreePar with initial version 2.5
Package: TreePar
Type: Package
Title: Estimating birth and death rates based on phylogenies
Version: 2.5
Date: 2013-05-07
Author: Tanja Stadler
Maintainer: Tanja Stadler
Depends: ape, Matrix, subplex, TreeSim (>= 1.6), deSolve
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (implemented as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (implemented as bd.densdep.optim). Note that the method takes into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. Both models can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are mission), but where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented as bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim (extending bd.shifts.optim). Furthermore rates may vary as a function of host types using bdtypes.stt.lik (multitype branching process extending functions in R package diversitree).
License: GPL-2
LazyLoad: yes
Packaged: 2013-06-09 16:28:20 UTC; tanja
NeedsCompilation: no
X-CRAN-Comment: This was archived on 2013-05-20 since the author did not update after request from the odesolve maintainer for the announced odesolve archival
Repository: CRAN
Date/Publication: 2013-06-09 19:39:33

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New package cems with initial version 0.2
Package: cems
Version: 0.2
Date: 2013-06-09
Author: Samuel Gerber
Maintainer: Samuel Gerber
Description: Conditional expectation manifolds are an approach to compute principal curves and surfaces.
Title: Conditional expectation manifolds.
Depends: R (>= 2.10), plotrix, RColorBrewer, rgl, vegan
License: GPL-2
Repository: CRAN
Packaged: 2013-06-09 00:00:20 UTC; samgerber
NeedsCompilation: yes
Date/Publication: 2013-06-09 08:18:51

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Sat, 08 Jun 2013

New package pbs with initial version 1.1
Package: pbs
Type: Package
Imports: graphics, stats, splines
Title: Periodic B Splines
Version: 1.1
Date: 2013-03-22
Author: Shuangcai Wang
Maintainer: swang1
Description: Periodic B Splines Basis
License: GPL-2
Packaged: 2013-06-07 19:00:51 UTC; wangs
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-08 06:57:39

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New package lshorth with initial version 0.1-6
Package: lshorth
Type: Package
Title: The Length of the Shorth
Version: 0.1-6
Date: 2012-04-03
Author: G. Sawitzki
Maintainer: G. Sawitzki
Description: Calculates the (localised) length of the shorth and supplies corresponding diagnostic plots.
URL: http://lshorth.r-forge.r-project.org/
License: LGPL
Encoding: UTF-8
Repository: CRAN
Repository/R-Forge/Project: lshorth
Repository/R-Forge/Revision: 98
Packaged: 2012-04-12 16:26:52 UTC; rforge
NeedsCompilation: no
Date/Publication: 2013-06-08 06:53:06

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Fri, 07 Jun 2013

New package PivotalR with initial version 0.1.0
Package: PivotalR
Type: Package
Title: R front-end to PostgreSQL and Pivotal (Greenplum) database, wrapper for MADlib
Version: 0.1.0
Date: 2013-06-03
Author: Predictive Analytics Team at Pivotal Inc. , with contributions from Woo Jung
Maintainer: Hai Qian
Contact: Predictive Analytics Team at Pivotal Inc.
Depends: R (>= 2.9.0), methods
Enhances: DBI, RPostgreSQL
Description: R wrapper of Pivotal Data Fabrics running on PostgreSQL or Pivotal (Greenplum) database with parallel and distributed computation ability for big data analytics. PivotalR is a package that enables users of R to interact with the Pivotal (Greenplum) Database as well as Pivotal HD/HAWQ for Big Data analytics. It does so by providing an interface to the operations on tables/views in the database. These operations are almost the same as those of data.frame. Thus the users of R do not need to learn SQL when they operate on the objects in the database. It also provides a wrapper for MADlib, which is an open-source library for parallel and scalable in-database analytics.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2013-06-04 17:39:24 UTC; qianh1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-07 18:40:47

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New package lmeSplines with initial version 1.1-0
Package: lmeSplines
Version: 1.1-0
Title: lmeSplines
Author: Rod Ball
Maintainer: Andrzej Galecki
Description: Add smoothing spline modelling capability to nlme. Fit smoothing spline terms in Gaussian linear and nonlinear mixed-effects models
Depends: nlme(>= 3.1-29)
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2013-06-07 18:25:34
Repository/R-Forge/Project: nlmeu
Repository/R-Forge/Revision: 94
Repository/R-Forge/DateTimeStamp: 2013-06-06 14:25:53
Packaged: 2013-06-06 18:15:35 UTC; rforge
NeedsCompilation: no

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New package poweRlaw with initial version 0.20.0
Package: poweRlaw
Type: Package
Title: Fitting heavy tailed distributions: the poweRlaw package
Version: 0.20.0
Date: 2013-06-05
Authors@R: person("Gillespie", "Colin", email="colin.gillespie@newcastle.ac.uk", role = c("aut", "cre"))
Author: Colin Gillespie
Maintainer: Colin Gillespie
Description: This package implements both the discrete and continuous maximum likelihood estimators for fitting the power-law distribution to data. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.
URL: https://github.com/csgillespie/poweRlaw
BugReports: https://github.com/csgillespie/poweRlaw/issues
Depends: stats, R (>= 2.15.0)
Imports: VGAM, parallel, methods
License: GPL-3
Collate: 'aaa_all_classes.R' 'all_classes_ctn.R' 'all_classes_discrete.R' 'AllGenerics.R' 'bootstrap_p.R' 'bootstrap.R' 'ctn_helper_functions.R' 'data_help_files.R' 'discrete_helper_functions.R' 'dist_cdf-methods.R' 'dist_data_cdf-methods.R' 'dist_ll-methods.R' 'dist_pdf-methods.R' 'dist_rand-methods.R' 'estimate_pars.R' 'estimate_xmin.R' 'initialize-methods.R' 'lines-methods.R' 'mle-methods.R' 'plcon.R' 'pldis.R' 'plot-methods.R' 'points-methods.R' 'poweRlaw-package.R' 'checks.R' 'compare_distributions.R'
Packaged: 2013-06-07 09:12:43 UTC; ncsg3
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-07 11:31:06

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Thu, 06 Jun 2013

New package LVMMCOR with initial version 0.01.1
Package: LVMMCOR
Version: 0.01.1
Date: 2013-05-10
Title: A Latent Variable Model for Mixed Continuous and Ordinal Responses
Author: Ehsan Bahrami Samani and Nourallah Tazikeh Miyandarreh
Maintainer: Ehsan Bahrami Samani
Description: A model for mixed ordinal and continuous responses is presented where the heteroscedasticity of the variance of the continuous response is also modeled. In this model ordinal response can be dependent on the continuous response. The aim is to use an approach similar to that of Heckman (1978) for the joint modelling of the ordinal and continuous responses. With this model, the dependence between responses can be taken into account by the correlation between errors in the models for continuous and ordinal responses
Depends: R (>= 2.14.0),nlme,MASS
License: GPL (>= 2)
Contact: +982129902910
Packaged: 2013-06-05 19:35:59 UTC; StatisticS
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-06 07:49:30

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New package IUPS with initial version 1.0
Package: IUPS
Type: Package
Title: Incorporating Uncertainties in Propensity Scores
Version: 1.0
Date: 2013-6-5
Author: Weihua An, Huizi Xu, and Zhida Zheng, Indiana University Bloomington
Maintainer: Weihua An
Depends: R (>= 2.14), R2jags, Matching, boot
SystemRequirements: JAGS (>= 3.3.0)
Description: This package includes functions to incorporate uncertainties in estimated propensity scores and provide adjusted standard errors for making valid causal inference.
License: GPL-3
Packaged: 2013-06-06 05:10:06 UTC; weihuaan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-06 07:56:42

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Wed, 05 Jun 2013

New package simMSM with initial version 1.0
Package: simMSM
Type: Package
Title: Simulation of event histories based on nonlinear hazard rate functions and potentially nonlinear covariate effects.
Version: 1.0
Date: 2013-06-04
Author: Holger Reulen
Maintainer: Holger Reulen
Description: This package provides R functions for simulation of event histories with nonlinear baseline hazard rate functions and nonlinear covariate effects using inversion sampling on all-cause hazard rate functions.
License: GPL (>= 2)
Packaged: 2013-06-05 12:57:47 UTC; Holger Reulen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-05 16:40:50

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New package rite with initial version 0.1
Package: rite
Version: 0.1
Date: 2013-06-01
Title: The Right Editor to Write R
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper
Depends: R (>= 3.0.0), tcltk, tcltk2
Suggests: knitr
Description: A simple yet powerful script editor built natively in R with tcltk.
License: GPL-2
URL: http://thomasleeper.com/software.html
Packaged: 2013-06-05 10:37:42 UTC; Thomas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-05 13:57:14

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New package micromapST with initial version 1.0
Package: micromapST
Type: Package
Version: 1.0
Date: 2013-06-04
Title: Linked Micromap Plots for U. S. States
Author: Dan Carr and Jim Pearson , with contributions from Linda Pickle .
Maintainer: Jim Pearson
Depends: R (>= 2.15.0)
Imports: graphics, RColorBrewer, grDevices, stats
Description: This package provides the users the ability to quickly create Linked Micromap plots of the 50 U.S. states and District of Columbia (51 areas). Linked Micromaps are visualizations of georeferenced data that link statistical graphics to an organized series of small maps. The Help description contains examples of how to use the micromapST function. This package contains the US and State boundary files and FIPS/State conversion tables used by the micromapST function and several data sets used in the micromapST examples. Copyrighted 2013 by Carr, Pearson and Pickle.
License: GPL (>= 2)
LazyData: yes
LazyLoad: yes
BuildResaveData: yes
Packaged: 2013-06-05 01:08:23 UTC; jpearson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-05 09:31:39

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New package GSE with initial version 3.0
Package: GSE
Type: Package
Title: Robust Estimation of Multivariate Location and Scatter in the Presence of Missing Data
Version: 3.0
Date: 2013-06-05
Author: Mike Danilov, Andy Leung, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung
Description: Robust Estimation of Multivariate Location and Scatter in the Presence of Missing Data
License: GPL (>= 2)
Depends: R (>= 2.14.1), Rcpp (>= 0.9.8), RcppArmadillo (>= 0.2.34), MASS, methods, ggplot2
Suggests: lattice, rrcov, xtable
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2013-06-05 07:51:44 UTC; Andy
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-05 10:30:41

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New package sybilEFBA with initial version 0.0.1
Package: sybilEFBA
Type: Package
Title: Using gene expression data to improve flux balance analysis predictions
Version: 0.0.1
Date: 2013-06-03
Authors@R: c(person("Abdelmoneim", "Amer Desouki", role = c("aut","cre"), email = "abdelmoneim.amer@uni-duesseldorf.de"))
Depends: R (>= 2.10.0), sybil, Matrix, glpkAPI (>= 1.2.1)
Suggests: cplexAPI (>= 1.2.6)
Description: In this package I implemented three different approaches to consider gene expression data (or protein measurements) when using standard FBA techniques.
LazyLoad: yes
License: GPL-3
Packaged: 2013-06-05 02:30:27 UTC; Abdelmonem
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-05 07:58:22

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New package mmeta with initial version 1.07
Package: mmeta
Type: Package
Title: Multivariate Meta-Analysis Using Sarmanov Beta Prior Distributions
Version: 1.07
Date: 2013-3-29
Author: Sheng Luo, Yong Chen, Xiao Su, Haitao Chu
Maintainer: Xiao Su
Description: This package implements a novel bivariate meta-analysis using Sarmanov beta prior distributions.
Depends: R (>= 2.10.0), aod, xtable, BRugs
License: GPL (>= 2)
LazyLoad: no
Packaged: 2013-06-04 21:22:08 UTC; xsu
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-05 08:08:27

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Tue, 04 Jun 2013

New package SCEPtERextras with initial version 0.1-0
Package: SCEPtERextras
Title: Additional grids for SCEPtER
Version: 0.1-0
Date: 2013-06-02
Authors@R: c(person("Matteo", "Dell'Omodarme", role = c("aut", "cre"), email = "mattdell@fastmail.fm"), person("Giada", "Valle", role = "aut"))
Description: Grid of stellar models computed with various initial helium abundances and different mixing-length values.
Depends: R (>= 2.10)
LazyData: yes
License: GPL (>= 2)
Maintainer: Matteo Dell'Omodarme
Packaged: 2013-06-04 09:05:01 UTC; matt
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 16:10:31

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New package SCEPtER with initial version 0.1-0
Package: SCEPtER
Title: Stellar CharactEristics Pisa Estimation gRid
Version: 0.1-0
Date: 2013-06-02
Authors@R: c(person("Matteo", "Dell'Omodarme", role = c("aut", "cre"), email = "mattdell@fastmail.fm"), person("Giada", "Valle", role = "aut"))
Description: A package to estimate stellar mass and radius given observational data of effective temperature, [Fe/H], and astroseismic parameters. The results are obtained adopting a maximum likelihood technique over a grid of computed stellar models.
Suggests: lattice
Depends: R (>= 2.10), MASS
LazyData: yes
License: GPL (>= 2)
Maintainer: Matteo Dell'Omodarme
Packaged: 2013-06-04 13:28:04 UTC; matt
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-04 16:09:42

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New package bigGP with initial version 0.1-2
Package: bigGP
Version: 0.1-2
Date: 2013-05-31
Title: Distributed Gaussian process calculations
Authors@R: c(person("Christopher", "Paciorek", email = "paciorek@stat.berkeley.edu", role = c("aut", "cre")), person("Benjamin", "Lipshitz", role = c("aut")), person(family = "Prabhat", role = c("ctb")), person("Cari", "Kaufman", role = c("ctb")), person("Tina", "Zhuo", role = c("ctb")), person("Rollin", "Thomas", role = c("ctb")))
Depends: R (>= 3.0.0), Rmpi (>= 0.6-2), methods
Suggests: rlecuyer, rsprng, fields
LazyData: Yes
Description: bigGP distributes Gaussian process calculations across nodes in a distributed memory setting, using Rmpi. The class provides high-level methods for maximum likelihood with normal data, prediction, calculation of uncertainty (i.e., posterior covariance calculations), and simulation of realizations. In addition, bigGP provides an API for basic matrix calculations with distributed covariance matrices, including Cholesky decomposition, back/forwardsolve, crossproduct, and matrix multiplication.
SystemRequirements: OpenMPI or MPICH2
OS_type: unix
License: GPL (>= 2)
URL: http://www.stat.berkeley.edu/~paciorek/code/bigGP
Collate: 'auxil.R' 'bigGP.R' 'collectDistribute.R' 'distributedComputation.R' 'krigeProblem.R'
Packaged: 2013-06-02 19:15:34 UTC; paciorek
Author: Christopher Paciorek [aut, cre], Benjamin Lipshitz [aut], Prabhat [ctb], Cari Kaufman [ctb], Tina Zhuo [ctb], Rollin Thomas [ctb]
Maintainer: Christopher Paciorek
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-04 16:01:13

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New package mopsocd with initial version 0.5.1
Package: mopsocd
Type: Package
Title: MOPSOCD: Multi-objective Particle Swarm Optimization with Crowding Distance
Version: 0.5.1
Date: 2013-06-04
Author: Pros Naval
Maintainer: Pros Naval
Description: A multi-objective optimization solver based on particle swarm optimization with crowding distance.
Suggests: scatterplot3d
License: GPL (>= 2)
Packaged: 2013-06-04 09:21:29 UTC; Pros Naval
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 12:24:06

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New package QZ with initial version 0.1-1
Package: QZ
Version: 0.1-1
Date: 2013-06-03
Title: Generalized Eigenvalues and QZ Decomposition
Author: Wei-Chen Chen, partly adapted and using routines from LAPACK.
Maintainer: Wei-Chen Chen
Depends: R (>= 2.15.0), methods
Enhances: fda
LazyLoad: yes
LazyData: yes
Description: QZ package provides generalized eigenvalues and QZ decomposition (generalized Schur form) for an N-by-N non-symmetric matrix A or paired matrices (A,B) with eigenvalues reordering mechanism. The package is mainly based complex*16 and double precision of LAPACK library (version 3.4.2.)
License: Mozilla Public License 2.0
Packaged: 2013-06-03 17:02:07 UTC; snoweye
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-06-04 09:46:25

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New package FGalgorithm with initial version 1.0
Package: FGalgorithm
Version: 1.0
Date: 2013-06-04
Title: Flury and Gautschi algorithms
Author: Dariush Najarzadeh
Maintainer: Dariush Najarzadeh
Description: This is a package for implementation of Flury-Gautschi algorithms.
License: GPL (>= 2)
Packaged: 2013-06-04 09:04:25 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 11:04:39

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New package BEST with initial version 0.1.0
Package: BEST
Type: Package
Title: Bayesian Estimation Supersedes the t-Test
Version: 0.1.0
Depends: rjags
BuildVignettes: no
Date: 2013-06-04
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith
Description: An alternative to t-tests, producing posterior estimates for group means and standard deviations and their differences and effect sizes.
License: GPL (>= 3)
Packaged: 2013-06-04 06:53:11 UTC; Mike
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 09:43:30

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New package RSADBE with initial version 1.0
Package: RSADBE
Type: Package
Title: Data related to the book "R Statistical Application Development by Example"
Version: 1.0
Date: 2013-05-13
Author: Prabhanjan Tattar
Maintainer: Prabhanjan Tattar
Description: The package contains all the data sets related to the book written by the maintainer of the package.
License: GPL-2
Packaged: 2013-06-04 06:06:06 UTC; prabhanjan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 09:00:58

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New package NPMVCP with initial version 1.1
Package: NPMVCP
Type: Package
Title: Nonparametric Multivariate Change Point Model
Version: 1.1
Date: 2013-06-03
Author: Mark D. Holland
Maintainer: Mark D. Holland
Description: Nonparametric Multivariate Change Point Model
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-06-03 23:30:39 UTC; Britta
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 08:54:27

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New package Causata with initial version 4.1-0
Package: Causata
Type: Package
Title: Analysis utilities for binary classification and Causata users.
Version: 4.1-0
Date: 2013-05-30
Author: Justin Hemann, David Barker, Suzanne Weller, Jason McFall
Maintainer: Justin Hemann
Description: The Causata package provides utilities for extracting data from the Causata application, training binary classification models, and exporting models as PMML for scoring.
Depends: R (>= 2.15.1)
Imports: XML, R.utils, rjson, RMySQL, RCurl, stringr, yaml, boot, foreach, data.table, glmnet, ggplot2
Suggests: doMC, testthat, pROC, knitr
License: GPL
LazyLoad: yes
VignetteBuilder: knitr
URL: www.causata.com
Packaged: 2013-06-04 05:56:53 UTC; Justin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-04 09:05:51

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Mon, 03 Jun 2013

New package nlts with initial version 0.2-0
Package: nlts
Title: (non)linear time series analysis
Description: R functions for (non)linear time series analysis. A core topic is order estimation through cross-validation.
Version: 0.2-0
Date: 2012/09/11
Depends: R (>= 2.2.0), locfit (>= 1.5.3), acepack
Author: Ottar N. Bjornstad
Maintainer: Ottar N. Bjornstad
URL: http://onb.ent.psu.edu/onb1/R
License: GPL
Packaged: 2013-06-03 18:37:03 UTC; onb1
NeedsCompilation: no
X-CRAN-Comment: Earlier versions of this package have been removed as they contained material not licensed under 'GPL'.
Repository: CRAN
Date/Publication: 2013-06-03 23:18:36

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New package l2boost with initial version 1.0
Package: l2boost
Type: Package
Title: l2boost - Friedman's boosting algorithm for regularized linear regression
Version: 1.0
Date: 2013-05-31
Authors@R: c(person("John", "Ehrlinger", role=c("aut", "cre"), email="john.ehrlinger@gmail.com"), person("Hemant", "Ishwaran", role="aut"))
Description: Efficient implementation of Friedman's boosting algorithm with l2-loss function and coordinate direction (design matrix columns) basis functions.
License: GPL (>= 2)
Depends: R (>= 2.14.0), MASS, parallel
Packaged: 2013-06-03 20:28:38 UTC; ehrlinj
Author: John Ehrlinger [aut, cre], Hemant Ishwaran [aut]
Maintainer: John Ehrlinger
Collate: 'VAR.R' 'break.ties.R' 'coef.l2boost.R' 'cv.l2boost.R' 'diabetes.R' 'elasticNetSim.R' 'error.bars.R' 'eval.fold.R' 'extract.corr.R' 'fitted.l2boost.R' 'get.discrete.solution.R' 'get.hybrid.solution.R' 'get.lars.solution.R' 'help.R' 'l2boost.R' 'mstep.long.R' 'mvnorm.l2boost.R' 'nu.limit.R' 'plot.l2boost.R' 'plot.lines.R' 'predict.l2boost.R' 'print.l2boost.R' 'print.summary.l2boost.R' 'resample.R' 'residuals.l2boost.R' 'summary.l2boost.R' 'which.max.ind.R' 'which.min.ind.R'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-03 23:15:58

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New package smoothie with initial version 1.0
Package: smoothie
Version: 1.0
Date: 2013-06-01
Title: Two-dimensional Field Smoothing
Author: Eric Gilleland
Maintainer: Eric Gilleland
Depends: R (>= 3.0.0)
Suggests: SpatialVx, fields
Description: Functions to smooth two-dimensional fields using FFT and the convolution theorem
License: GPL (>= 2)
URL: http://www.ral.ucar.edu/staff/ericg
BugReports: http://www.ral.ucar.edu/staff/ericg
Packaged: 2013-06-03 14:01:54 UTC; ericg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-03 17:53:52

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New package pcurve with initial version 0.6-4
Package: pcurve
Version: 0.6-4
Date: 2011/01/22
Title: Principal curve analysis
Author: S original by Trevor Hastie S+ library by Glenn De'ath R port by Chris Walsh
Depends: R(>= 1.9.0), mgcv, vegan, MASS, stats
Description: Fits a principal curve to a numeric multivariate dataset in arbitrary dimensions. Produces diagnostic plots.
Maintainer: Gavin Simpson
License: GPL
Repository: CRAN
Repository/R-Forge/Project: pcurve
Repository/R-Forge/Revision: 2
Repository/R-Forge/DateTimeStamp: 2013-05-31 14:50:23
Date/Publication: 2013-06-03 07:22:57
Packaged: 2013-05-31 18:19:15 UTC; rforge
NeedsCompilation: yes

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Sun, 02 Jun 2013

New package GWmodel with initial version 1.1-9
Package: GWmodel
Version: 1.1-9
Date: 2013-06-02
Title: Geographically weighted models
Author: Binbin Lu, Paul Harris, Isabella Gollini, Martin Charlton, Chris Brunsdon
Maintainer: Binbin Lu
Depends: R (>= 3.0.0),maptools (>= 0.5-2), robustbase
Suggests: mvoutlier, RColorBrewer, gstat
Description: Functions for computing geographically weighted models
Copyright: We gratefully acknowledge support from Science Foundation Ireland under the National Development Plan through the award of a Strategic Research Centre grant 07-SRC-I1168
License: GPL (>= 2)
URL: http://www.stratag.ie/index.php?id=gw_models_project
Packaged: 2013-06-02 04:31:10 UTC; ronan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-02 16:59:24

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Sat, 01 Jun 2013

New package ndtv with initial version 0.2
Package: ndtv
Type: Package
Title: Network Dynamic Temporal Visualizations
Version: 0.2
Date: 2013-05-31
Authors@R: c( person("Skye", "Bender-deMoll", role=c("cre","aut"), email="skyebend@uw.edu"), person("Martina", "Morris", role=c("ctb"), email="morrism@u.washington.edu"))
Depends: R (>= 2.15), network (>= 1.7.2),networkDynamic (>= 0.4.1),animation,sna,statnet.common
Suggests: tergm (>= 3.1),testthat
Enhances: networkDynamic
Description: Renders dynamic network data from networkDynamic objects as animated movies or other representations of relational structure and node attributes that change over time.
License: GPL-3 + file LICENSE
URL: http://statnet.org
Packaged: 2013-06-01 06:51:51 UTC; skyebend
Author: Skye Bender-deMoll [cre, aut], Martina Morris [ctb]
Maintainer: Skye Bender-deMoll
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-01 15:59:12

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Fri, 31 May 2013

New package Simile with initial version 1.3
Package: Simile
Type: Package
Title: Interact with Simile models
Version: 1.3
Depends: tcltk
Date: 2013-04-23
Author: Simulistics Ltd
Maintainer: Jasper Taylor
Description: Allows a Simile model saved as a compiled binary to be loaded, parameterized, executed and interrogated. This version works with Simile v5.97 on.
License: Unlimited
LazyLoad: yes
Packaged: 2013-05-31 11:20:35 UTC; jaspert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-31 14:19:14

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New package enRich with initial version 1.0
Package: enRich
Type: Package
Title: An R package for analysis of multiple ChIP-seq data
Version: 1.0
Date: 2013-05-22
Author: Yanchun Bao , Veronica Vinciotti
Maintainer: Yanchun Bao
Description: enRich is an R package for joint statistical modelling of ChIP-seq data, accounting for technical/biological replicates, multiple conditions and different ChIP efficiencies of the individual experiments.
Depends: R(>= 2.14), parallel
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-05-31 12:00:04 UTC; masryyb
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-31 14:22:44

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New package protoclass with initial version 1.0
Package: protoclass
Maintainer: Jacob Bien
Author: Jacob Bien and Robert Tibshirani
Version: 1.0
License: GPL-3
Title: Interpretable classification with prototypes
Description: Greedy algorithm described in Bien and Tibshirani (2011) Prototype Selection for Interpretable Classification. Annals of Applied Statistics. 5(4). 2403-2424
Depends: class
Suggests: testthat, roxygen2
Collate: 'protoclass.r' 'protoclass-package.r'
Packaged: 2013-05-31 08:12:01 UTC; jbien
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-31 11:11:41

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Thu, 30 May 2013

New package distillery with initial version 1.0
Package: distillery
Version: 1.0
Date: 30 May 2013
Title: Distillery
Author: Eric Gilleland
Maintainer: Eric Gilleland
Depends: R (>= 2.10.0)
Description: Some method functions primarily used in common with packages extRemes and SpatialVx.
License: GPL (>= 2)
URL: http://www.ral.ucar.edu/staff/ericg
Packaged: 2013-05-30 16:13:04 UTC; ericg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-30 18:57:35

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New package netClass with initial version 1.0
Package: netClass
Version: 1.0
Date: 2013-05-27
Title: netClass: An R Package for Network-Based Microarray Classification
Author: Yupeng Cun
Maintainer: Yupeng Cun
Description: netClass is an R packages for feature (gene) selection, which employ the biological network information to microarray classification. We implemented average gene expression of pathway (aep), pathway activities classification (PAC), Hub network Classification, filter via top ranked genes(FrSVM), smoothed t-statistic(stSVM) for two classes microarray classification which employed the prior information.
Depends: R (>= 2.12), AnnotationDbi, pathClass, Matrix,graph, igraph, samr
Suggests: multicore, Biobase, KEGG.db
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-05-30 11:00:24 UTC; cun
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-30 15:01:38

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New package mht with initial version 2.122
Package: mht
Type: Package
Title: Multiple Hypotheses Testing For Variable Selection
Version: 2.122
Date: 2013-05-30
Author: F.Rohart
Maintainer: F.Rohart
Description: Multiple Hypotheses Testing For Variable Selection
License: GPL-3
Depends: glmnet
Packaged: 2013-05-30 10:50:01 UTC; florian
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-30 14:26:28

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New package AppliedPredictiveModeling with initial version 1.1-1
Package: AppliedPredictiveModeling
Type: Package
Title: Functions and Data Sets for 'Applied Predictive Modeling'
Version: 1.1-1
Date: 2013-05-29
Author: Max Kuhn, Kjell Johnson
Maintainer: Max Kuhn
Description: A few functions and several data set for the Springer book 'Applied Predictive Modeling'
URL: http://appliedpredictivemodeling.com/
Depends: R (>= 2.10), CORElearn, MASS, plyr, reshape2
Suggests: caret, lattice, ellipse
License: GPL
Packaged: 2013-05-29 19:34:07 UTC; kuhna03
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-30 07:31:33

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Wed, 29 May 2013

New package sirt with initial version 0.31-20
Package: sirt
Type: Package
Title: Supplementary Item Response Theory Models
Version: 0.31-20
Date: 2013-05-29
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch
Description: Supplementary item response theory models to complement existing functions in R.
Depends: R (>= 2.15.0), MASS, combinat, pbivnorm, mvtnorm, sfsmisc, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.800.1)
Suggests: lme4, psych, sm, gregmisc, GPArotation, splines, ic.infer
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2)
URL: https://sites.google.com/site/alexanderrobitzsch/software
Packaged: 2013-05-29 14:22:49 UTC; robitzsch
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-29 17:35:02

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New package RSDA with initial version 1.0
Package: RSDA
Type: Package
Title: RSDA - R to Symbolic Data Analysis
Version: 1.0
Date: 2013-05-28
Author: Oldemar Rodriguez R.
Maintainer: Oldemar Rodriguez
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin DIDAY in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
License: GPL (>= 2)
Depends: ggplot2, scales, scatterplot3d, FactoMineR
Packaged: 2013-05-29 15:06:16 UTC; oldemarrodriguez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 17:33:11

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New package pastis with initial version 0.1
Package: pastis
Type: Package
Title: Phylogenetic Assembly with Soft Taxonomic Inferences
Author: Klaas Hartmann, Gavin Thomas, Arne Mooers, Jeffrey Joy, Aki Mimoto, Walter Jetz
Maintainer: Gavin Thomas
Depends: caper (>= 0.5.0), ape (>= 3.0.0)
Description: A pre-processor for mrBayes that assimilates sequences, taxonomic information and tree constraints as per xxx. The main functions of interest for most users will be pastis_simple, pastis_main and conch. The main analysis is conducted with pastis_simple or pastis_main followed by a manual execution of mrBayes (>3.2). The placement of taxa not contained in the tree constraint can be investigated using conch.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
URL: http://to.be.determined
Authors@R: c(person(given="Klaas", family="Hartmann", email="klaas.hartmann@utas.edu.au", role=c("aut", "cre")), person(given="Gavin", family="Thomas", email="gavin.thomas@sheffield.ac.uk", role=c("aut", "cre")))
Version: 0.1
Date: 2013-05-27
Packaged: 2013-05-28 08:24:18 UTC; gavinthomas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 11:55:32

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New package SPMS with initial version 1.0
Package: SPMS
Type: Package
Title: Sub-Pathway Minner Software
Version: 1.0
Date: 2013-05-08
Author: Xiaomeng Ni
Maintainer: Xiaomeng Ni
Description: Use new methods to mine subpathway,but user need to prepare for KEGG pathway data and store them in "xml" folder under "paths"(paths library is the default directory which is seted by user) library,prepare KEGG pathway map data and store them in "png" folder under the "paths"(paths library is the default directory which is seted by user) library in advance.
License: GPL-2
Imports: Matrix
Suggests: base, RBGL, XML, graphics, png, graph, EBImage, igraph
LazyLoad: yes
Packaged: 2013-05-29 06:45:04 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 10:50:26

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New package StAMPP with initial version 1.0
Package: StAMPP
Type: Package
Title: Statistical Analysis of Mixed Ploidy Populations
Depends: R (>= 2.14.0), parallel, doParallel, foreach, adegenet, pegas
Version: 1.0
Date: 2013-04-05
Author: LW Pembleton
Maintainer: LW Pembleton
Description: StAMPP allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
License: GPL-3
Packaged: 2013-05-28 09:50:37 UTC; Luke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 07:53:24

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New package rfisheries with initial version 0.0.3
Package: rfisheries
Title: R interface for fisheries data
Version: 0.0.3
Date: 2012-12-12
Authors@R: c(person("Karthik", "Ram", role = c("aut", "cre"), email = "karthik.ram@gmail.com"), person("Carl", "Boettiger", role = "aut"), person("Andrew", "Dyck", role = "aut"))
Maintainer: Karthik Ram
Description: A programmatic interface to openfisheries.org
Depends: R (>= 2.15), plyr, RCurl, RJSONIO
Imports: RCurl
URL: http://www.github.com/ropensci/rfisheries
BugReports: http://www.github.com/ropensci/rfisheries/issues/new
License: CC0
Collate: 'country_codes.R' 'landings.R' 'species_codes.R'
Packaged: 2013-05-29 01:20:20 UTC; karthik
Author: Karthik Ram [aut, cre], Carl Boettiger [aut], Andrew Dyck [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 07:54:47

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New package pvsR with initial version 0.1
Package: pvsR
Type: Package
Title: An R package to interact with the Project Vote Smart API for scientific research
Depends: R (>= 2.14.2), XML, nnet
Version: 0.1
Date: 2013-05-27
Author: Ulrich Matter
Maintainer: Ulrich Matter
Description: The pvsR package facilitates data retrieval from Project Vote Smart's rich online data base on US politics via the Project Vote Smart application programming interface (PVS API). The functions in this package cover most PVS API classes and methods and return the requested data in a data frame.
License: GPL-2
Note: In order to use this package you need your personal Project Vote Smart API key. To get an API-key you need to sign up for access to PVS' API (see http://votesmart.org/share/api for details). Whenever you are using pvsR make sure that your personal PVS API key is saved as a character string in the variable pvs.key (pvs.key <- "yourkey"). If there is no valid PVS API key saved in the variable pvs.key the functions in this package won't work. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
NeedsCompilation: no
Packaged: 2013-05-29 00:13:14 UTC; ueli
Repository: CRAN
Date/Publication: 2013-05-29 07:44:16

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New package branchLars with initial version 1.0
Package: branchLars
Type: Package
Title: Cost-efficient Variable Selection
Version: 1.0
Date: 2013-5-27
Author: Li Hua Yue
Maintainer: Li Hua Yue
Depends: lars, Rgraphviz, R(>= 3.0)
Description: Select cost-efficient factors using Branching LARS method
License: GPL (>= 2)
Packaged: 2013-05-29 00:46:04 UTC; TuTu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-29 07:53:23

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Tue, 28 May 2013

New package fitTetra with initial version 1.0
Package: fitTetra
Type: Package
Title: fitTetra is an R package for assigning tetraploid genotype scores
Version: 1.0
Date: 2013-04-23
Author: Roeland Voorrips and Gerrit Gort
Maintainer: Gerrit Gort
Suggests: doMC, foreach, RSvgDevice, devEMF
Description: Package fitTetra contains three functions that can be used to assign genotypes to a collection of tetraploid samples based on bialleleic marker assays. Functions fitTetra (to fit several models for one marker from the data and select the best fitting) or saveMarkerModels (calls fitTetra for multiple markers and saves the results to files) will probably be the most convenient to use. Function CodomMarker offers more control and fits one specified model for a given marker.
License: GPL (>= 2.2)
Packaged: 2013-05-28 16:10:03 UTC; gort001
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 22:43:11

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New package VSURF with initial version 0.5
Package: VSURF
Type: Package
Title: Variable Selection Using Random Forests
Version: 0.5
Date: 2013-05-28
Author: Robin Genuer, Jean-Michel Poggi and Christine Tuleau-Malot
Maintainer: Robin Genuer
Description: Three steps variable selection procedure based on random forests. Initially developed to handle high dimensional data (for which number of variables largely exceeds number of observations), the package is very versatile and can treat most dimensions of data, for regression and supervised classification problems. First step is dedicated to eliminate irrelevant variables from the dataset. Second step aims to select all variables related to the response for interpretation purpose. Third step refines the selection by eliminating redundancy in the set of variables selected by the second step, for prediction purpose.
License: GPL (>= 2)
Depends: randomForest, rpart
Packaged: 2013-05-28 14:47:12 UTC; robin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 17:36:16

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New package DTMCPack with initial version 0.1-2
Package: DTMCPack
Type: Package
Title: Suite of functions related to discrete-time discrete-state Markov Chains
Version: 0.1-2
Date: 2013-05-22
Author: William Nicholson
Maintainer: William Nicholson
Description: A series of functions which aid in both simulating and determining the properties of finite, discrete-time, discrete state markov chains. Two functions (DTMC, MultDTMC) produce n iterations of a Markov Chain(s) based on transition probabilities and an initial distribution. The function FPTime determines the first passage time into each state. The function statdistr determines the stationary distribution of a Markov Chain.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-05-28 14:33:14 UTC; will
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 16:40:32

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New package TSclust with initial version 1.0
Package: TSclust
Type: Package
Title: Time series clustering utilities
Version: 1.0
Date: 2013-01-07
Encoding: UTF-8
Author: Pablo Montero Manso, José Antonio Vilar
Maintainer: Pablo Montero
Description: This package contains a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
License: GPL-2
Depends: R (>= 2.14.0), nlme,locpol, KernSmooth, dtw, longitudinalData, wmtsa
Suggests: proxy
Packaged: 2013-05-28 11:18:18 UTC; pmont
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 13:53:55

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New package CSS with initial version 1.0
Package: CSS
Type: Package
Title: Extract information from an html document with CSS selectors
Version: 1.0
Date: 2013-01-31
Author: Francois Guillem
Maintainer: Francois Guillem
Description: The package provides functions that facilitate extraction of information from an html document by using css selectors instead of xpath queries.
License: GPL (>= 2)
Depends: XML, stringr
Suggests: testthat
Packaged: 2013-05-28 09:07:07 UTC; francois
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 11:14:38

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New package ODMconverter with initial version 1.0
Package: ODMconverter
Type: Package
Title: tools to convert ODM files
Version: 1.0
Date: 2013-05-28
Author: Martin Dugas
Maintainer: Martin Dugas
Depends: R (>= 2.13.1), XML, xlsx
Description: Transformation of ODM files into R format, office format and vice versa. CDISC ODM format is commonly used in clinical trials. Semantic annotation (such as UMLS, SNOMED or LOINC codes) are transformed accordingly.
License: GPL
LazyLoad: yes
Packaged: 2013-05-28 06:57:08 UTC; dugasmar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-28 10:32:54

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Mon, 27 May 2013

New package Tides with initial version 1.0
Package: Tides
Version: 1.0
Title: Tides
Author: Tom Cox
Maintainer: Tom Cox
Description: Functions to calculate characteristics of quasi periodic time series, e.g. observed estuarine water levels
License: GPL
LazyData: yes
Packaged: 2013-05-27 09:12:20 UTC; tom
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-27 16:56:02

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New package GIGrvg with initial version 0.1
Package: GIGrvg
Type: Package
Title: Random variate generator for the GIG distribution
Version: 0.1
Date: 2013-05-27
Author: Josef Leydold and Wolfgang Hormann
Maintainer: Josef Leydold
Description: Random variate generator for the GIG distribution
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-05-27 10:40:09 UTC; leydold
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-27 13:13:40

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New package SesIndexCreatoR with initial version 1.0-2
Package: SesIndexCreatoR
Type: Package
Title: Computation and visualization of socioeconomic indices and categories distributions
Version: 1.0-2
Date: 2013-05-16
Authors@R: c(person("Benoit", "Lalloue", role = c("aut", "cre"), email = "benoit.lalloue@ehesp.fr"), person("Severine", "Deguen", role = c("ths", "aut"), email = "severine.deguen@ehesp.fr"), person("Jean-Marie", "Monnez", role =c("ths", "aut"), email = "jean-marie.monnez@univ-lorraine.fr"), person("Nolwenn", "Le Meur", role = c("aut")))
Author: Benoit Lalloue
Maintainer: Benoit Lalloue
Description: This package allows computing and visualizing socioeconomic indices and categories distributions from datasets of socioeconomic variables (These tools were developed as part of the EquitArea Project, a public health program).
Depends: FactoMineR, class, R (>= 3.0.0)
URL: www.equitarea.org
Encoding: latin1
License: GPL-2 | GPL-3
Packaged: 2013-05-24 17:15:46 UTC; Ben
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-27 10:56:29

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Sun, 26 May 2013

New package circlize with initial version 0.0.2
Package: circlize
Type: Package
Title: circos layout in R
Version: 0.0.2
Date: 2013-05-25
Author: Zuguang Gu
Maintainer: Zuguang Gu
Depends: R (>= 2.10.0)
Description: The circlize package implements circos layout (http://circos.ca/) in R. It can do almost everything that circos can do. And due to the natural born feature of drawing statistical graphics in R, this package can provide a more flexible way to visualize information in a circular style.
LazyLoad: yes
URL: https://github.com/jokergoo/circlize
License: GPL (>= 2)
Packaged: 2013-05-26 11:51:16 UTC; IBM
Repository: CRAN
Date/Publication: 2013-05-26 14:46:49
NeedsCompilation: no

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New package McSpatial with initial version 2.0
Package: McSpatial
Type: Package
Title: Nonparametric spatial data analysis
Version: 2.0
Date: 2013-5-20
Author: Daniel McMillen
Maintainer: Daniel McMillen
Description: Locally weighted regression, semiparametric and conditionally parametric regression, fourier and cubic spline functions, GMM and linearized spatial logit and probit, k-density functions and counterfactuals, nonparametric quantile regression and conditional density functions, Machado-Mata decomposition for quantile regressions, spatial AR model, repeat sales models, conditionally parametric logit and probit
License: GPL
LazyLoad: yes
Depends: lattice, locfit, maptools, quantreg, RANN, SparseM
Suggests: car, classInt, mlogit, RColorBrewer, spatstat, spdep
Packaged: 2013-05-26 08:34:40 UTC; Dan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-26 11:08:53

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New package ggROC with initial version 1.0
Package: ggROC
Title: package for roc curve plot with ggplot2
Version: 1.0
Date: 2013-05-24
Author: Honglong Wu
Maintainer: Honglong Wu
Depends: R (>= 2.14.0), ggplot2
Suggests: ggplot2
Description: package for roc curve plot with ggplot2
License: GPL (> 2)
Packaged: 2013-05-26 08:55:34 UTC; user
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-26 11:08:59

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Sat, 25 May 2013

New package sparsediscrim with initial version 0.1.0
Package: sparsediscrim
Title: Sparse Discriminant Analysis
Version: 0.1.0
Date: 2013-05-25
Author: John A. Ramey
Maintainer: John A. Ramey
Description: A collection of sparse and regularized discriminant analysis methods intended for small-sample, high-dimensional data sets. The package includes the High-Dimensional Regularized Discriminant Analysis classifier. Furthermore, the package includes several Diagonal Discriminant Analysis methods, which are special cases of the well-known Naive Bayes classifier.
Imports: corpcor, bdsmatrix, mvtnorm
License: MIT
URL: https://github.com/ramey/sparsediscrim, http://ramhiser.com
Collate: 'dlda.r' 'dqda.r' 'sdlda.r' 'sdqda.r' 'stein-shrinkage.r' 'estimates.r' 'helper-intercept.r' 'data-intraclass.r' 'data-block-autocorrelation.r' 'tong-shrinkage.r' 'hdrda.r' 'helper-cov.r' 'helper-cv.r' 'helper.r'
Packaged: 2013-05-25 17:19:33 UTC; johnramey
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-25 20:04:01

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New package SDD with initial version 1.0
Package: SDD
Type: Package
Title: Serial Dependence Diagrams
Version: 1.0
Date: 2013-02-17
Author: Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza
Description: This package allows for computing (and by default plotting) different types of serial dependence diagrams.
License: GPL-2
LazyLoad: yes
Depends: R (>= 2.15.0)
Imports: Hmisc,sm,tseries,stats,rpanel,rgl
Packaged: 2013-05-25 11:20:26 UTC; Angelo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-25 15:30:25

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Fri, 24 May 2013

New package msgl with initial version 0.1.1
Package: msgl
Type: Package
Title: High dimensional multiclass classification using sparse group lasso
Version: 0.1.1
Date: 2013-20-05
Author: Martin Vincent (Sparse group lasso), Conrad Sanderson (Armadillo), Jaakko Jarvi (Boost Tuple) and Jens Maurer (Boost Random)
Maintainer: Martin Vincent
Description: Sparse group lasso multiclass classification, suitable for high dimensional problems with many classes (see url). Fast algorithm for solving the multinomial sparse group lasso optimization problem. 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. Armadillo is licensed under the MPL 2.0 (see url). The Armadillo C++ library is primarily developed at NICTA (Australia) by Conrad Sanderson, with contributions from around the world. Furthermore the package utilize various Boost libraries, in particular the Tuple library by Jaakko Jarvi and the Random library by Jens Maurer. The Boost libraries are licensed under the Boost Software License (see url).
URL: http://arxiv.org/abs/1205.1245 http://arma.sourceforge.net/, http://www.mozilla.org/MPL/2.0/, http://www.boost.org/, http://www.boost.org/users/license.html
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.13.0), Matrix
Collate: 'msgl_multinomial.R'
Packaged: 2013-05-24 18:52:34 UTC; martin
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 21:40:44

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New package tlnise with initial version 2.0
Package: tlnise
Depends: R (>= 3.0.0)
Suggests: MASS
Imports: stats
Version: 2.0
Date: 2013-05-24
Title: Two-level normal independent sampling estimation
Author: S-PLUS original by Phil Everson; R port by Roger D. Peng
Maintainer: Roger D. Peng
Description: Functions for two level normal models as described in Everson and Morris (2000). J. R. Statist. Soc. B, 62 prt 2, pp.399--412.
License: GPL-3
URL: http://www.swarthmore.edu/NatSci/peverso1/TLNise/tlnise.htm
Packaged: 2013-05-24 14:37:36 UTC; rdpeng
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 18:24:21

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New package SparseTSCGM with initial version 1.0
Package: SparseTSCGM
Type: Package
Title: Sparse time series chain graphical models
Version: 1.0
Date: 2013-05-24
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz
Depends: R (>= 3.0.0), glasso, longitudinal, flare, mvtnorm, network
Description: Compute and plot sparse autoregressive coefficient and precision matrices for time series chain graphical models.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2013-05-24 12:05:56 UTC; P261204
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 15:38:46

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New package compositionsGUI with initial version 1.0
Package: compositionsGUI
Type: Package
Title: Graphical User Environment for Compositional Data Analysis
Version: 1.0
Date: 2013-05-14
Author: Jiri Eichler, Karel Hron, Raimon Tolosana-Delgado, Gerald van den Boogaart, Matthias Templ, Peter Filzmoser
Maintainer: Jiri Eichler
Depends: robCompositions, compositions, mvoutlier, robustbase, RGtk2, MASS, nnet, boot
Description: The package provides graphical user interface and teaching tool for compositional data analysis using R. It contains data loading from various sources (external sources, installed R packages), preprocessing (imputation of missing values and rounded zeros), basic summary statistics as well as log-ratio transformations, necessary for a reasonable statistical treatment of compositional data (isometric, centred, additive log-ratio transformations). Further, also statistical methods like outlier detection and principal component analysis, together with the corresponding graphical tools, are provided. Finally, the package contains plotting functions, suitable for compositional data analysis, like ternary and quaternary diagrams, scatterplots of log-ratio transformed data, and diagrams with categorical/continuous covariates.
License: GPL (>= 2)
Packaged: 2013-05-16 20:20:57 UTC; templ
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 12:34:41

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New package Demerelate with initial version 0.8-0
Package: Demerelate
Version: 0.8-0
Date: 2012-05-24
Title: Functions to calculate relatedness on diploid genetic data
Authors@R: c(person("Philipp","Kraemer",role=c("aut", "cre"),email="Philipp.Kraemer@uni-oldenburg.de"),person("Gabriele","Gerlach",role="aut",email="Gabriele.Gerlach@uni-oldenburg.de"))
Author: Philipp Kraemer and Gabriele Gerlach
Maintainer: Philipp Kraemer
Depends: R (>= 2.15.0), fts, mlogit, sfsmisc
Suggests: MASS
Description: Functions to calculate pairwise relatedness on diploid genetic datasets. Different estimators for relatedness can be combined with information on geographical distances. Information on heterozygosity, allele- and genotype diversity as well as genetic F-statistics are provided for each population.
License: GPL (>= 2)
URL: http://www.r-project.org
BugReports: http://Demerelate.bugtracker.url
Packaged: 2013-05-24 08:10:41 UTC; philipp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 10:29:00

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New package twostageTE with initial version 1.0
Package: twostageTE
Type: Package
Title: Two-Stage Threshold Estimation
Version: 1.0
Date: 2013-03-05
Author: Shawn Mankad, George Michailidis, Moulinath Banerjee
Maintainer: Shawn Mankad
Description: Implements a variety of nonparametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
License: GPL-2
Depends: isotone
Packaged: 2013-05-23 22:28:03 UTC; smankad
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 07:38:34

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Thu, 23 May 2013

New package InferenceSMR with initial version 1.0
Package: InferenceSMR
Type: Package
Title: Inference about the standardized mortality ratio when evaluating the effect of a screening program on survival.
Version: 1.0
Date: 2013-05-22
Author: Denis Talbot, Thierry Duchesne, Jacques Brisson, Nathalie Vandal
Maintainer: Denis Talbot
Description: The InferenceSMR package provides functions to make inference about the standardized mortality ratio (SMR) when evaluating the effect of a screening program. The package is based on methods described in Sasieni (2003) and Talbot et al. (2011).
License: GPL (>= 2)
Depends: survival
Packaged: 2013-05-23 14:10:09 UTC; Nilidas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-23 17:41:26

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New package SODC with initial version 1.0
Package: SODC
Type: Package
Title: Optimal Discriminant Clustering(ODC) and Sparse Optimal Discriminant Clustering(SODC)
Version: 1.0
Date: 2013-05-15
Author: Yanhong Wang
Maintainer: Yanhong Wang
Description: To implement two clustering methods, ODC and SODC, for clustering datasets using optimal scoring, can also be used as an dimension reduction tool.
License: GPL-2
Depends: magic,ppls,psych,MASS
Packaged: 2013-05-23 13:34:01 UTC; matyxwx
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-23 15:53:51

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Wed, 22 May 2013

New package SnowballC with initial version 0.5
Package: SnowballC
Type: Package
Version: 0.5
Date: 2013-05-22
Title: Snowball stemmers based on the C libstemmer UTF-8 library
Authors@R: person("Milan", "Bouchet-Valat", email="nalimilan@club.fr", role=c("aut", "cre"))
Description: An R interface to the C libstemmer library that implements Porter's word stemming algorithm for collapsing words to a common root to aid comparison of vocabulary. Currently supported languages are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.
License: BSD
Copyright: Dr Martin Porter (2001) for the libstemmer C library, and Milan Bouchet-Valat (2013) for the R package contents
URL: https://r-forge.r-project.org/projects/r-temis/
BugReports: https://r-forge.r-project.org/tracker/?group_id=1437
Packaged: 2013-05-22 12:55:04 UTC; milan
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-22 18:27:08

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