Fri, 31 Oct 2014

New package hermite with initial version 1.0
Package: hermite
Type: Package
Title: Generalized Hermite distribution
Version: 1.0
Date: 2014-10-30
Encoding: UTF-8
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler
Description: Probability functions for the generalized Hermite distribution
Depends: R (>= 2.15.0)
Repository: CRAN
License: GPL (>= 2)
Packaged: 2014-10-31 15:08:23 UTC; dmorinya
NeedsCompilation: no
Date/Publication: 2014-10-31 16:16:01

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Thu, 30 Oct 2014

New package genpathmox with initial version 0.1
Package: genpathmox
Title: Generalized PATHMOX Algorithm for PLS-PM, LS and LAD Regression
Version: 0.1
Authors@R: "Giuseppe Lamberti [aut, cre]"
Description: genpathmox provides a very interesting solution for handling segmentation variables in complex statistical methodology. It contains en extended version of the PATHMOX algorithm in the context of partial least square path modeling (Sanchez, 2009) including the F-block test (to detect the responsible latent endogenous equations of the difference), the F-coefficient (to detect the path coefficients responsible of the difference) and the invariance test (to realize a comparison between the sub-models' latent variables). Furthermore, the package contains a generalized version of the PATHMOX algorithm to approach different methodologies: linear regression and least absolute regression models.
Depends: R (>= 3.1.1),plspm, quantreg,mice,diagram, methods
License: GPL-3
LazyData: true
Packaged: 2014-10-30 14:37:42 UTC; giuseppelamberti
Author: "Giuseppe Lamberti" [aut, cre]
Maintainer: "Giuseppe Lamberti"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 19:35:26

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New package fPortfolio with initial version 3011.81
Package: fPortfolio
Title: Rmetrics - Portfolio Selection and Optimization
Date: 2014-10-30
Version: 3011.81
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz
Description: Environment for teaching "Financial Engineering and Computational Finance".
Depends: R (>= 2.15.1), methods, timeDate, timeSeries, fBasics, fAssets
Imports: fCopulae, robustbase, MASS, Rglpk, slam, Rsymphony, Rsolnp, kernlab, quadprog, rneos
Suggests: Rsocp, Rnlminb2, Rdonlp2, dplR, bcp, fGarch, mvoutlier
Additional_repositories: http://r-forge.r-project.org/
Note: SEVERAL PARTS ARE STILL PRELIMINARY AND MAY BE CHANGED IN THE FUTURE. THIS TYPICALLY INCLUDES FUNCTION AND ARGUMENT NAMES, AS WELL AS DEFAULTS FOR ARGUMENTS AND RETURN VALUES.
LazyData: yes
License: GPL (>= 2)
URL: https://www.rmetrics.org
Packaged: 2014-10-30 14:13:59 UTC; Tobi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 15:54:08

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New package PrevMap with initial version 1.0
Package: PrevMap
Type: Package
Title: PrevMap - an R package for prevalence mapping
Version: 1.0
Date: 2014-06-25
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
Depends: geoR, maxLik, raster, pdist
Description: The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is also an extension of the 'geoR' package which should be installed first together with the 'maxLik', 'raster' and 'pdist' packages.
LazyData: true
License: GPL (>= 2)
Packaged: 2014-10-30 09:40:57 UTC; giorgi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 11:18:02

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New package webutils with initial version 0.2
Package: webutils
Type: Package
Title: Utility Functions for Web Applications
Version: 0.2
Date: 2014-10-29
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: Utility functions for developing web applications. Includes parsers for application/x-www-form-urlencoded as well as multipart/form-data and examples of using the parser with either httpuv or rhttpd.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/webutils
BugReports: https://github.com/jeroenooms/webutils/issues
Imports: tools, utils, jsonlite
Suggests: httpuv
Packaged: 2014-10-30 00:32:01 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 07:46:54

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Wed, 29 Oct 2014

New package exCon with initial version 0.1-0
Package: exCon
Type: Package
Title: Interactive Exploration of Contour Data
Version: 0.1-0
Date: 2014-10-29
Authors@R: c(person("Bryan", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu"), person("Kristina", "Mulry", role = "ctb"))
Description: exCon is an interactive tool to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. exCon creates an interactive web page showing the contoured data set along with slices from the original matrix parallel to each dimension. The page is written in d3/javascript.
License: GPL-3
Imports: jsonlite
URL: https://github.com/bryanhanson/exCon
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/exCon/issues
Depends: R (>= 3.0)
Packaged: 2014-10-29 19:41:42 UTC; bryanhanson
Author: Bryan Hanson [aut, cre], Kristina Mulry [ctb]
Maintainer: Bryan Hanson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 22:05:54

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New package DAMOCLES with initial version 1.0
Package: DAMOCLES
Type: Package
Title: Dynamic Assembly Model Of Colonization, Local Extinction and Speciation
Version: 1.0
Date: 2014-09-09
Depends: R (>= 2.14.2), geiger, caper, ape, deSolve, matrixStats
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne
License: GPL-2
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account the phylogenetic history
Packaged: 2014-09-09 18:19:08 UTC; p223208
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 09:29:22

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New package rqPen with initial version 1.0
Package: rqPen
Type: Package
Title: R Package for Penalized Quantile Regression
Version: 1.0
Date: 2014-10-25
Author: Ben Sherwood
Depends: R (>= 3.0.0),quantreg
Maintainer: Ben Sherwood
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
ByteCompile: TRUE
License: MIT + file LICENSE
Packaged: 2014-10-29 01:29:00 UTC; bsherwoo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:44:31

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New package addreg with initial version 1.2
Package: addreg
Title: Additive Regression for Discrete Data
Description: Methods for fitting identity-link GLMs and GAMs to discrete data. The package uses EM-type algorithms with more stable convergence properties than standard methods.
Version: 1.2
Date: 2014-10-29
Author: Mark Donoghoe
Maintainer: Mark Donoghoe
Depends: R (>= 3.0.1)
Imports: splines, combinat, glm2
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-28 22:19:48 UTC; 42674999
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:36:11

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Tue, 28 Oct 2014

New package MfUSampler with initial version 0.9
Package: MfUSampler
Type: Package
Title: Multivariate-from-Univariate (MfU) MCMC Sampler
Version: 0.9
Date: 2014-10-27
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Convenience Functions for Multivariate MCMC Using Univariate Samplers, including Slice Sampler with Stepout and Shrinkage (Neal, 2003), and Adaptive Rejection Sampler (Gilks and Wild, 1992).
License: GPL (>= 2)
Depends: ars
Suggests: sns
Packaged: 2014-10-28 18:54:28 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 22:00:52

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New package CateSelection with initial version 1.0
Package: CateSelection
Type: Package
Title: Categorical Variable Selection Methods
Version: 1.0
Date: 2014-10-28
Author: Yi Xu and Jixiang Wu
Maintainer: Yi Xu
Description: A multi-factor dimensionality reduction based forward selection method for genetic association mapping.
License: GPL (>= 2)
Depends: R(>= 2.10)
Repository: CRAN
Packaged: 2014-10-28 20:38:02 UTC; Xu
NeedsCompilation: no
Date/Publication: 2014-10-28 21:58:29

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New package safi with initial version 1.0
Package: safi
Type: Package
Title: Sensitivity Analysis for Functional Input
Version: 1.0
Date: 2014-10-28
Author: Jana Fruth, Malte Jastrow
Maintainer: Jana Fruth
Description: Design and sensitivity analysis for computer experiments with scalar-valued output and functional input, e.g. over time or space. The aim is to explore the behavior of the sensitivity over the functional domain.
License: GPL (>= 2)
Packaged: 2014-10-28 15:53:50 UTC; Jana
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 17:35:33

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New package settings with initial version 0.1.1
Package: settings
Type: Package
Title: Software Option Settings Manager for R
Version: 0.1.1
Date: 2014-10-22
Author: Mark van der Loo
Maintainer: Mark van der Loo
Description: Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names and default values. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes.
URL: https://github.com/markvanderloo/settings
License: GPL-3
VignetteBuilder: knitr
Suggests: testthat, knitr
Packaged: 2014-10-28 07:43:29 UTC; mark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 11:18:40

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Mon, 27 Oct 2014

New package bio3d with initial version 2.1-3
Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-3
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1)
Depends: R (>= 3.1.0)
LazyData: yes
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-24 21:47:52 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 19:03:11

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New package h2o with initial version 2.8.1.1
Package: h2o
Type: Package
Title: H2O R Interface
Version: 2.8.1.1
Date: 2014-05-15
Author: Anqi Fu, Spencer Aiello, Ariel Rao, Tom Kraljevic and Petr Maj, with contributions from the 0xdata team
Maintainer: Tom Kraljevic
Description: Run H2O via its REST API from within R.
License: Apache License (== 2.0)
Depends: R (>= 2.13.0), RCurl, rjson, statmod, survival, stats, tools, utils, methods
Collate: Wrapper.R Internal.R Classes.R ParseImport.R models.R Algorithms.R zzz.R
NeedsCompilation: no
SystemRequirements: Java (>= 1.6)
Suggests: plyr
URL: http://www.0xdata.com
Packaged: 2014-10-23 02:24:40 UTC; jenkins
Repository: CRAN
Date/Publication: 2014-10-27 18:11:24

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New package qdm with initial version 0.1-0
Package: qdm
Version: 0.1-0
Date: 2014-10-16
Title: Fitting a Quadrilateral Dissimilarity Model to Same-Different Judgments
Authors@R: c(person("Nora", "Umbach", role = c("aut", "cre"), email = "nora.umbach@web.de"), person("Florian", "Wickelmaier", role = "aut"))
Depends: R (>= 3.1.0), stats, graphics
Description: This package provides different specifications of a Quadrilateral Dissimilarity Model which can be used to fit same-different judgments in order to get a predicted matrix that satisfies regular minimality [Colonius & Dzhafarov, 2006, Measurement and representations of sensations, Erlbaum]. From such a matrix, Fechnerian distances can be computed.
License: GPL (>= 2)
Packaged: 2014-10-27 13:33:02 UTC; noraumbach
Author: Nora Umbach [aut, cre], Florian Wickelmaier [aut]
Maintainer: Nora Umbach
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 15:30:23

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Sat, 25 Oct 2014

New package managelocalrepo with initial version 0.1.4
Package: managelocalrepo
Type: Package
Title: Manage a CRAN-style Local Repository
Version: 0.1.4
Date: 2014-10-25
Author: Imanuel Costigan
Maintainer: Imanuel Costigan
Description: This will allow easier management of a CRAN-style repository on local networks (i.e. not on CRAN). This might be necessary where hosted packages contain intellectual property owned by a corporation.
License: GPL-2
Depends: R (>= 3.0)
Imports: stringr (>= 0.6.2), assertthat (>= 0.1), tools (>= 3.0)
Packaged: 2014-10-25 03:44:33 UTC; imanuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:55

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New package HiDimDA with initial version 0.2-2
Package: HiDimDA
Type: Package
Title: High Dimensional Discriminant Analysis
Version: 0.2-2
Date: 2014-10-24
Author: Antonio Pedro Duarte Silva
Maintainer: Antonio Pedro Duarte Silva
Depends: R (>= 2.10.0)
Imports: splines
Suggests: MASS
LazyLoad: yes
LazyData: yes
Description: Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.
License: GPL (>= 3)
URL: http://www.r-project.org
Repository: CRAN
Packaged: 2014-10-24 13:48:10 UTC; apedro
NeedsCompilation: yes
Date/Publication: 2014-10-25 07:51:03

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New package choroplethrMaps with initial version 1.0
Package: choroplethrMaps
Type: Package
Title: Contains maps used by the choroplethr package
Version: 1.0
Date: 2014-10-22
Author: Ari Lamstein
Maintainer: Ari Lamstein
Description: Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world.
License: BSD_3_clause + file LICENSE
URL: https://github.com/trulia/choroplethrMaps/, https://groups.google.com/forum/#!forum/choroplethr
BugReports: https://github.com/trulia/choroplethrMaps/issues
Suggests: ggplot2
Packaged: 2014-10-25 02:51:32 UTC; arilamstein
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:52

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New package BayesMixSurv with initial version 0.9
Package: BayesMixSurv
Type: Package
Title: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
Version: 0.9
Date: 2014-10-24
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
License: GPL (>= 2)
Depends: survival
Packaged: 2014-10-25 01:34:35 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:48

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Fri, 24 Oct 2014

New package highD2pop with initial version 1.0
Package: highD2pop
Type: Package
Title: Two-Sample Tests for Equality of Means in High Dimension
Version: 1.0
Date: 2012-11-02
Author: Karl Gregory
Maintainer: Karl Gregory
Description: Performs the generalized component test from Gregory et al (2015), as well as the tests from Chen and Qin (2010), Srivastava and Kubokawa (2013), and Cai, Liu, and Xia (2014) for equality of two population mean vectors when the length of the vectors exceeds the sample size.
License: GPL (>= 2)
LazyLoad: true
LazyData: true
ZipData: no
Depends: fastclime
Packaged: 2014-10-24 14:25:33 UTC; karlgregory
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-25 01:28:48

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New package ruv with initial version 0.9.4
Package: ruv
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: The algorithms in this package attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, and RUV-rinv, along with various supporting algorithms. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specifiy a set of negative control variables, as described in the references.
Version: 0.9.4
Date: 2014-10-24
Author: Johann Gagnon-Bartsch
Maintainer: Johann Gagnon-Bartsch
License: GPL
URL: http://www.stat.berkeley.edu/~johann/ruv
LazyLoad: yes
Packaged: 2014-10-24 09:52:13 UTC; johann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-24 13:55:18

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New package PANICr with initial version 0.0.0.2
Package: PANICr
Title: PANIC Tests of Nonstationarity
Description: This package contains a methodology that makes use of the factor structure of large dimensional panels to understand the nature of nonstationarity inherent in data. This is referred to as PANIC - Panel Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC (2004) includes valid pooling methods that allow panel tests to be constructed. PANIC (2004) can detect whether the nonstationarity in a series is pervasive, or variable specific, or both. PANIC (2010) includes two new tests on the idiosyncratic component that estimates the pooled autoregressive coefficient and sample moment, respectively. The PANIC model approximates the number of factors based on Bai and Ng (2002)
Depends: R(>= 2.10.0)
Version: 0.0.0.2
License: GPL-3
LazyData: no
Author: Steve Bronder
Maintainer: Steve Bronder
URL: stevebronder.com
Suggests: knitr
VignetteBuilder: knitr
Imports: MCMCpack
Packaged: 2014-10-24 06:46:57 UTC; brond_000
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-24 10:55:46

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New package PHENIX with initial version 1.0
Package: PHENIX
Type: Package
Title: Phenotypic Integration Index
Version: 1.0
Date: 2014-10-15
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
Imports: ppcor
Encoding: UTF-8
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might overestimate the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) and a bootstrapping method to test the significance of both integration indices.
License: GPL (>= 2)
Packaged: 2014-10-23 20:33:24 UTC; ajesusmp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-24 07:51:38

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New package P2C2M with initial version 0.5
Package: P2C2M
Type: Package
Title: Posterior Predictive Checks of Coalescent Models
Version: 0.5
Date: 2014-10-23
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl
Depends: R (>= 3.0.0)
Imports: ape (>= 3.1-4), apTreeshape (>= 1.4-5), ggplot2 (>= 1.0.0), rPython (>= 0.0-5), stringr (>= 0.6.2)
Suggests: genealogicalSorting (>= 0.92), phybase (>= 1.3.1), Rmpi (>= 0.6-5), xtermStyle (>= 2.2-4)
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST and *BEAST, respectively. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is necessary.
License: GPL (>= 2)
OS_type: unix
NeedsCompilation: yes (automatic)
SystemRequirements: Python (= 2.7)
Packaged: 2014-10-23 06:55:27 UTC; michael
Repository: CRAN
Date/Publication: 2014-10-24 07:51:37

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Thu, 23 Oct 2014

New package rsml with initial version 1.0
Package: rsml
Type: Package
Title: Root System Markup Language (RSML) file processing
Version: 1.0
Date: 2014-07-22
Author: Guillaume Lobet
Maintainer: Guillaume Lobet
Description: Read and analyse Root System Markup Language (RSML) files.
License: GPL-2
Imports: XML,rgl
Packaged: 2014-10-23 14:10:40 UTC; guillaumelobet
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 17:25:08

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New package matR with initial version 0.9
Package: matR
Type: Package
Title: Metagenomics Analysis Tools for R
Authors@R: c (person ("Daniel", "Braithwaite", role = c ("aut", "cre"), email = "contact.dtb@gmail.com"), person ("Kevin", "Keegan", role = "aut", email = "keegan@mcs.anl.gov"), person (c ("University", "of"), "Chicago", role = "cph"))
Version: 0.9
Depends: R (>= 2.10), MGRASTer, BIOM.utils, graphics, stats, utils
Imports:
Suggests: RJSONIO, qvalue, ecodist, gplots, scatterplot3d
URL: https://github.com/MG-RAST/matR/
Date: 2014-10-22
Description: An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software.
License: BSD_2_clause + file LICENSE
Copyright: University of Chicago
LazyData: yes
Collate: utils.R biom-ext.R client.R graphics.R analysis-support.R analysis-misc.R distx.R rowstats.R transform.R boxplot.R princomp.R image.R init.R
Packaged: 2014-10-23 07:39:09 UTC; dan
Author: Daniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph]
Maintainer: Daniel Braithwaite
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 11:50:13

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Wed, 22 Oct 2014

New package sigloc with initial version 0.0.4
Package: sigloc
Version: 0.0.4
Date: 2013-04-23
Title: Signal Location Estimation
Author: Sergey S. Berg
Maintainer: Sergey S. Berg
Depends: R (>= 2.15.3), nleqslv, ellipse
Description: A collection of tools for estimating the location of a transmitter signal from radio telemetry studies using the maximum likelihood estimation (MLE) approach described in Lenth (1981).
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2014-10-22 20:22:57 UTC; Serge
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 23:14:50

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New package TDboost with initial version 1.0
Package: TDboost
Title: A Boosted Nonparametric Tweedie Model
Version: 1.0
Date: 2013-10-11
Author: Yi Yang , Wei Qian , Hui Zou
Maintainer: Yi Yang
Depends: R (>= 2.12.0), lattice
Description: A fully nonparametric Tweedie model using the gradient boosting. It is capable of fitting a flexible nonlinear model and capturing interactions among predictors.
LazyData: yes
License: GPL-3
Packaged: 2014-10-22 16:33:11 UTC; emeryyi
NeedsCompilation: yes
Date/Publication: 2014-10-22 20:48:02
Repository: CRAN

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New package glmvsd with initial version 1.0
Package: glmvsd
Type: Package
Title: Variable Selection Deviation (VSD) Measures and Instability Tests for High-dimensional Generalized Linear Models
Version: 1.0
Date: 2014-09-19
Author: Ying Nan , Yi Yang , Yuhong Yang
Maintainer: Yi Yang
Depends: stats, glmnet, ncvreg, MASS
Description: Variable selection deviation measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
License: GPL-2
URL: https://github.com/emeryyi/glmvsd
Packaged: 2014-10-22 16:08:33 UTC; emeryyi
Date/Publication: 2014-10-22 20:49:00
NeedsCompilation: no
Repository: CRAN

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New package traj with initial version 1.0
Package: traj
Title: Trajectory Analysis
Description: Implements the three step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Version: 1.0
Date: 2014-07-10
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik
License: GPL-2
LazyData: true
Depends: R (>= 3.0.3)
Imports: cluster, psych, pastecs, NbClust, graphics, grDevices, stats, utils, GPArotation
Packaged: 2014-10-22 15:47:16 UTC; Dan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 18:20:51

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New package saeSim with initial version 0.6.0
Package: saeSim
Type: Package
Title: Simulation Tools for Small Area Estimation
Date: 2014-10-22
Version: 0.6.0
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz
URL: https://wahani.github.io/saeSim
BugReports: https://github.com/wahani/saeSim/issues
Depends: R(>= 3.1), methods
Imports: dplyr(>= 0.2), ggplot2, MASS, spdep, parallel
Suggests: testthat, knitr
Description: Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel.
License: GPL-3 | file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-22 12:28:59 UTC; swarnholz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 16:04:46

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New package lmenssp with initial version 1.0
Package: lmenssp
Type: Package
Title: Linear Mixed Effects Models with Non-stationary Stochastic Processes
Version: 1.0
Date: 2014-10-21
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar
Depends: MASS, nlme
Description: Fit, filter and smooth mixed models with non-stationary processes
License: GPL (>= 2)
Packaged: 2014-10-22 08:38:04 UTC; asar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 13:13:04

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New package FDGcopulas with initial version 1.0
Package: FDGcopulas
Type: Package
Title: Multivariate Dependence with FDG Copulas
Version: 1.0
Date: 2014-09-19
Author: Gildas Mazo, Stephane Girard
Maintainer: Gildas Mazo
Description: FDG copulas are a class of copulas featuring an interesting balance between flexibility and tractability. This package provides tools to construct, calculate the pairwise dependence coefficients of, simulate from, and fit FDG copulas. The acronym FDG stands for 'one-Factor with Durante Generators', as an FDG copula is a one-factor copula -- that is, the variables are independent given a latent factor -- whose linking copulas belong to the Durante class of bivariate copulas (also referred to as exchangeable Marshall-Olkin or semilinear copulas).
License: GPL (>= 3)
Depends: Rcpp (>= 0.10.6), methods
LinkingTo: Rcpp
Imports: numDeriv, randtoolbox
Packaged: 2014-10-22 07:24:07 UTC; mazo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-22 09:33:34

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New package indicoio with initial version 0.3
Package: indicoio
Title: A simple R Wrapper for the indico set of APIs - http://indico.io
Version: 0.3
Author: Alexander Gedranovich
Maintainer: Madison May
Description: R-based client for Machine Learning APIs at http://indico.io. Provides wrappers for following APIs: Positive/Negative Sentiment Analysis, Political Sentiment Analysis, Image Feature Extraction, Facial Emotion Recognition, Facial Feature Extraction, Language Detection
Depends: R (>= 3.0.2), httr, rjson, stringr, png
License: MIT + file LICENSE
LazyData: true
Suggests: testthat, jpeg
Packaged: 2014-10-22 00:37:34 UTC; mmay
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 08:58:17

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Tue, 21 Oct 2014

New package DetMCD with initial version 0.0.1
Package: DetMCD
Type: Package
Title: DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter)
Version: 0.0.1
Date: 2013-01-13
Depends: matrixStats, pcaPP (>= 1.8-1), robustbase, MASS
Suggests: mvtnorm
LinkingTo: Rcpp, RcppEigen
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
License: GPL (>= 2)
LazyLoad: yes
Authors@R: c(person("Vakili", "Kaveh", role = c("aut", "cre"), email = "vakili.kaveh.email@gmail.com"), person("Mia", "Hubert", role = "ths", email = "mia.hubert@wis.kuleuven.be"))
Maintainer: Vakili Kaveh
Author: Vakili Kaveh [aut, cre], Mia Hubert [ths]
Packaged: 2014-10-21 16:15:15 UTC; kaveh
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 20:01:49

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New package scrm with initial version 1.3-1
Package: scrm
Type: Package
Title: Simulating the Evolution of Biological Sequences
Version: 1.3-1
Date: 2014-10-21
Authors@R: c( person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut', 'cre', 'cph')), person('Zhu', 'Sha', role=c('aut', 'cph')), person('Dirk', 'Metzler', role='ths'), person('Gerton', 'Lunter', role=c('aut', 'cph', 'ths')) )
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution.
URL: https://github.com/scrm/scrm-r
License: GPL (>= 3)
Suggests: testthat (>= 0.9.0), knitr, ape
Imports: Rcpp (>= 0.11.2)
SystemRequirements: C++11
VignetteBuilder: knitr
LinkingTo: Rcpp
Packaged: 2014-10-21 11:42:11 UTC; paul
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 17:48:23

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New package rtkpp with initial version 0.8.2
Package: rtkpp
Type: Package
Title: STK++ integration to R using Rcpp.
Version: 0.8.2
Encoding: UTF-8
Date: 2014-02-08
Authors@R: c(person("Serge", "Iovleff", role=c("aut","cre"), email="serge.iovleff@stkpp.org"), person("Vincent", "Kubicki", role="ctb", email="Vincent.Kubicki@inria.fr"), person("Quentin", "Grimonprez", role="ctb", email="Quentin.Grimonprez@inria.fr"), person("Parmeet", "Bhatia", role="ctb", email="bhatia.parmeet@gmail.com"))
Copyright: Inria, and specifically inst/COPYRIGHTS for the STK++ library
Maintainer: Serge Iovleff
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
License: GPL (>= 2) | LGPL (>= 2) | file LICENSE
BugReports: https://www.stkpp.org
LazyLoad: yes
Depends: R (>= 3.0.2), Rcpp
LinkingTo: Rcpp
Imports: methods
URL: http://www.stkpp.org
NeedsCompilation: yes
SystemRequirements: GNU make
Collate: 'ClusterAlgo.R' 'ClusterInit.R' 'ClusterStrategy.R' 'IClusterModel.R' 'ClusterCategorical.R' 'ClusterDiagGaussian.R' 'ClusterGamma.R' 'ClusterModelNames.R' 'ClusterPlot.R' 'global.R' 'rtkpp.R' 'rtkppFlags.R' 'inlineCxxPlugin.R'
Packaged: 2014-10-21 12:37:40 UTC; iovleff
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Repository: CRAN
Date/Publication: 2014-10-21 17:48:19

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New package cdcsis with initial version 1.0
Package: cdcsis
Type: Package
Title: Conditional Distance Correlation and Its Related Feature Screening Method
Version: 1.0
Date: 2014-09-01
Author: Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin Wang
Depends: R(>= 3.0.1), stats
Imports: ks
Suggests: MASS, energy
Maintainer: Canhong Wen
Description: Gives conditional distance correlation and performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data. The conditional distance correlation is a novel conditional dependence measurement of two random variables given a third variable. The conditional distance correlation sure independence screening is used for screening variables in ultrahigh dimensional setting.
License: GPL (>= 2)
Packaged: 2014-10-21 14:47:45 UTC; wencanh
Repository: CRAN
Collate: 'cdcov.R' 'cdcor.R' 'cdcor.ada.R' 'bw.R' 'cdcsis.R'
NeedsCompilation: yes
Date/Publication: 2014-10-21 17:48:22

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New package openssl with initial version 0.1
Package: openssl
Type: Package
Title: Bindings to OpenSSL
Version: 0.1
Date: 2014-10-20
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: This package interfaces to the OpenSSL libraries libssl and libcrypto. Currently it only implements bindings to the OpenSSL random number generator in order to generate crypto secure random bytes in R.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/openssl
BugReports: https://github.com/jeroenooms/openssl/issues
SystemRequirements: OpenSSL (libssl-dev or openssl-devel)
Packaged: 2014-10-20 19:30:34 UTC; jeroen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 08:27:55

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Mon, 20 Oct 2014

New package tclust with initial version 1.2-3
Package: tclust
Version: 1.2-3
Date: 2014-10-20
Title: Robust Trimmed Clustering
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov
Description: Robust Trimmed Clustering
Depends: R (>= 2.12.0), mvtnorm, sn, mclust, cluster
License: GPL-3
Repository: CRAN
NeedsCompilation: yes
Packaged: 2014-10-20 13:49:50 UTC; TodorovV
Date/Publication: 2014-10-21 02:02:38

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New package ore with initial version 1.0.0
Package: ore
Version: 1.0.0
Date: 2014-10-20
Title: An R Interface to the Oniguruma Regular Expression Library
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
Depends: R (>= 2.12.1)
Suggests: crayon, rex, testthat
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Encoding: UTF-8
License: BSD_3_clause + file LICENCE
URL: https://github.com/jonclayden/ore
Packaged: 2014-10-20 15:15:03 UTC; jon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-20 19:18:10

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New package JMdesign with initial version 1.0
Package: JMdesign
Type: Package
Title: Joint Modeling of Longitudinal and Survival Data - Power Calculation
Version: 1.0
Date: 2012-06-01
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix Sigma_theta is unknown.
License: GPL-2
Depends: methods
Packaged: 2014-10-20 15:06:06 UTC; sthollow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 19:18:02

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New package restlos with initial version 0.1-3
Package: restlos
Type: Package
Title: Robust Estimation of Location and Scatter
Version: 0.1-3
Date: 2014-10-13
Author: Steffen Liebscher and Thomas Kirschstein
Maintainer: Steffen Liebscher
Description: The restlos package provides algorithms for robust estimation of location and scatter based on minimum spanning trees (pMST), self-organizing maps (Flood Algorithm), and Delaunay triangulations (RDELA). The functions are also suitable for outlier detection.
Depends: som, rgl, geometry, igraph
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-10-20 07:58:57 UTC; Steffen
X-CRAN-Comment: Archived on 2014-10-03 as depends on nnclust which has been archived.
Date/Publication: 2014-10-20 10:30:59

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New package commentr with initial version 0.1
Package: commentr
Type: Package
Title: Print Nicely Formatted Comments for use in Script Files
Version: 0.1
License: GPL-2
Date: 2014-10-13
Author: Erik Bulow
Maintainer: Erik Bulow
Description: Functions to produce nicely formatted comments to use in R-scripts (or Latex/HTML/markdown etc). A comment with formatting is printed to the console and can then be copied to a script.
Imports: stringr
Suggests: testthat
BugReports: https://github.com/cancercentrum/commentr/issues
Packaged: 2014-10-20 07:46:08 UTC; erikbulow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 10:30:16

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Sat, 18 Oct 2014

New package multispatialCCM with initial version 1.0
Package: multispatialCCM
Title: Multispatial Convergent Cross Mapping
Version: 1.0
Date: 2014-10-18
Author: Adam Clark
Maintainer: Adam Clark
Depends: R (>= 3.0.2)
Description: The multispatial convergent cross mapping algorithm can be used as a test for causal associations between pairs of processes represented by time series. This is a combination of convergent cross mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh et al., 2008, American Naturalist, 171, 71–80. The algorithm allows CCM to be implemented on data that are not from a single long time series. Instead, data can come from many short time series, which are stitched together using bootstrapping.
License: GPL (>= 2)
Encoding: UTF-8
Packaged: 2014-10-18 23:48:53 UTC; atclark
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:55:59

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New package logconPH with initial version 1.0
Package: logconPH
Type: Package
Title: CoxPH Model with Log Concave Baseline Distribution
Version: 1.0
Date: 2014-08-19
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
License: GPL-2
Packaged: 2014-10-18 23:32:43 UTC; Cliff
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:49:27

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New package landpred with initial version 1.0
Package: landpred
Type: Package
Title: Landmark Prediction of a Survival Outcome
Version: 1.0
Author: Layla Parast
Maintainer: Layla Parast
Description: This package includes functions for landmark prediction of a survival outcome incorporating covariate and short-term event information. For more information about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and Tianxi Cai. Incorporating short-term outcome information to predict long-term survival with discrete markers. Biometrical Journal 53.2 (2011): 294-307.
License: GPL
Imports: survival
Packaged: 2014-10-17 22:28:12 UTC; parast
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-18 06:36:04

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Fri, 17 Oct 2014

New package RMKdiscrete with initial version 0.1
Package: RMKdiscrete
Version: 0.1
Date: 2014-10-17
Title: Sundry Discrete Probability Distributions
Author: Robert M. Kirkpatrick
Maintainer: Robert M. Kirkpatrick
Description: Sundry discrete probability distributions and helper functions.
Depends: stats, R (>= 2.15.0)
NeedsCompilation: yes
Repository: CRAN
License: GPL (>= 2)
Packaged: 2014-10-17 16:15:33 UTC; Rob
Date/Publication: 2014-10-17 20:23:16

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New package highTtest with initial version 1.0
Package: highTtest
Type: Package
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Version: 1.0
Date: 2014-10-14
Authors@R: c(person("Hongyuan", "Cao", role = c("aut"), email = "caohong@missouri.edu"), person("Michael", "Kosorok", role = c("aut"), email = "kosorok@unc.edu"), person("Shannon","Holloway", role=c("aut","cre"), email="sthollow@ncsu.edu"))
Description: Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.
License: GPL-2
Depends: methods, colorfulVennPlot
Packaged: 2014-10-17 16:31:13 UTC; sthollow
Author: Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 19:54:38

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New package sisVIVE with initial version 1.0
Package: sisVIVE
Type: Package
Title: Some Invalid Some Valid Instrumental Variables Estimator
Version: 1.0
Date: 2014-07-31
Author: Hyunseung Kang
Maintainer: Hyunseung Kang
Depends: lars
Suggests: MASS
Description: Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome. The paper, Instrumental Variables Estimation with Some Invalid Instruments and its Application to Mendelian Randomization by Hyunseung Kang, Anru Zhang, T. Tony Cai, and Dylan S. Small (on arXiv) has more details on this procedure.
License: GPL-2
Packaged: 2014-10-17 14:29:30 UTC; khyuns
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:39:17

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New package MRH with initial version 1.0
Package: MRH
Type: Package
Title: Multi-Resolution Estimation of the Hazard Rate
Version: 1.0
Date: 2013-10-28
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times.
License: GPL-2
Depends: survival, KMsurv
Suggests: R.rsp
VignetteBuilder: R.rsp
Imports: coda, HI
Packaged: 2014-10-17 15:44:27 UTC; Yolanda
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 17:52:12

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New package mdscore with initial version 0.1-2
Package: mdscore
Type: Package
Title: Improved Score Tests for Generalized Linear Models
Version: 0.1-2
Date: 2014-10-15
Depends: R (>= 3.1.1), MASS
Suggests: Sleuth3
Authors@R: c(person("Antonio Hermes M.","da Silva-Junior", email = "hermes@ccet.ufrn.br", role = c("aut", "cre")), person("Damiao N.","da Silva", email = "damiao@ccet.ufrn.br", role = "aut"), person("Silvia L. P.", "Ferrari", email = "silviaferrari.usp@gmail.com", role = "ctb"))
Author: Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva [aut], Silvia L. P. Ferrari [ctb]
Maintainer: Antonio Hermes M. da Silva-Junior
Description: A set of functions to obtain modified score test for generalized linear models.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-10-17 12:28:47 UTC; mlfd58
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:50:40

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New package likert with initial version 1.2
Package: likert
Type: Package
Title: Functions to analyze and visualize likert type items
Version: 1.2
Date: 2014-09-28
Author: Jason Bryer , Kimberly Speerschneider
Maintainer: Jason Bryer
URL: http://jason.bryer.org/likert, http://github.com/jbryer/likert
BugReports: https://github.com/jbryer/likert/issues
Description: Functions to analyze and visualize likert type items
License: GPL
LazyLoad: yes
VignetteBuilder: utils
Depends: R (>= 3.0),ggplot2,xtable
Imports: psych,reshape,gridExtra,grid,plyr
Suggests: devtools,shiny
Packaged: 2014-10-17 14:01:18 UTC; jbryer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:43:09

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New package ecoval with initial version 1.0
Package: ecoval
Type: Package
Title: Procedures for Ecological Assessment of Surface Waters
Version: 1.0
Date: 2014-10-17
Author: Nele Schuwirth and Peter Reichert with contributions by Simone Langhans
Maintainer: Nele Schuwirth
Description: Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.
License: GPL (>= 2)
Depends: utility, rivernet
LazyData: true
Packaged: 2014-10-17 14:19:43 UTC; schuwine
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:36:36

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New package CLME with initial version 1.0-1
Package: CLME
Title: Constrained Inference for Linear Mixed Effects Models.
Version: 1.0-1
Depends: R (>= 3.0.2)
Imports: MASS, quadprog, shiny, methods, Iso
Suggests: nnet
Date: 2014-09-09
Description: Implements constrained inference for linear mixed effects models using residual bootstrap methodology.
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema
BugReports: https://github.com/jelsema/CLME/issues
BuildVignettes: true
LazyLoad: yes
License: GPL-2 | GPL-3
Packaged: 2014-10-17 16:02:45 UTC; jelsemacm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 18:22:17

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New package pBrackets with initial version 1.0
Package: pBrackets
Version: 1.0
Date: 2014-10-17
Title: Plot Brackets
Author: Andreas Schulz
Maintainer: Andreas Schulz
Depends: R (>= 3.0.0)
Imports: grid
Description: Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.
License: GPL (>= 2.0)
Packaged: 2014-10-17 09:30:23 UTC; scu9a
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 13:08:28

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New package segmag with initial version 1.2.2
Package: segmag
Type: Package
Version: 1.2.2
Date: 2014-10-06
Title: Determine Event Boundaries in Event Segmentation Experiments
Maintainer: Frank Papenmeier
Author: Frank Papenmeier [aut, cre], Konstantin Sering [ctb]
Authors@R: c(person("Frank","Papenmeier", role=c("aut","cre"), email="frank.papenmeier@uni-tuebingen.de"), person("Konstantin","Sering", role="ctb"))
Description: This package contains functions that help to determine event boundaries in event segmentation experiments by bootstrapping a critical segmentation magnitude under the null hypothesis that all key presses were randomly distributed across the experiment. Segmentation magnitude is defined as the sum of Gaussians centered at the times of the segmentation key presses performed by the participants. Within a participant, the maximum of the overlaid Gaussians is used to prevent an excessive influence of a single participant on the overall outcome (e.g. if a participant is pressing the key multiple times in succession). Further functions are included, such as plotting the results.
License: GPL (>= 3)
Suggests: testthat
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Packaged: 2014-10-06 15:55:49 UTC; fpapenmeier
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 10:30:45

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Thu, 16 Oct 2014

New package rivernet with initial version 1.0
Package: rivernet
Type: Package
Title: Read, Analyze and Plot River Networks
Version: 1.0
Date: 2014-10-16
Author: Peter Reichert
Maintainer: Peter Reichert
Description: Functions for reading, analysing and plotting river networks. For this package, river networks consist of sections and nodes with associated attributes, e.g. to characterise their morphological, chemical and biological state. The package provides functions to read this data from text files, to analyse the network structure and network paths and regions consisting of sections and nodes that fulfill prescribed criteria, and to plot the river network and associated properties.
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-16 07:39:29 UTC; reichert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 23:51:16

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New package enigma with initial version 0.1.0
Package: enigma
Title: R Client for the Enigma API
Description: Enigma (https://enigma.io) holds many public datasets from governments, companies, universities, and organizations. Enigma provides an API for data, metadata, and statistics on each of the datasets. enigma is an R client to interact with the Enigma API, including getting the data and metadata for datasets in Enigma, as well as collecting statistics on datasets. In addition, you can download a gzipped csv file of a dataset if you want the whole dataset. An API key from Enigma is required to use enigma.
Version: 0.1.0
Date: 2014-10-16
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"))
License: MIT + file LICENSE
LazyData: true
Imports: httr, jsonlite, plyr
Suggests: testthat
Packaged: 2014-10-16 21:25:40 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 00:42:42

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New package statar with initial version 0.1
Package: statar
Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Version: 0.1
Authors@R: person("Matthieu","Gomez", email = "mattg@princeton.edu", role = c("aut", "cre"))
Description: statar includes a set of functions for vectors: mode, tag, bin and winsorize. statar includes a set of functions for data.tables: summarize (in tables or graphs), panel data operations (lag, fill in gaps, fill in missing values) and SQL-type joins.
License: GPL-2
URL: https://github.com/matthieugomez/statar
BugReports: https://github.com/matthieugomez/statar/issues
Depends: R (>= 3.1.0)
Imports: data.table, dplyr (>= 0.3), ggplot2, grid, Hmisc, lazyeval, lubridate, matrixStats, stringr, tidyr
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-10-16 15:26:12 UTC; Matthieu
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 22:56:33

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New package RCMIP5 with initial version 1.0
Package: RCMIP5
Title: Tools for Manipulating and Summarizing CMIP5 Data
Description: Working with CMIP5 data can be tricky, forcing scientists to write custom scripts and programs. The `RCMIP5` package aims to ease this process, providing a standard, robust, and high-performance set of scripts to (i) explore what data have been downloaded, (ii) identify missing data, (iii) average (or apply other mathematical operations) across experimental ensembles, (iv) produce both temporal and spatial statistical summaries, (v) regrid data, and (vi) produce easy-to-work-with graphical and data summaries.
Imports: abind (>= 1.4-0), plyr (>= 1.8.1), reshape2 (>= 1.4), foreach (>= 1.4.2), digest
Depends: R (>= 2.11.0)
Suggests: ggplot2 (>= 0.9.3), ncdf4 (>= 1.9), ncdf (>= 1.6), doParallel (>= 1.0.8), fields(>= 7.1), testthat (>= 0.9), knitr
Version: 1.0
Authors@R: c( person("Ben", "Bond-Lamberty", role = c("aut")), person("Kathe", "Todd-Brown", role = c("aut", "cre"), email = "ktoddbrown@gmail.com") )
License: MIT + file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-15 03:07:51 UTC; ben
Author: Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre]
Maintainer: Kathe Todd-Brown
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 14:03:50

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New package RcmdrPlugin.steepness with initial version 0.3-2
Package: RcmdrPlugin.steepness
Type: Package
Title: Steepness Rcmdr Plug-in
Version: 0.3-2
Date: 2014-29-09
Author: David Leiva & Han de Vries
Maintainer: David Leiva
Depends: Rcmdr (>= 2.1-2), tcltk, steepness
Description: This package provides a GUI for the steepness package, it is written as an Rcmdr plug-in.
License: GPL (>= 2)
Packaged: 2014-09-29 21:07:02 UTC; dleivaur
NeedsCompilation: no
X-CRAN-Comment: Archived on 2013-03-23 and again on 2014-05-30 as steepness was.
Repository: CRAN
Date/Publication: 2014-10-16 14:05:53

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New package logbin with initial version 1.0
Package: logbin
Title: Relative Risk Regression Using the Log Binomial Model
Description: Methods for fitting log-link GLMs and GAMs for binomial data. The package uses EM-type algorithms with more stable convergence properties than standard methods.
Version: 1.0
Date: 2014-10-16
Author: Mark Donoghoe
Maintainer: Mark Donoghoe
Depends: R (>= 3.0.1)
Imports: splines, glm2
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-16 03:19:53 UTC; mdonoghoe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 07:58:44

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Wed, 15 Oct 2014

New package rfoaas with initial version 0.0.4
Package: rfoaas
Type: Package
Title: R Interface to FOAAS
Version: 0.0.4
Date: 2014-10-15
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Description: R access to the FOAAS (F... Off As A Service) web service
License: GPL (>= 2)
Packaged: 2014-10-15 10:55:44.845568 UTC; edd
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 01:17:17

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New package metaMix with initial version 0.1
Package: metaMix
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Version: 0.1
Author: Sofia Morfopoulou
Maintainer: Sofia Morfopoulou
Depends: R (>= 3.0.1)
Imports: data.table (>= 1.9.2), Matrix, gtools, Rmpi, ggplot2
Suggests: knitr
VignetteBuilder: knitr
Description: metaMix resolves complex metagenomic mixtures by analysing deep sequencing data, using a Mixture Model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture.
License: GPL-3
LazyData: true
SystemRequirements: Open MPI (>=1.4.3)
Packaged: 2014-10-15 11:36:19 UTC; psofaki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-16 01:26:14

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New package windex with initial version 1.0
Package: windex
Type: Package
Title: windex: Analysing convergent evolution using the Wheatsheaf index
Version: 1.0
Date: 2014-09-05
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle
Description: Analysing convergent evolution using the Wheatsheaf index.
License: GPL-2
Depends: geiger (>= 2.0), ape, scatterplot3d, utils, R (>= 3.0.0)
Packaged: 2014-10-14 13:49:37 UTC; aminter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 00:01:11

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New package ggRandomForests with initial version 1.0.0
Package: ggRandomForests
Type: Package
Title: Creating and Plotting Data Objects for Understanding Random Forests
Version: 1.0.0
Date: 2014-10-15
Author: John Ehrlinger
Maintainer: John Ehrlinger
License: GPL (>= 3)
URL: https://github.com/ehrlinger/ggRandomForests
Description: The ggRandomForests package contains tools for creating and plotting data structures to visually understand random forest models. The functions are designed for use with the randomForestSRC package. This package is structured to extract intermediate data objects from the random forest. S3 Plot functions, which use the ggplot2 package, are included for each data object.
Depends: R (>= 3.1.0), ggplot2, randomForestSRC, reshape2, survival, dplyr
Suggests: testthat
Packaged: 2014-10-15 18:13:42 UTC; ehrlinj
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:53:25

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New package cwhmisc with initial version 5.0
Package: cwhmisc
Version: 5.0
Date: 2014-10-15
Title: Miscellaneous Functions for math, plotting, printing, statistics, strings, and tools
Author: Christian W. Hoffmann
Maintainer: Christian W. Hoffmann
Depends: R (>= 2.0), lattice, grid
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
License: GPL (>= 2)
Packaged: 2014-10-15 14:05:48 UTC; hoffmann
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:37:39

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New package bio3d with initial version 2.1-1
Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-1
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat
Depends: R (>= 3.0.0)
LazyData: yes
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-15 20:07:48 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:56:55

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New package gets with initial version 0.1
Package: gets
Type: Package
Title: General-to-Specific (GETS) Model Selection
Version: 0.1
Depends: R (>= 2.4.1), zoo, lgarch
Date: 2014-10-14
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
Description: Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or a log-ARCH-X model of the log-variance. The three main functions of the package are arx, getsm and getsv. The first function estimates an AR-X model with log-ARCH-X errors. The second function undertakes GETS model selection of the mean specification of an arx object, whereas the third function undertakes GETS model selection of the log-variance specification of an arx object.
License: GPL-2
Packaged: 2014-10-15 09:28:20 UTC; admin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 13:16:36

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New package vetools with initial version 1.3-28
Encoding: UTF-8
Package: vetools
Depends: R (>= 2.10), sp
Imports: stringr, tis, lubridate, maptools, plyr, xts, scales
Maintainer: Andrew Sajo-Castelli
License: GPL
Title: Tools for Venezuelan Environmental Data
LazyData: false
Type: Package
Authors@R: c(person("Andrew", "Sajo-Castelli", email="asajo@usb.ve", role = c("aut", "cre")), person("Desiree", "Villalta", role = "ctb"),person("Lelys", "Bravo", role = "ctb"))
Description: Integrated data management library that offers a variety of tools concerning the loading and manipulation of environmental data available from different Venezuelan governmental sources. Facilities are provided to plot temporal and spatial data as well as understand the health of a collection of meteorological data.
Version: 1.3-28
Revision: $Rev: 4 $
BugReports: https://github.com/talassio/vetools/issues
Packaged: 2014-10-15 05:41:42 UTC; cesma
Author: Andrew Sajo-Castelli [aut, cre], Desiree Villalta [ctb], Lelys Bravo [ctb]
NeedsCompilation: no
Repository: CRAN
Date: 2013-08-01 14:10:01
Date/Publication: 2014-10-15 08:47:53

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New package nsgp with initial version 1.0.5
Package: nsgp
Title: Non-Stationary Gaussian Process Regression
Version: 1.0.5
Date: 2014-10-14
Author: Markus Heinonen
Maintainer: Markus Heinonen
Depends: R (>= 3.0.0)
Imports: MASS
Description: A Gaussian process regression using a Gaussian kernel for both one-sample and two-sample cases. Includes non-stationary Gaussian kernel (exponential decay function) and several likelihood ratio tests for differential testing along target points.
License: GPL-2
URL: http://amis-group.fr/software/nsgp
Packaged: 2014-10-14 14:29:42 UTC; markusheinonen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 06:54:09

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Tue, 14 Oct 2014

New package spark with initial version 1.0.0
Package: spark
Title: Sparklines in the R Terminal
Version: 1.0.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: Sparklines in the terminal. Essentially an R implementation of the original shell project: http://zachholman.com/spark/
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/gaborcsardi/spark
BugReports: https://github.com/gaborcsardi/pretty/spark
Imports: magrittr
Suggests: crayon, testthat
Packaged: 2014-10-14 13:44:34 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 02:45:14

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New package rex with initial version 0.1.0
Package: rex
Type: Package
Title: Simpler Regular Expressions
Version: 0.1.0
Date: 2013-01-16
Author: Kevin Ushey, Jim Hester
Maintainer: Jim Hester
Description: A simpler, human-readable interface for the construction of regular expressions.
Imports: magrittr, lazyeval
License: MIT + file LICENSE
Suggests: testthat, knitr, dplyr, ggplot2
VignetteBuilder: knitr
Collate: 'aaa.R' 'utils.R' 'escape.R' 'capture.R' 'character_class.R' 'counts.R' 'lookarounds.R' 'match.R' 'or.R' 'rex-mode.R' 'rex.R' 'shortcuts.R' 'wildcards.R' 'zzz.R'
Packaged: 2014-10-13 20:22:57 UTC; james.hester
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-14 05:27:22

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Mon, 13 Oct 2014

New package flam with initial version 1.0
Package: flam
Type: Package
Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Version: 1.0
Date: 2014-10-13
Author: Ashley Petersen
Maintainer: Ashley Petersen
Imports: MASS
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
License: GPL (>= 2)
Packaged: 2014-10-13 17:51:08 UTC; ajpete
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-13 21:53:48

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New package dataRetrieval with initial version 1.4.0
Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
Version: 1.4.0
Date: 2014-10-13
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov"), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"))
Description: Collection of functions to help retrieve USGS data from either web services or user-provided data files.
License: Unlimited | file LICENSE
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright
Depends: R (>= 3.0)
Imports: zoo, XML, RCurl, reshape2, lubridate
Suggests: xtable, EGRET, knitr, testthat
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
Additional_repositories: http://usgs-r.github.com
Packaged: 2014-10-13 15:59:48 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 21:59:18

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New package prettyunits with initial version 1.0.0
Package: prettyunits
Title: Pretty, Human Readable Formatting of Quantities
Version: 1.0.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/gaborcsardi/prettyunits
BugReports: https://github.com/gaborcsardi/prettyunits/issues
Imports: magrittr, assertthat
Suggests: testthat
Packaged: 2014-10-13 13:22:50 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 17:32:18

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New package CP with initial version 1.5
Package: CP
Type: Package
Title: Conditional Power Calculations
Version: 1.5
Date: 2014-10-13
Author: Andreas Kuehnapfel
Maintainer: Andreas Kuehnapfel
Depends: R(>= 3.0.1)
Imports: survival
Description: Functions for calculating the conditional power for different models in survival time analysis within randomized clinical trials with two different treatments to be compared and survival as an endpoint.
License: GPL-3
URL: https://www.imise.uni-leipzig.de
LazyLoad: yes
LazyData: yes
Packaged: 2014-10-13 07:35:22 UTC; akuehnapfel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 13:35:27

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New package QualInt with initial version 1.0.0
Package: QualInt
Title: Test for Qualitative Interactions
Version: 1.0.0
Author: Lixi Yu, Eun-Young Suh, Guohua (James) Pan
Maintainer: Lixi Yu
Description: Used for testing for qualitative interactions between treatment effects and patient subgroups. Here the term treatment effect means a comparison result of two treatments within each patient subgroup. Models included in this package are Gaussian, binomial and Cox models. Methods included here are interval based graphical approach and Gail Simon LRT.
Depends: survival, ggplot2
License: GPL-2
LazyLoad: yes
Packaged: 2014-10-13 06:18:25 UTC; Lixi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 09:58:21

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Sun, 12 Oct 2014

New package RNetLogo with initial version 1.0-1
Package: RNetLogo
Version: 1.0-1
Date: 2014-10-12
Title: Provides an Interface to the Agent-Based Modelling Platform NetLogo
Author: Jan C. Thiele
Maintainer: Jan C. Thiele
Description: Interface to use and access Wilensky's NetLogo (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the NetLogo Mathematica Link http://ccl.northwestern.edu/netlogo/docs/mathematica.html
Depends: R (>= 2.12.1), rJava (>= 0.6-3), igraph
Suggests: parallel
SystemRequirements: Java (>= 6.0), NetLogo (>= 5.0)
License: GPL-2
LazyLoad: yes
URL: http://rnetlogo.r-forge.r-project.org/
Packaged: 2014-10-12 13:24:12 UTC; jthiele
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-12 18:56:10

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Sat, 11 Oct 2014

New package BSGW with initial version 0.9
Package: BSGW
Type: Package
Title: Bayesian Survival Model using Generalized Weibull Regression
Version: 0.9
Date: 2014-10-11
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Bayesian survival model using Weibull regression on both scale and shape parameters.
License: GPL (>= 2)
Depends: survival
Packaged: 2014-10-11 22:19:22 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-12 02:02:48

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New package RAdwords with initial version 0.1
Package: RAdwords
Type: Package
Title: RAdwords: Loading Adwords data into R
Description: The aim of RAdwords is loading Adwords data into R. Therefore the package implements three main features. First, the package provides an authentication process for R with the Adwords API via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.
Version: 0.1
Author: Johannes Burkhardt , Matthias Bannert
Maintainer: Johannes Burkhardt
Depends: R (>= 3.0.3)
Imports: RCurl, rjson
License: GPL (>= 2) | MIT + file LICENSE
URL: https://github.com/jburkhardt/RAdwords
Packaged: 2014-10-11 15:44:41 UTC; jburkhardt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-11 18:33:25

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New package mfblock with initial version 1.0
Package: mfblock
Type: Package
Title: Fitting and Simulation of a block multifactor model
Version: 1.0
Date: 2014-09-11
Author: Marc Fortier
Maintainer: Marc Fortier
Imports: boot,nloptr
Description: Implementation of the simulated method of moments (smm) of Oh and Patton for copula-based multivariate models
License: GPL-3
Depends: skewt
NeedsCompilation: TRUE
Packaged: 2014-10-10 21:40:10 UTC; root
Repository: CRAN
Date/Publication: 2014-10-11 07:07:36

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Fri, 10 Oct 2014

New package BNSP with initial version 1.0.0
Package: BNSP
Title: Bayesian Non- and Semi-parametric Model Fitting
Version: 1.0.0
Date: 2014-10-10
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models
Depends: R (>= 3.1.0)
License: GPL (>= 2)
URL: http://www.bbk.ac.uk/ems/faculty/papageorgiou
Packaged: 2014-10-10 14:30:48 UTC; papgeo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-10 23:54:56

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New package HierO with initial version 0.1
Package: HierO
Type: Package
Title: A graphical user interface for calculating power and sample size for hierarchical data
Version: 0.1
Date: 2014-10-10
Author: Kari Tokola
Maintainer: Kari Tokola
Description: HierO is a graphical user interface (GUI) tool for calculating optimal statistical power and sample size for hierarchical data structure. HierO constructs a user defined sample size optimization problem to GAMS (General Algebraic Modeling System)form and uses Rneos package to send the problem to NEOS server for solving.
License: GPL-2
Depends: methods, rneos
Imports: XMLRPC, RCurl, bitops, XML, tcltk, tcltk2
Additional_repositories: http://www.omegahat.org/R
Packaged: 2014-10-10 12:38:01 UTC; kt61380
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-10 21:54:10

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New package adwave with initial version 1.0
Package: adwave
Type: Package
Title: Wavelet Analysis of Genomic Data from Admixed Populations
Version: 1.0
Date: 2014-10-03
Depends: R (>= 2.10), waveslim
Author: Jean Sanderson
Maintainer: Murray Cox
Description: Implements wavelet-based approaches for describing population admixture. Principal Components Analysis (PCA) is used to define the population structure and produce a localized admixture signal for each individual. Wavelet summaries of the PCA output describe variation present in the data and can be related to population-level demographic processes. For more details, see accompanying paper.
License: GPL (>= 2)
Packaged: 2014-10-10 09:36:22 UTC; jean
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-10 21:54:19

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New package RSQLServer with initial version 0.1.1
Package: RSQLServer
Type: Package
Title: SQL Server R Database Interface (DBI)
Version: 0.1.1
Date: 2014-10-10
Authors@R: as.person(c("Imanuel Costigan [aut,cre]", "The jTDS Project (for MSSQL Server driver) [aut]", "Simon Urbanek [ctb]", "The Legion Of The Bouncy Castle [cph,ctb]"))
Maintainer: Imanuel Costigan
Description: RSQLServer wraps the jTDS Project's JDBC 3.0 SQL Server driver and extends the RJDBC classes and DBI methods. It defines a SQLServerDriver, SQLServerConnection & SQLServerRsult S4 classes as extensions of the RJDBC equivalent classes. Most of the DBI methods will simply be calls to methods defined by RJDBC classes. However, the dbConnect and some of the dbGetInfo methods are specific to SQL Server. The jTDS drivers do extend to Sybase SQL Server, but currently, only Microsoft SQL Server is supported by this package.
License: GPL-2
Depends: methods, DBI (>= 0.3.1), rJava (>= 0.9-6)
Imports: RJDBC (>= 0.2-4)
SystemRequirements: Java (>= 1.3)
Collate: 'DBDriver.R' 'DBConnection.R' 'DBResult.R' 'RSQLServer.R' 'Utils.R' 'onLoad.R'
Packaged: 2014-10-10 08:55:42 UTC; imanuel
Author: Imanuel Costigan [aut, cre], The jTDS Project [aut] (for MSSQL Server driver), Simon Urbanek [ctb], The Legion Of The Bouncy Castle [cph, ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-10 12:10:24

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New package sptm with initial version 14.10-8
Package: sptm
LazyLoad: yes
LazyData: yes
Version: 14.10-8
Date: 14.10-08
Title: SemiParametric Transformation Model Methods
Author: Youyi Fong , Krisztian Sebestyen
Maintainer: Youyi Fong
Depends: R (>= 3.0.0), survival, survey
Imports: kyotil
Suggests: RUnit, mvtnorm, Matrix, MASS
Description: Semiparametric transformation model, calibration weights
License: GPL (>= 2)
Packaged: 2014-10-09 22:23:29 UTC; yfong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-10 07:27:16

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Thu, 09 Oct 2014

New package ENiRG with initial version 0.1
Package: ENiRG
Type: Package
Title: Ecological Niche in R and GRASS
Version: 0.1
Date: 2014-05-21
Author: Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes Gonzalez-Wanguemert
Maintainer: Fernando Garcia Canovas
Description: The package allows to perform the Ecological Niche Factor Analysis, calculate habitat suitability maps and classify the habitat in suitability classes. Computations are executed in a throw-away GRASS environment from R in order to be able to perform analysis with large data sets.
License: GPL (>= 2)
Depends: ade4, raster, R.utils, sp, spgrass6
Imports: gdata, fgui, miniGUI, tcltk
Packaged: 2014-10-09 10:30:36 UTC; fcgarcia
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-09 14:33:32

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New package CEC with initial version 0.9.1
Package: CEC
Title: Cross-Entropy Clustering
Version: 0.9.1
Date: 2014-10-09
Author: Konrad Kamieniecki
Maintainer: Konrad Kamieniecki
Description: Cross-Entropy Clustering (CEC) divides the data into Gaussian type clusters. It performs the automatic reduction of unnecessary clusters, while at the same time allows the simultaneous use of various type Gaussian mixture models.
ByteCompile: true
Encoding: UTF-8
NeedsCompilation: yes
License: GPL-3
Packaged: 2014-10-08 20:18:08 UTC; konrad
Repository: CRAN
Date/Publication: 2014-10-09 14:30:45

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New package anominate with initial version 0.5
Package: anominate
Type: Package
Title: alpha-NOMINATE Ideal Point Estimator
Version: 0.5
Date: 2014-10-06
Author: Royce Carroll , Christopher Hare , Jeffrey B. Lewis , James Lo , Keith T. Poole , and Howard Rosenthal
Maintainer: Christopher Hare
Depends: coda, wnominate, oc, pscl, MCMCpack
Description: Fits ideal point model described in Carroll, Lewis, Lo, Poole and Rosenthal, "The Structure of Utility in Models of Spatial Voting," American Journal of Political Science 57(4): 1008--1028.
License: GPL-2
URL: http://www.voteview.com/alphanominate.asp
Packaged: 2014-10-09 01:51:51 UTC; Christopher
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-09 14:49:04

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Wed, 08 Oct 2014

New package HiDimMaxStable with initial version 0.1
Package: HiDimMaxStable
Version: 0.1
Date: 2014-10-07
Encoding: UTF-8
Title: Inference on High Dimensional Max-Stable Distributions
Authors@R: c(person("Alexis","Bienvenüe",role=c("aut","cre"), email="alexis.bienvenue@univ-lyon1.fr"), person("Christian","Robert",role="aut"))
Depends: R (>= 2.2.0), methods, copula
Imports: mnormt, partitions, maxLik, mnormpow, VGAM
Suggests: rgl, snowfall, MASS, SpatialExtremes
Description: Inference of high dimensional max-stable distributions, from the paper "Likelihood based inference for high-dimensional extreme value distributions", by A. Bienvenüe and C. Robert, arXiv:1403.0065 [stat.AP].
License: GPL (>= 2)
URL: http://arxiv.org/abs/1403.0065
Packaged: 2014-10-08 19:15:57 UTC; alexis
Author: Alexis Bienvenüe [aut, cre], Christian Robert [aut]
Maintainer: Alexis Bienvenüe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-08 21:57:23

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New package bdscale with initial version 1.0
Package: bdscale
Version: 1.0
Date: 2014-10-08
Title: Remove weekends and holidays from ggplot2 axes
Author: Dave Mills
Maintainer: Dave Mills
Depends: R (>= 3.0)
Imports: ggplot2, scales
Suggests: magrittr, dplyr
URL: http://github.com/dvmlls/bdscale
Description: Provides a continuous date scale, omitting weekends and holidays
License: GPL-2
Packaged: 2014-10-08 20:14:28 UTC; David.Mills
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-08 22:27:33

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Tue, 07 Oct 2014

New package saps with initial version 1.0.0
Package: saps
Title: Significance Analysis of Prognostic Signatures
Description: Functions implementing the Significance Analysis of Prognostic Signatures method (SAPS). SAPS provides a robust method for identifying biologically significant gene sets associated with patient survival. Three basic statistics are computed. First, patients are clustered into two survival groups based on differential expression of a candidate gene set. P_pure is calculated as the probability of no survival difference between the two groups. Next, the same procedure is applied to randomly generated gene sets, and P_random is calculated as the proportion achieving a P_pure as significant as the candidate gene set. Finally, a pre-ranked Gene Set Enrichment Analysis (GSEA) is performed by ranking all genes by concordance index, and P_enrich is computed to indicate the degree to which the candidate gene set is enriched for genes with univariate prognostic significance. A SAPS_score is calculated to summarize the three statistics, and optionally a Q-value is computed to estimate the significance of the SAPS_score by calculating SAPS_scores for random gene sets.
Version: 1.0.0
biocViews: BiomedicalInformatics, GeneExpression, GeneSetEnrichment, DifferentialExpression, Survival
Authors@R: c( person("Daniel", "Schmolze", email = "saps@schmolze.com", role = c("aut", "cre")), person("Andrew", "Beck", email = "abeck2@bidmc.harvard.edu", role = "aut"), person("Benjamin", "Haibe-Kains", email = "benjamin.haibe.kains@utoronto.ca", role = "aut"))
Maintainer: Daniel Schmolze
Depends: R (>= 2.14.0), survival
Imports: piano, survcomp, reshape2
Suggests: snowfall, knitr
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Packaged: 2014-10-08 01:32:33 UTC; Daniel
Author: Daniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin Haibe-Kains [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-08 04:52:36

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New package PLordprob with initial version 1.0
Package: PLordprob
Type: Package
Title: Multivariate Ordered Probit Model via Pairwise Likelihood
Version: 1.0
Date: 2014-09-29
Author: Euloge Clovis Kenne Pagui [aut,cre], Antonio Canale [aut], Alan Genz [ctb], Adelchi Azzalini [ctb]
Maintainer: Euloge Clovis Kenne Pagui
Depends: mnormt
Description: Multivariate ordered probit model, i.e. the extension of the scalar ordered probit model where the observed variables have dimension greater than one. Estimation of the parameters is done via maximization of the pairwise likelihood, a special case of the composite likehood obtained as product of bivariate marginal distributions. The package uses the Fortran 77 subroutine SADMVN by Alan Genz, with minor adaptations made by Adelchi Azzalini in his "mvnormt" package for evaluating the two-dimensional Gaussian integrals involved in the pairwise log-likelihood. Optimization of the latter objective function is performed via quasi-Newton box-constrained optimization algorithm, as implemented in nlminb.
License: GPL-2
Packaged: 2014-10-07 14:29:04 UTC; kenne
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-07 18:28:10

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New package MareyMap with initial version 1.2
Package: MareyMap
Title: Estimation of meiotic recombination rates using marey maps.
Version: 1.2
Date: 07/10/2014
Depends: R (>= 2.10)
Imports: tcltk, tkrplot, tools
Suggests: methods
Author: Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Maintainer: Aurelie Siberchicot
License: GPL (>= 2)
Description: A package to graphically estimate local recombination rates across a genome using marey maps.
URL: http://pbil.univ-lyon1.fr/software/mareymap
LazyData: no
Encoding: UTF-8
Packaged: 2014-10-07 09:23:27 UTC; aurelie
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-07 12:04:50

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New package ibelief with initial version 1.0
Package: ibelief
Type: Package
Title: An R Package for Implementing Belief Functions
Version: 1.0
Author: Kuang Zhou ; Arnaud Martin
Maintainer: Kuang Zhou
Description: This package contains several basic functions to implement belief functions.
LazyData: FALSE
Depends: R (>= 3.0.2)
License: GPL (>= 2)
Packaged: 2014-10-07 09:03:25 UTC; zhoukuang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-07 11:20:18

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New package vegan3d with initial version 0.65-0
Package: vegan3d
Title: Static and dynamic 3D plots for vegan package
Version: 0.65-0
Date: 2014-10-06
Authors@R: c(person("Jari", "Oksanen", role=c("aut","cre"), email="jari.oksanen@oulu.fi"), person("Roeland", "Kindt", role="aut"), person(given=c("Gavin", "L."), family="Simpson", role="aut", email="ucfagls@gmail.com"))
Depends: vegan (>= 2.0-10)
Imports: rgl, scatterplot3d
Description: Static and dynamic 3D plots to be used with ordination results and in diversity analysis, especially with the vegan package
License: GPL-2
BugReports: https://github.com/vegandevs/vegan3d/issues
URL: https://github.com/vegandevs/vegan3d
Packaged: 2014-10-07 07:44:05 UTC; jarioksa
Author: Jari Oksanen [aut, cre], Roeland Kindt [aut], Gavin L. Simpson [aut]
Maintainer: Jari Oksanen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-07 10:53:45

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New package TEEReg with initial version 1.0
Package: TEEReg
Type: Package
Title: Trimmed Elemental Estimation for Linear Models
Version: 1.0
Date: 2014-10-06
Author: Wei Jiang and Matthew S. Mayo
Maintainer: Wei Jiang
Description: For fitting multiple linear regressions, the ordinary least squares approach is sensitive to outliers and/or violations of model assumptions. The trimmed elemental estimators are more robust to such situations. This package contains functions for computing the trimmed elemental estimates, as well as for creating the bias-corrected and accelerated bootstrap confidence intervals in the context of trimmed elemental regressions.
License: GPL (>= 2)
Packaged: 2014-10-07 08:07:58 UTC; Will Jiang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-07 10:37:09

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