Sun, 21 Dec 2014

New package convevol with initial version 1.0
Package: convevol
Title: Quantifies and assesses the significance of convergent evolution
Version: 1.0
Authors@R: "C. Tristan Stayton [aut, cre]"
Description: Quantifies and assesses the significance of convergent evolution.
Depends: R (>= 3.1.2), ape, geiger, MASS, phytools
Imports: cluster
License: GPL-2
LazyData: true
Packaged: 2014-12-21 20:18:58 UTC; tstayton
Author: "C. Tristan Stayton" [aut, cre]
Maintainer: "C. Tristan Stayton"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-22 05:00:28

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New package FeatureHashing with initial version 0.7
Package: FeatureHashing
Type: Package
Title: Implement Feature Hashing on Model Matrix
Version: 0.7
Date: 2014-08-01
Authors@R: as.person(c( "Wush Wu [aut, cre]", "Austin Appleby (for the included Murmurhash3 sources) [ctb]"))
Author: Wush Wu [aut, cre], Austin Appleby [ctb] (for the included Murmurhash3 sources)
Maintainer: Wush Wu
Description: Feature hashing, also called as the hashing trick, is a method to transform features to vector. Without looking the indices up in an associative array, it applies a hash function to the features and uses their hash values as indices directly. This package implements the method of feature hashing proposed in Weinberger et. al. (2009) with Murmurhash3 and provides a formula interface in R. See the README.md for more information.
License: GPL (>= 3)
Depends: methods
Imports: Rcpp (>= 0.11), Matrix
LinkingTo: Rcpp
Suggests: pack
SystemRequirements: C++11
BugReports: https://github.com/wush978/FeatureHashing/issues
URL: https://github.com/rstats-db/RSQLite
Packaged: 2014-12-21 16:37:48 UTC; wush
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-21 18:00:50

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New package Rdsdp with initial version 1.0.0
Package: Rdsdp
Version: 1.0.0
Title: R Interface to DSDP Semidefinite Programming Library
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu
Description: R interface to DSDP semidefinite programming library. Installs version 5.8 of DSDP from DSDP website. An existing installation of DSDP may be used by passing the proper configure arguments to the installation command.
LazyLoad: yes
License: GPL-3
URL: www.mcs.anl.gov/hs/software/DSDP
NeedsCompilation: yes
Packaged: 2014-12-18 20:52:32 UTC; zhisu
Repository: CRAN
Date/Publication: 2014-12-21 07:02:03

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New package rDEA with initial version 1.0-2
Package: rDEA
Version: 1.0-2
Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Authors@R: c(person("Jaak", "Simm", role = c("aut", "cre"), email = "jaak.simm@gmail.com"), person("Galina", "Besstremyannaya", role = c("aut") ))
Imports: slam (>= 0.1-9), truncreg(>= 0.2-1), truncnorm(>= 1.0-7), maxLik
Suggests: testthat
SystemRequirements: GLPK (>= 4.52)
License: GPL-2 | GPL-3
URL: https://github.com/jaak-s/rDEA
Packaged: 2014-12-20 23:31:26 UTC; jaak
Author: Jaak Simm [aut, cre], Galina Besstremyannaya [aut]
Maintainer: Jaak Simm
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-21 07:06:51

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New package htmlTable with initial version 1.0
Package: htmlTable
Version: 1.0
Date: 2014-12-19
Title: Advanced Tables for Markdown/HTML
Author: Max Gordon
Maintainer: Max Gordon
Description: A package for creating tables with state of the art layout containing row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout the underlying CSS structure is simple in order to maximize compatibility with MS Word/LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.
License: GPL (>= 3)
URL: http://gforge.se/packages/
BugReports: https://github.com/gforge/htmlTable/issues
Biarch: yes
Imports: stringr, magrittr, Hmisc, methods
Suggests: testthat, XML, knitr, xtable, reshape
Encoding: UTF-8
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2014-12-20 16:22:58 UTC; Max
Repository: CRAN
Date/Publication: 2014-12-21 07:02:08

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New package aplore3 with initial version 0.7
Package: aplore3
Title: Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic Regression" (3rd ed.)
Version: 0.7
Authors@R: "Luca Braglia [aut, cre]"
Description: This package is a unofficial companion to the textbook "Applied Logistic Regression" by D.W. Hosmer, S. Lemeshow and R.X. Sturdivant (3rd ed.). See ?aplore3 for more info.
URL: https://github.com/lbraglia/aplore3
BugReports: https://github.com/lbraglia/aplore3/issues
Depends: R (>= 3.1.1)
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Suggests: knitr, MASS, vcdExtra, nnet, survival, pROC
Packaged: 2014-12-20 22:27:04 UTC; l
Author: "Luca Braglia" [aut, cre]
Maintainer: "Luca Braglia"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-21 07:02:05

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Sat, 20 Dec 2014

New package SCEPtERbinary with initial version 0.1-1
Package: SCEPtERbinary
Title: Stellar CharactEristics Pisa Estimation gRid for Binary Systems
Version: 0.1-1
Date: 2014-04-12
Authors@R: c(person("Matteo", "Dell'Omodarme", role = c("aut", "cre"), email = "mattdell@fastmail.fm"), person("Giada", "Valle", role = "aut"))
Description: SCEPtER pipeline for estimating the stellar age for double-lined detached binary systems. The observational constraints adopted in the recovery are the effective temperature, the metallicity [Fe/H], the mass, and the radius of the two stars. The results are obtained adopting a maximum likelihood technique over a grid of pre-computed stellar models.
Suggests: lattice
Depends: R (>= 2.10), MASS, parallel, SCEPtER
LazyData: no
License: GPL (>= 2)
Maintainer: Matteo Dell'Omodarme
Packaged: 2014-12-20 14:36:03 UTC; matt
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-20 17:38:25

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New package NORTARA with initial version 1.0.0
Package: NORTARA
Title: Generation of Multivariate Data with Arbitrary Marginals
Version: 1.0.0
Authors@R: person("Po", "Su", email = "desolator@sjtu.edu.cn", role = c("aut", "cre"))
Description: An implementation of a specific method for generating n-dimensional random vectors with given marginal distributions and correlation matrix. The method uses the NORTA (NORmal To Anything) approach which generates a standard normal random vector and then transforms it into a random vector with specified marginal distributions and the RA (Retrospective Approximation) algorithm which is a generic stochastic root-finding algorithm. The marginals can be continuous or discrete. See the vignette of package for more details.
URL: https://github.com/superdesolator/NORTARA
BugReports: https://github.com/superdesolator/NORTARA/issues
Depends: R (>= 3.1.2)
License: MIT + file LICENSE
LazyData: true
Imports: corpcor(>= 1.6.7), Matrix(>= 1.1-4)
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-20 14:29:55 UTC; Administrator
Author: Po Su [aut, cre]
Maintainer: Po Su
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-20 15:46:33

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New package orgR with initial version 0.9.0
Package: orgR
Type: Package
Title: Analyse Text Files Created by Emacs' Org mode
Version: 0.9.0
Date: 2014-12-15
Author: Yi Tang
Maintainer: Yi Tang
Description: Provides functionality to process text files created by Emacs' Org mode, and decompose the content to the smallest components (headlines, body, tag, clock entries etc). Emacs is an extensible, customizable text editor and Org mode is for keeping notes, maintaining TODO lists, planning projects. Allows users to analyze org files as data frames in R, e.g., to convieniently group tasks by tag into project and calculate total working hours. Also provides some help functions like search.parent, gg.pie (visualise working hours in ggplot2) and tree.headlines (visualise headline stricture in tree format) to help user managing their complex org files.
License: GPL (>= 2)
Depends: ggthemes (>= 1.7.0), ggplot2 (>= 1.0.0), lubridate(>= 1.3.3), data.table (>= 1.9.4), stringr (>= 0.6.2)
Packaged: 2014-12-19 15:02:11.908 UTC; yitang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-20 07:48:40

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Fri, 19 Dec 2014

New package biogram with initial version 1.0
Package: biogram
Type: Package
Title: N-Gram Analysis of Biological Sequences
Version: 1.0
LazyData: true
Date: 2014-12-19
Authors@R: c( person("Michal", "Burdukiewicz", email = "michalburdukiewicz@gmail.com", role = c("cre", "aut")), person("Piotr", "Sobczyk", role = "aut"), person("Chris", "Lauber", role = "aut"))
Description: Tools for extraction and analysis of various n-grams (sequences of n items) derived from biological sequences (proteins or nucleic acids). To deal with the dimensionality of the n-gram data, biogram uses QuiPT (quick permutation test) for fast feature-filtering.
License: GPL-3
URL: https://github.com/michbur/biogram
Depends: R (>= 3.0.0), slam
Imports: bit
Suggests: testthat
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-12-19 11:17:38 UTC; michal
Author: Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Chris Lauber [aut]
Maintainer: Michal Burdukiewicz
Date/Publication: 2014-12-19 15:58:01

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New package nlsem with initial version 0.1
Package: nlsem
Version: 0.1
Date: 2014-12-19
Title: Fitting Structural Equation Mixture Models
Authors@R: c(person("Nora", "Umbach", role = c("aut", "cre"), email = "nora.umbach@web.de"), person("Katharina", "Naumann", role = "aut"), person("David", "Hoppe", role = "aut"), person("Holger", "Brandt", role = "aut"), person("Augustin", "Kelava", role="ctb"), person("Bernhard", "Schmitz", role="ctb"))
Depends: R (>= 3.1.0), gaussquad, mvtnorm, nlme
Description: Estimation of structural equation models with nonlinear effects and underlying nonnormal distributions.
License: GPL (>= 2)
Packaged: 2014-12-19 09:42:10 UTC; noraumbach
Author: Nora Umbach [aut, cre], Katharina Naumann [aut], David Hoppe [aut], Holger Brandt [aut], Augustin Kelava [ctb], Bernhard Schmitz [ctb]
Maintainer: Nora Umbach
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-19 12:07:02

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Thu, 18 Dec 2014

New package srd with initial version 1.0
Package: srd
Type: Package
Title: Draws Scaled Rectangle Diagrams
Version: 1.0
Date: 2014-07-15
Author: Roger Marshall
Maintainer: Roger Marshall
Description: Draws scaled rectangle diagrams to represent a 2^k contingency table, for k<=6
License: GPL-2
Imports: plyr,animation,colorspace,stringr,survival
Packaged: 2014-12-18 22:35:36 UTC; rmar073
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-19 01:58:45

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New package spanr with initial version 1.0
Package: spanr
Type: Package
Title: Search Partition Analysis
Version: 1.0
Date: 2014-07-15
Author: Roger Marshall
Maintainer: Roger Marshall
Description: Carries out a search for an optimal partition in terms of a regular Boolean expression
License: GPL-2
Imports: plyr, stringr, survival
Packaged: 2014-12-18 22:25:39 UTC; rmar073
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-19 01:49:50

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New package GPC with initial version 0.1
Package: GPC
Type: Package
Title: Generalized Polynomial Chaos
Version: 0.1
Depends: R (>= 2.7.0), randtoolbox, orthopolynom, ks, lars
Date: 2013-02-01
Author: Miguel Munoz Zuniga and Jordan Ko
Maintainer: Miguel Munoz Zuniga
Description: A generalized polynomial chaos expansion of a model taking as input independent random variables is achieved. A statistical and a global sensitivity analysis of the model are also carried out.
License: GPL-3
Packaged: 2014-12-18 17:17:50 UTC; munozzum
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 21:08:58

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New package selfingTree with initial version 0.2
Package: selfingTree
Type: Package
Title: Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing
Version: 0.2
License: BSD_3_clause + file LICENSE
Copyright: (c) 2014, Pioneer Hi-Bred International, Inc.
Date: 2014-12-18
Authors@R: person(given = "Frank",family = "Technow", email = "Frank.Technow@pioneer.com", comment = "Pioneer Hi-Bred International, Inc., Johnston, Iowa", role = c("aut","cre"))
Author: Frank Technow [aut, cre] (Pioneer Hi-Bred International, Inc., Johnston, Iowa)
LazyData: TRUE
Maintainer: Frank Technow
Depends: R (>= 2.15.1),foreach
Description: A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.
Packaged: 2014-12-18 15:43:52 UTC; frank
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 17:31:18

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New package RoughSetKnowledgeReduction with initial version 0.1
Package: RoughSetKnowledgeReduction
Type: Package
Title: Simplification of Decision Tables using Rough Sets
Version: 0.1
Date: 2012-03-13
Author: Alber Sanchez
Maintainer: Alber Sanchez
Description: Rough Sets were introduced by Zdzislaw Pawlak on his book "Rough Sets: Theoretical Aspects of Reasoning About Data". Rough Sets provide a formal method to approximate crisp sets when the set-element belonging relationship is either known or undetermined. This enables the use of Rough Sets for reasoning about incomplete or contradictory knowledge. A decision table is a prescription of the decisions to make given some conditions. Such decision tables can be reduced without losing prescription ability. This package provides the classes and methods for knowledge reduction from decision tables as presented in the chapter 7 of the aforementioned book. This package provides functions for calculating the both the discernibility matrix and the essential parts of decision tables.
License: MIT + file LICENSE
Depends: methods
Collate: DecisionTable.R ConditionReduct.R DiscernibilityMatrix.R ValueReduct.R
Packaged: 2014-12-07 14:02:21 UTC; alber
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 09:11:32

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New package multiband with initial version 0.1.0
Package: multiband
Title: Period Estimation for Multiple Bands
Description: Algorithms for performing joint parameter estimation in astronomical survey data acquired in multiple bands.
Version: 0.1.0
Maintainer: Eric C. Chi
Author: Eric C. Chi, James P. Long
Depends: R (>= 3.0.2)
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-12-18 05:28:46 UTC; ericchi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 07:12:06

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Wed, 17 Dec 2014

New package RcmdrPlugin.RMTCJags with initial version 1.0
Package: RcmdrPlugin.RMTCJags
Type: Package
Title: R MTC Jags Rcmdr Plugin
Version: 1.0
Date: 2014-12-16
Author: Marcelo Goulart Correia
Maintainer: Marcelo Goulart Correia
Depends: R (>= 3.0.0)
Imports: Rcmdr, runjags, rmeta, igraph, coda, rjags
SystemRequirements: jags (>= 3.0.0)
Description: This package provides an Rcmdr "plug-in" for perform Mixed Treatment Comparison for binary outcome using BUGS code from Bristol University (Lu and Ades)
License: GPL (>= 2)
Packaged: 2014-12-05 16:45:08 UTC; instituto
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 23:13:09

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New package MenuCollection with initial version 1.0
Package: MenuCollection
Type: Package
Title: Collection of Configurable GTK+ Menus
Version: 1.0
Date: 2014-07-19
Author: Gianmarco Polotti
Maintainer: Gianmarco Polotti
Description: Set of configurable menus built with GTK+ to graphically interface new functions.
Depends: R (>= 3.0.0), RGtk2, RGtk2Extras
Imports: gplots, grDevices, graphics
Suggests:
License: GPL-2
Packaged: 2014-12-17 20:46:32 UTC; PolGia0
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 23:13:05

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New package GPareto with initial version 1.0.0
Package: GPareto
Type: Package
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Version: 1.0.0
Date: 2014-12-17
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois
Description: Gaussian process regression models, a.k.a. kriging models, are applied to global multiobjective optimization of black-box functions. Multiobjective Expected Improvement and Stepwise Uncertainty Reduction sequential infill criteria are available. A quantification of uncertainty on Pareto fronts is provided using conditional simulations.
License: GPL-3
Depends: DiceKriging (>= 1.5.3), emoa, methods
Imports: Rcpp (>= 0.11.1), rgenoud, pbivnorm, pso, randtoolbox, KrigInv, MASS
Suggests: DiceDesign (>= 1.4)
LinkingTo: Rcpp
Packaged: 2014-12-17 09:42:42 UTC; a073501
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 13:08:28

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New package stpp with initial version 1.0-5
Package: stpp
Type: Package
Title: Space-Time Point Pattern simulation, visualisation and analysis
Version: 1.0-5
Date: 2014-12-11
Author: Edith Gabriel, Peter J Diggle, stan function by Barry Rowlingson
Maintainer: Edith Gabriel
Depends: R (>= 2.10), splancs, KernSmooth, spatstat
Suggests: rpanel, rgl
Description: A package for analysing, simulating and displaying space-time point patterns
License: GPL-3
LazyLoad: yes
Packaged: 2014-12-16 13:46:14 UTC; math
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 09:25:40

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Tue, 16 Dec 2014

New package RSNPset with initial version 0.3
Package: RSNPset
Type: Package
Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Version: 0.3
Date: 2014-12-16
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
Description: RSNPset is an implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. The package provides three standard score statistics (Cox, Binomial, and Gaussian) but is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.
License: GPL-3
Imports: fastmatch (>= 1.0-4), foreach (>= 1.4.1), doRNG (>= 1.5.3), qvalue (>= 1.34), Rcpp (>= 0.10.4)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-16 19:06:52 UTC; abs33
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 01:59:36

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New package refset with initial version 0.1.0
Package: refset
Type: Package
Title: Subsets with Reference Semantics
Version: 0.1.0
Date: 2014-11-20
Author: David Hugh-Jones
Maintainer: David Hugh-Jones
Description: Provides subsets with reference semantics, i.e. subsets which automatically reflect changes in the original object, and which optionally update the original object when they are changed.
License: GPL-2
NeedsCompilation: no
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat
Packaged: 2014-12-16 21:42:46 UTC; david
Repository: CRAN
Date/Publication: 2014-12-17 01:57:34

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New package FPDclustering with initial version 1.0
Package: FPDclustering
Type: Package
Title: PD-Clustering and Factor PD-Clustering
Version: 1.0
Date: 2014-12-16
Author: Cristina Tortora and Paul D. McNicholas
Maintainer: Cristina Tortora
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. Facto PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It allows clustering of high dimensional data sets.
Depends: ThreeWay
License: GPL (>= 2)
Packaged: 2014-12-16 18:46:17 UTC; ctortora
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 01:54:43

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New package rSPACE with initial version 1.0
Package: rSPACE
Type: Package
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Version: 1.0
Date: 2014-12-15
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
License: GPL (>= 2)
Imports: raster, RMark, ggplot2, tcltk2, sp, grid, plyr, tcltk
Packaged: 2014-12-16 18:20:03 UTC; marthamellis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-16 22:38:08

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New package PRROC with initial version 1.0
Package: PRROC
Type: Package
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Version: 1.0
Date: 2014-12-16
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
License: GPL-3
Packaged: 2014-12-16 21:03:40 UTC; dev
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 22:34:59

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New package NeuralNetTools with initial version 1.0.0
Package: NeuralNetTools
Type: Package
Title: Visualization and Analysis Tools for Neural Networks
Version: 1.0.0
Date: 2014-12-10
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
BugReports: https://github.com/fawda123/NeuralNetTools/issues
License: CC0
LazyData: true
Imports: ggplot2, neuralnet, nnet, reshape2, RSNNS, scales
Depends: R (>= 3.1.1)
Authors@R: person(given = "Marcus W.", family = "Beck", role = c("aut","cre"), email = "mbafs2012@gmail.com")
Packaged: 2014-12-16 16:06:56 UTC; Marcus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 17:43:30

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New package spca with initial version 0.6.0
Package: spca
Type: Package
Title: Sparse Principal Component Analysis
Version: 0.6.0
Date: 2014-12-14
Author: Giovanni Maria Merola
Maintainer: Giovanni Merola
URL: http://github.com/merolagio/spca
BugReports: http://github.com/merolagio/spca/issues
Description: Computes Least Squares Sparse Principal Components either by a Branch-and-Bound search or with an iterative Backward Elimination algorithm. Sparse solutions can be plotted, printed and compared using the methods included.
Depends: R (>= 3.1)
VignetteBuilder: knitr
Suggests: formatR, knitr (>= 1.8.0), ggplot2, reshape2
Imports: MASS
License: GPL-3
LazyData: true
Packaged: 2014-12-16 11:39:18 UTC; Glovani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 13:19:52

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New package WaveletComp with initial version 1.0
Package: WaveletComp
Type: Package
Title: Computational Wavelet Analysis
Version: 1.0
Date: 2014-12-15
Author: Angi Roesch and Harald Schmidbauer
Maintainer: Angi Roesch
Description: Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.
Depends: R (>= 2.10)
License: GPL-2
URL: http://www.hs-stat.com/projects/WaveletComp/WaveletComp_guided_tour.pdf
Packaged: 2014-12-16 07:19:23 UTC; angi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 09:26:23

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New package networkD3 with initial version 0.1.1
Package: networkD3
Type: Package
Title: Tools for Creating D3 JavaScript Network Graphs from R
Description: Creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
Version: 0.1.1
Date: 2014-12-16
Author: Christopher Gandrud, J.J. Allaire, and B.W. Lewis
Maintainer: Christopher Gandrud
URL: http://github.com/christophergandrud/networkD3/
License: GPL (>= 3)
Depends: R (>= 3.0.0)
Imports: htmlwidgets (>= 0.3.2), plyr, rjson
Suggests: htmltools (>= 0.2.6), RCurl
Enhances: knitr, shiny
Packaged: 2014-12-16 06:52:00 UTC; christophergandrud
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:22:39

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New package BinNonNor with initial version 1.0
Package: BinNonNor
Type: Package
Title: Data Generation with Binary and Continuous Non-normal Components
Version: 1.0
Date: 2014-12-15
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
Description: Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012).
License: GPL (>= 2)
Depends: BB, corpcor, mvtnorm, Matrix
Packaged: 2014-12-15 19:20:02 UTC; arcelik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:17:47

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Mon, 15 Dec 2014

New package RcppDL with initial version 0.0.3
Package: RcppDL
Type: Package
Title: Deep Learning Methods via Rcpp
Version: 0.0.3
Date: 2014-12-12
Author: Qiang Kou, Yusuke Sugomori
Maintainer: Qiang Kou
Description: This package is based on the C++ code from Yusuke Sugomori, which implements basic machine learning methods with many layers (deep learning), including dA (Denoising Autoencoder), SdA (Stacked Denoising Autoencoder), RBM (Restricted Boltzmann machine) and DBN (Deep Belief Nets).
License: GPL-3
Imports: methods, Rcpp (>= 0.11.2)
LinkingTo: Rcpp
URL: https://github.com/thirdwing/RcppDL
BugReports: https://github.com/thirdwing/RcppDL/issues
Packaged: 2014-12-15 20:35:49 UTC; qkou
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-16 01:02:30

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New package leaderCluster with initial version 1.2
Package: leaderCluster
Type: Package
Title: Leader Clustering Algorithm
Version: 1.2
Date: 2014-12-11
Author: Taylor B. Arnold
Maintainer: Taylor B. Arnold
Description: The leader clustering algorithm provides a means for clustering a set of data points. Unlike many other clustering algorithms it does not require the user to specify the number of clusters, but instead requires the approximate radius of a cluster as its primary tuning parameter. The package provides a fast implementation of this algorithm in n-dimensions using Lp-distances (with special cases for p=1,2, and infinity) as well as for spatial data using the Haversine formula, which takes latitude/longitude pairs as inputs and clusters based on great circle distances.
License: LGPL-2
Packaged: 2014-12-15 15:30:02 UTC; taylor
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-16 00:58:11

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New package ztable with initial version 0.1.0
Package: ztable
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Version: 0.1.0
Authors@R: "Keon-Woong Moon [aut, cre]"
Description: Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm or coxph objects.
Depends: R (>= 3.1.2)
License: GPL-2
LazyData: true
Suggests: MASS, survival, testthat, knitr
VignetteBuilder: knitr
Packaged: 2014-12-15 16:29:35 UTC; cardiomoon
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-15 20:04:46

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Sat, 13 Dec 2014

New package qqtest with initial version 1.0
Package: qqtest
Type: Package
Title: Quantile Quantile Plots Self Calibrating For Visual Testing
Version: 1.0
Date: 2014-12-02
Authors@R: person("Wayne", "Oldford", email="rwoldford@uwaterloo.ca", role=c("aut", "cre"))
Maintainer: Wayne Oldford
Description: Provides the function qqtest which incorporates uncertainty in its qqplot display(s) so that the user might have a better sense of the evidence against the specified distributional hypothesis. qqtest draws a quantile quantile plot for visually assessing whether the data come from a test distribution that has been defined in one of many ways. The vertical axis plots the data quantiles, the horizontal those of a test distribution. The default behaviour generates 1000 samples from the test distribution and overlays the plot with pointwise interval estimates for the ordered quantiles from the test distribution. A small number of independently generated exemplar quantile plots are also overlaid. Both the interval estimates and the exemplars provide different comparative information to assess the evidence provided by the qqplot for or against the hypothesis that the data come from the test distribution (default is normal or gaussian). Finally, a visual test of significance (a lineup plot) can also be displayed to test the null hypothesis that the data come from the test distribution.
License: GPL-3
Depends: R (>= 2.10.0)
Imports: grDevices, MASS
Packaged: 2014-12-13 19:36:06 UTC; rwoldford
Author: Wayne Oldford [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-14 01:15:35

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New package rodd with initial version 0.1-1
Package: rodd
Type: Package
Title: Optimal Discriminating Designs
Version: 0.1-1
Date: 2014-10-28
Authors@R: c(person("Roman", "Guchenko", role = c("aut", "cre"), email = "RomanGuchenko@yandex.ru"))
Depends: R (>= 3.0.0)
Imports: numDeriv, quadprog, Matrix, rootSolve, matrixcalc
Suggests: mvtnorm
Description: A collection of functions for numerical construction of optimal discriminating designs. At the current moment T-optimal designs (which maximize the lower bound for the power of F-test for regression model discrimination) and their robust analogues can be calculated with the package.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2014-12-13 19:04:46 UTC; Roman
Author: Roman Guchenko [aut, cre]
Maintainer: Roman Guchenko
Repository: CRAN
Date/Publication: 2014-12-14 01:05:16

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New package mixor with initial version 1.0.1
Package: mixor
Type: Package
Title: Mixed-Effects Ordinal Regression Analysis
Version: 1.0.1
Date: 2014-12-12
Author: Donald Hedeker , Kellie J. Archer, Rachel Nordgren, Robert D. Gibbons
Maintainer: Kellie J. Archer
Description: Provides the function 'mixord' for fitting a mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and variance-covariance matrix, and estimating contrasts for the fitted models.
License: GPL (>= 2)
Depends: R (>= 2.10)
Suggests: survival
BuildResaveData: best
Biarch: yes
NeedsCompilation: yes
LazyLoad: true
Packaged: 2014-11-12 00:26:45 UTC; kjarcher
Repository: CRAN
Date/Publication: 2014-12-13 08:02:46

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New package gemmR with initial version 1.3-2
Package: gemmR
Type: Package
Title: General Monotone Model
Version: 1.3-2
Date: 2014-09-08
Authors@R: c(person("Jeffrey", "Chrabaszcz", role = c("aut", "cre"), email = "jchrabaszcz@gmail.com"), person("Joe", "Tidwell", role = "aut"), person("Michael", "Dougherty", role = c("aut")))
LazyData: yes
Description: An R-language implementation of the General Monotone Model proposed by Michael Dougherty and Rick Thomas. It is a procedure for estimating weights for a set of independent predictors that minimize the rank-order inversions between the model predictions and some outcome.
License: GPL-3
Depends: Rcpp(>= 0.11), doMC(>= 1.3.1), foreach (>= 1.4.2)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
BugReports: https://github.com/jchrszcz/gemmR/issues
Collate: 'gemmquick.R' 'RcppExports.R'
Packaged: 2014-12-12 22:13:31 UTC; jchrszcz
Author: Jeffrey Chrabaszcz [aut, cre], Joe Tidwell [aut], Michael Dougherty [aut]
Maintainer: Jeffrey Chrabaszcz
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-13 08:02:40

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Fri, 12 Dec 2014

New package gimme with initial version 0.1
Package: gimme
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and individual-level relations in time series data from within a structural equation modeling framework.
Version: 0.1
Author: Stephanie Lane
Maintainer: Stephanie Lane
Depends: R (>= 3.0.2), lavaan (>= 0.5-17), qgraph
License: GPL-2
LazyData: yes
Packaged: 2014-12-12 15:35:00 UTC; stlane
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-12 20:34:47

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New package tcR with initial version 1.0
Package: tcR
Type: Package
Title: Data Analysis of T-cell Receptor Repertoires
Version: 1.0
Date: 2014-12-12
Author: Vadim Nazarov, Mikhail Pogorelyy
Maintainer: Vadim Nazarov
Description: Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
License: Apache License 2.0
Depends: R (>= 2.10), ggplot2 (>= 1.0.0), dplyr (>= 0.2), gridExtra (>= 0.9.0), reshape2 (>= 1.2.0)
Imports: utils (>= 3.1.0), Rcpp (>= 0.11.1), grid (>= 3.0.0), data.table (>= 1.9.0), gtable (>= 0.1.2), roxygen2 (>= 3.0.0), stringdist (>= 0.7.3)
LinkingTo: Rcpp
Packaged: 2014-12-12 11:34:00 UTC; n-san
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-12 14:50:19

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New package InvariantCausalPrediction with initial version 0.1-4
Package: InvariantCausalPrediction
Type: Package
Title: Invariant Causal Prediction
Version: 0.1-4
Date: 2014-12-10
Author: Nicolai Meinshausen
Depends: glmnet, mboost
Maintainer: Nicolai Meinshausen
Description: Confidence intervals for causal prediction in a regression setting. An experimental version is also available for classification.
License: GPL
Packaged: 2014-12-12 10:22:33 UTC; nicolai
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-12 14:44:35

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New package ibmdbR with initial version 1.34.3
Package: ibmdbR
Version: 1.34.3
Title: IBM In-Database Analytics for R
Author: IBM Corporation
Maintainer: Michael Wurst
Depends: R (>= 2.15.1), methods, RODBC, MASS
Description: Functionality required to efficiently use R with IBM DB2(c) for Linux, Unix and Windows as well as IBM dashDB(c). Many basic and complex R operations are pushed down into the database, which removes the main memory boundary of R and allows to take advantage of parallel processing in the underlying database.
License: GPL-3
LazyLoad: Yes
Packaged: 2014-12-12 13:10:02 UTC; mwurst
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-12 14:54:03

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New package subrank with initial version 0.9.1
Package: subrank
Type: Package
Title: Computes copula using ranks and subsampling
Version: 0.9.1
Date: 2014-12-12
Author: Jerome Collet
Maintainer: Jerome Collet
Description: essentially a discussion tool about estimation of copula using ranks and subsampling.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2014-12-11 20:15:24 UTC; collet
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-12 11:11:34

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Thu, 11 Dec 2014

New package RecordLinkage with initial version 0.4-6
Package: RecordLinkage
Version: 0.4-6
Title: Record Linkage in R
Author: Andreas Borg , Murat Sariyar
Maintainer: Andreas Borg
Contact: reclinkmainz@googlemail.com
Description: Provides functions for linking and de-duplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain.
License: GPL (>= 2)
Depends: R (>= 2.10.0), DBI, RSQLite(>= 0.9-1), ff, ffbase
Imports: e1071, rpart, ada, ipred, stats, evd, methods, data.table (>= 1.7.8), nnet, xtable
Suggests: RUnit
LinkingTo: RSQLite
URL: https://r-forge.r-project.org/projects/recordlinkage/, http://journal.r-project.org/archive/2010-2/RJournal_2010-2_Sariyar+Borg.pdf
Collate: register-S3-classes.r RLBigData-classes.r RLResult-class.r accessor-methods.r evt.r classify.r classifySupv-methods.r genSamples.r strcmp.r compare.r getPairs.r summary.r em-methods.r internals.r em.r mygllm.r epilink-methods.r phonetics.r onAttach.r getPairs-methods.r serialization.r tools.r stochastic.r
Packaged: 2014-12-11 09:26:14 UTC; rforge
Repository: CRAN
Repository/R-Forge/Project: recordlinkage
Repository/R-Forge/Revision: 437
Repository/R-Forge/DateTimeStamp: 2014-12-11 09:20:46
Date/Publication: 2014-12-11 19:37:43
NeedsCompilation: yes

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New package EffectTreat with initial version 0.1-1
Package: EffectTreat
Type: Package
Title: Prediction of Therapeutic Success
Version: 0.1-1
Date: 2014-12-11
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association(i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics.
Depends:
License: GPL (>= 2)
BugReports: Wim Van der Elst
Repository: CRAN
Packaged: 2014-12-11 15:59:18 UTC; wimvde
NeedsCompilation: no
Date/Publication: 2014-12-11 19:32:48

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New package clusterCrit with initial version 1.2.4
Package: clusterCrit
Type: Package
Title: Clustering Indices
Version: 1.2.4
Date: 2014-12-11
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes
Description: compute clustering validation indices
License: GPL (>= 2)
URL: http:www.r-project.org
Collate: main.R zzz.R
Encoding: latin1
Suggests: RUnit, rbenchmark
Packaged: 2014-12-11 10:15:06 UTC; bernardo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-11 13:20:18

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New package medflex with initial version 0.4.0
Package: medflex
Title: Flexible Mediation Analysis using Natural Effect Models
Version: 0.4.0
Date: 2014-12-10
Authors@R: c( person("Johan", "Steen", email = "johan.steen@gmail.com", role = c("aut", "cre")), person("Tom", "Loeys", email = "tom.loeys@ugent.be", role = "aut"), person("Beatrijs", "Moerkerke", email = "beatrijs.moerkerke@ugent.be", role = "aut"), person("Stijn", "Vansteelandt", email = "stijn.vansteelandt@ugent.be", role = "aut"), person("Joris", "Meys", email = "joris.meys@ugent.be", comment = "technical support", role = "ctb"), person("Theis", "Lange", email = "thlan@sund.ku.dk", comment = "valuable suggestions", role = "ctb"))
Description: medflex allows to run flexible mediation analyses using natural effect models as described in Lange, Vansteelandt and Bekaert (2012), Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013).
Depends: R (>= 3.1.2), multcomp (>= 1.3-6)
License: GPL-2
LazyData: true
Imports: boot (>= 1.3-8)
Suggests: arm (>= 1.7-05), car (>= 2.0-21), gam (>= 1.09.1), glmnet (>= 1.9-8), Matrix (>= 1.1-4), rpart (>= 4.1-8), SuperLearner (>= 2.0-15), VGAM (>= 0.9-5)
Packaged: 2014-12-10 23:05:29 UTC; johansteen
Author: Johan Steen [aut, cre], Tom Loeys [aut], Beatrijs Moerkerke [aut], Stijn Vansteelandt [aut], Joris Meys [ctb] (technical support), Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-11 08:02:18

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Wed, 10 Dec 2014

New package filenamer with initial version 0.2
Package: filenamer
Type: Package
Title: Easy Management of File Names
Version: 0.2
Date: 2014-12-07
Author: David J. H. Shih
Maintainer: David J. H. Shih
Description: Create descriptive file names with ease. New file names are automatically (but optionally) time stamped and placed in date stamped directories. Streamline your analysis pipeline with input and output file names that have informative tags and proper file extensions.
URL: https://bitbucket.org/djhshih/filenamer
BugReports: https://bitbucket.org/djhshih/filenamer/issues
License: GPL (>= 3)
Suggests: io, testthat
Packaged: 2014-12-10 19:34:46 UTC; davids
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-10 23:15:50

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New package spiders with initial version 1.0
Package: spiders
Type: Package
Title: Fits predator preferences model
Version: 1.0
Date: 2014-12-04
Author: Edward A. Roualdes and Simon Bonner
Maintainer: Edward A. Roualdes
Description: Fits and simulates data from our predator preferences model
Depends: R (>= 3.0.2)
Imports: plyr
Suggests: testthat
License: GPL (>= 2.0)
Packaged: 2014-12-10 16:37:08 UTC; easy-e
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-10 21:15:29

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New package snplist with initial version 0.13
Package: snplist
Type: Package
Title: Tools to create Gene Sets
Version: 0.13
Date: 2014-12-03
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
License: GPL-3
Depends: R (>= 3.0.0), RSQLite (>= 0.11.4)
Imports: biomaRt (>= 2.16.0), Rcpp (>= 0.10.5), R.utils (>= 1.27.1), DBI (>= 0.3.1)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
Packaged: 2014-12-04 17:24:15 UTC; abs33
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-10 21:14:31

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New package jomo with initial version 0.1-0
Package: jomo
Type: Package
Title: A package for Multilevel Joint Modelling Multiple Imputation
Version: 0.1-0
Date: 2014-10-24
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno
Description: Building on Schafer's pan and on standalone program REALCOM, jomo is a package for multilevel joint modelling multiple imputation. Binary and categorical variables are handled through latent normal variables and algorithms for cluster specific covariance matrices are introduced.
License: GPL-2
Suggests: BaBooN
Packaged: 2014-12-10 16:21:43 UTC; lsh366965
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-10 17:36:11

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New package bnormnlr with initial version 1.0
Package: bnormnlr
Type: Package
Title: Bayesian Estimation for Normal Heteroscedastic Nonlinear Regression Models
Version: 1.0
Date: 2014-12-08
Author: Nicolas Molano-Gonzalez, Marta Corrales Bossio, Maria Fernanda Zarate, Edilberto Cepeda-Cuervo.
Maintainer: Nicolas Molano-Gonzalez
Description: Implementation of Bayesian estimation in normal heteroscedastic nonlinear regression Models following Cepeda-Cuervo, (2001).
License: GPL-2
Depends: mvtnorm, numDeriv
Suggests: car, coda, MASS
Packaged: 2014-12-10 14:05:43 UTC; A80873475
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-10 16:26:13

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New package sprm with initial version 1.1
Package: sprm
Type: Package
Title: Sparse and Non-Sparse Partial Robust M Regression
Version: 1.1
Date: 2014-12-10
Author: Sven Serneels, BASF Corp and Irene Hoffmann
Maintainer: Irene Hoffmann
Description: Robust methods for dimension reduction and regression analysis are implemented that yield estimates with a partial least squares alike interpretability. Partial robust M regression is robust to both vertical outliers and leverage points. Sparse partial robust M regression is a related robust method with sparse coefficient estimate, and therefore with intrinsic variable selection.
License: GPL (>= 3)
Depends: ggplot2, grid
Imports: cvTools, reshape2, pcaPP
Packaged: 2014-12-10 11:00:00 UTC; hoffmann
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-10 14:41:27

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New package OneArmPhaseTwoStudy with initial version 0.1
Package: OneArmPhaseTwoStudy
Type: Package
Title: Planing, Monitoring and Evaluating Oncological Phase 2 Studies
Version: 0.1
Date: 2014-08-05
Author: Marius Wirths
Maintainer: Marius Wirths
Description: Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate "Simon's two-stage designs" and so called "subset designs". If you are unfamiliar with this package a good starting point is to take a closer look at the functions "getSolutions" and "getSolutionsSub1".
License: GPL (>= 2)
Depends: methods, Rcpp (>= 0.9.11)
LinkingTo: Rcpp
RcppModules: simon, sub1
Packaged: 2014-12-10 09:56:19 UTC; wirthsmarius
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-10 13:41:13

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Tue, 09 Dec 2014

New package timma with initial version 0.99.0
Package: timma
Type: Package
Title: Target Inhibition Interaction using Maximization and Minimization Averaging
Version: 0.99.0
Date: 2014-09-08
Author: Liye
Maintainer: Liye He
Description: Target Inhibition Interaction using Maximization/Minimization Averaging
License: Artistic License 2.0
Imports: Rcpp (>= 0.11.2), QCA (>= 1.1-3)
LinkingTo: Rcpp, RcppArmadillo
biocViews: Software, StatisticalMethod
Packaged: 2014-12-09 19:27:51 UTC; localadmin_lzhe
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-09 22:34:23

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New package smnet with initial version 1.0
Package: smnet
Type: Package
Title: Smoothing For Stream Network Data
Version: 1.0
Date: 2014-12-09
Depends: SSN, spam
Imports: splines, dfoptim, RSQLite, igraph, DBI
Author: Alastair Rushworth
Maintainer: Alastair Rushworth
Description: Fits flexible additive models to data on stream networks, taking account of flow-connectivity of the network. Models are fit using penalised least squares.
License: GPL-2
LazyLoad: yes
Packaged: 2014-12-09 15:36:43 UTC; alastair
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-09 17:51:37

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New package MRSP with initial version 0.4.3
Package: MRSP
Type: Package
Title: Multinomial Response Models with Structured Penalties
Version: 0.4.3
Date: 2014-12-09
Author: Wolfgang Poessnecker
Maintainer: Wolfgang Poessnecker
Description: Fits regularized multinomial response models using penalized loglikelihood methods with structured penalty terms.
License: GPL (>= 2)
Depends: methods, parallel, compiler, matrixcalc, Formula, R (>= 2.14.1)
Imports: base
LazyData: yes
NeedsCompilation: yes
Repository: CRAN
Collate: MRSP-prespecifier.r MRSP-classes-7.r FISTA-classes-3.r FISTA-generics-2.r FISTA-27.r MRSP-methods-15.r MRSP-cfunctions-2.r MRSP-helpers-21.r MRSP-fista-7.r MRSP-family-23.r MRSP-fit-39.r MRSP-formula-2.r MRSP-3.r zzz.r
Packaged: 2014-12-09 14:08:16 UTC; poessnecker
Date/Publication: 2014-12-09 16:11:35

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New package iFes with initial version 1.0
Package: iFes
Type: Package
Title: Incremental Feature Selection Algorithm accelerated by GPU
Version: 1.0
Date: 2014-12-05
Depends: R (>= 2.10), ROCR, parallel, doParallel, foreach
SystemRequirements: Nvidia's CUDA toolkit (>= release 5.5)
Author: Qinghan Meng, Fengfeng Zhou
Maintainer: Qinghan Meng
Description: Incremental gene selection algorithm(iFes) expands the screening targets in each step of the forward stepwise algorithm, and proposes a novel feature selection algorithm iFes with both high accuracies and low feature numbers. Logistic regression classification algorithm accelerated by NVIDIA GPU is utilized to measure how good the currently chosen feature subset is.
License: GPL-2
Packaged: 2014-12-09 13:45:29 UTC; qhmeng
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-09 18:02:13

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New package htmlwidgets with initial version 0.3.2
Package: htmlwidgets
Type: Package
Title: HTML Widgets for R
Version: 0.3.2
Date: 2014-12-03
Author: Ramnath Vaidyanathan, Joe Cheng, JJ Allaire, Yihui Xie, and Kenton Russell
Maintainer: JJ Allaire
Description: A framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.
License: MIT + file LICENSE
VignetteBuilder: knitr
Imports: htmltools (>= 0.2.6), RJSONIO, yaml
Suggests: knitr (>= 1.8)
Enhances: shiny (>= 0.10.2.1),
Packaged: 2014-12-09 12:55:41 UTC; jjallaire
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-09 14:54:14

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New package urltools with initial version 0.5
Package: urltools
Type: Package
Title: Vectorised Tools for URL Handling and Parsing
Version: 0.5
Date: 2014-12-07
Author: Oliver Keyes
Maintainer: Oliver Keyes
Description: A toolkit for handling URLs that so far includes functions for URL encoding and decoding, parsing, and parameter extraction. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.
License: MIT + file LICENSE
LinkingTo: Rcpp
Imports: Rcpp
Suggests: testthat, knitr
BugReports: https://github.com/Ironholds/urltools/issues
VignetteBuilder: knitr
Packaged: 2014-12-09 02:42:01 UTC; ironholds
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-09 07:12:40

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New package RDataCanvas with initial version 0.1
Package: RDataCanvas
Type: Package
Title: Basic Runtime Support for Datacanvas.io
Version: 0.1
Authors@R: c(person("Xiaolin", "Zhang", role = c("aut", "cre"), email = "leoncamel@gmail.com"))
Description: Provides basic functionalities for writing a module for http://datacanvas.io. The http://datacanvas.io is a big data analytics platform that helps data scientists to build, manage and share data pipelines.
Depends: R (>= 3.0.0)
License: BSD_3_clause + file LICENSE
URL: https://github.com/DataCanvasIO/RDataCanvas
BugReports: https://github.com/DataCanvasIO/RDataCanvas/issues
LazyData: true
Imports: jsonlite
Suggests: testthat
Packaged: 2014-12-09 05:57:45 UTC; xiaolin
Author: Xiaolin Zhang [aut, cre]
Maintainer: Xiaolin Zhang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-09 08:43:09

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New package GeneticSubsetter with initial version 0.5
Package: GeneticSubsetter
Type: Package
Title: Identify Favorable Subsets of Germplasm Collections
Version: 0.5
Date: 2015-11-24
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner
Description: Finds subsets of sets of genotypes with a high mean Polymorphism Information Content (PIC), and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
License: GPL (>= 2)
Imports: rrBLUP
Packaged: 2014-12-08 23:24:39 UTC; ryan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-09 06:56:03

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Mon, 08 Dec 2014

New package MetSizeR with initial version 1.1
Package: MetSizeR
Type: Package
Title: GUI Tool for Estimating Sample Sizes for Metabolomic Experiments
Version: 1.1
Date: 2013-09-08
Author: Gift Nyamundanda, Isobel Claire Gormley, Yue Fan, William M Gallagher, Lorraine Brennan
Maintainer: Gift Nyamundanda
Description: An easy to use Graphical User Interface for estimating sample sizes required for metabolomic experiments even when experimental pilot data is not available.
Depends: mvtnorm,MetabolAnalyze,cairoDevice, gWidgets, gWidgetsRGtk2
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-12-08 12:21:11 UTC; Gift
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-08 22:15:50

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New package V8 with initial version 0.1
Package: V8
Type: Package
Title: Embedded JavaScript Engine
Version: 0.1
Date: 2014-12-07
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: V8 is an open source JavaScript engine developed by Google.
License: MIT + file LICENSE
URL: http://github.com/jeroenooms/v8, https://code.google.com/p/v8/
BugReports: http://github.com/jeroenooms/V8/issues
SystemRequirements: V8 development library: libv8-dev (deb), v8-devel (rpm)
NeedsCompilation: yes
Imports: Rcpp, jsonlite
LinkingTo: Rcpp
Packaged: 2014-12-08 03:59:36 UTC; jeroen
Repository: CRAN
Date/Publication: 2014-12-08 07:09:10

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New package thermocouple with initial version 1.0.0
Package: thermocouple
Type: Package
Title: Temperature Measurement with Thermocouples, RTD and IC Sensors
Version: 1.0.0
Encoding: UTF-8
Authors@R: c(person(given = "Jose", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"))
Description: Temperature measurement data, equations and methods for Thermocouples, wire RTD, thermistors and IC thermometers
License: GPL (>= 3)
LazyData: yes
Depends: R (>= 2.7.0)
Packaged: 2014-12-07 23:27:28.378 UTC; poky
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-08 07:17:11

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New package seqminer with initial version 3.4
Package: seqminer
Type: Package
Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL format) into R
Version: 3.4
Date: 2014-12-07
Author: Xiaowei Zhan and Dajiang Liu , with contributions of Heng Li (this author wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R
Copyright: We have used the following software and made minimal necessary changes: Tabix, Heng Li (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.
License: GPL | file LICENSE
URL: http://seqminer.genomic.codes
Packaged: 2014-12-07 21:22:35 UTC; zhanxw
Repository: CRAN
Date/Publication: 2014-12-08 07:38:24
Depends: stringr
Suggests: testthat, SKAT
SystemRequirements: zlib headers and libraries, optionally also bzip2 and POSIX-compliant regex functions.
NeedsCompilation: yes

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New package RSurveillance with initial version 0.1.0
Package: RSurveillance
Type: Package
Title: Design and Analysis of Disease Surveillance Activities
Version: 0.1.0
Date: 2014-11-15
Author: Evan Sergeant
Maintainer: Evan Sergeant
Description: This package provides a range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation.
License: GPL-2 | GPL-3
LazyLoad: yes
Imports: epitools, epiR
Packaged: 2014-12-08 01:07:28 UTC; evan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-08 07:06:21

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Sun, 07 Dec 2014

New package dashboard with initial version 0.1.0
Package: dashboard
Type: Package
Title: Interactive Data Visualization with D3.js
Version: 0.1.0
Date: 2014-12-05
Author: Johann Laurent
Maintainer: Johann Laurent.
Description: The dashboard package allows users to create web pages which display interactive data visualizations working in a standard modern browser. It displays them locally using the Rook server. Nor knowledge about web technologies nor Internet connection are required. D3.js is a JavaScript library for manipulating documents based on data. D3 helps the dashboard package bring data to life using HTML, SVG and CSS.
Depends: R (>= 2.13.0)
Imports: Rook
License: GPL-2
NeedsCompilation: no
Packaged: 2014-12-07 20:05:36 UTC; johannlaurent
Repository: CRAN
Date/Publication: 2014-12-07 22:48:31

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New package rtdists with initial version 0.2-6
Package: rtdists
Type: Package
Title: Response time distributions
Depends: R (>= 3.0.0)
Suggests: testthat
Imports: evd, msm, gsl
Description: Provides response time distributions (density/PDF, distribution function/CDF, and random generation): (a) Ratcliff diffusion model based on C code by Andreas and Jochen Voss and (b) linear ballistic accumulator (LBA) with different distribution underlying the drift rate.
URL: https://github.com/rtdists/rtdists/
License: GPL (>= 3)
Authors@R: c( person(given="Scott", family="Brown", role=c("aut")), person(given="Matthew", family="Gretton", role=c("aut")), person(given="Andrew", family="Heathcote", role=c("aut")), person(given="Andreas", family="Voss", role=c("ctb")), person(given="Jochen", family="Voss", role=c("ctb")), person(given="Andrew", family="Terry", role=c("ctb")), person(given="Henrik", family="Singmann", email="singmann+rtdists@gmail.com", role=c("aut", "cre")) )
Version: 0.2-6
Date: 2014-12-06
Packaged: 2014-12-06 22:45:16 UTC; Henrik
Author: Scott Brown [aut], Matthew Gretton [aut], Andrew Heathcote [aut], Andreas Voss [ctb], Jochen Voss [ctb], Andrew Terry [ctb], Henrik Singmann [aut, cre]
Maintainer: Henrik Singmann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-07 06:44:55

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Sat, 06 Dec 2014

New package knockoff with initial version 0.1
Package: knockoff
Type: Package
Title: Knockoff Filter
Version: 0.1
Date: 2014-12-05
Author: Rina Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
Description: The knockoff filter for controlling the false discovery rate
License: GPL-3
Imports: glmnet, RJSONIO
Suggests: lars, knitr, testthat
VignetteBuilder: knitr
Packaged: 2014-12-06 00:33:17 UTC; epatters
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-06 15:09:57

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New package algstat with initial version 0.0.2
Package: algstat
Type: Package
Title: Algebraic statistics in R
Version: 0.0.2
Date: 2014-12-04
Authors@R: c(person("David", "Kahle", role = c("aut","cre"), email = "david.kahle@gmail.com"), person("Luis", "Garcia-Puente", role = "aut", email = "lgarcia@shsu.edu"))
Maintainer: David Kahle
Description: algstat provides functionality for algebraic statistics in R. Current applications include exact inference in log-linear models for contingency table data, analysis of ranked and partially ranked data, and general purpose tools for multivariate polynomials, building on the mpoly package. To aid in the process, algstat has ports to Macaulay2, Bertini, LattE-integrale and 4ti2.
Depends: mpoly
LinkingTo: Rcpp
Imports: stringr, reshape2, Rcpp
License: GPL-2
SystemRequirements: Optionally Latte-integrale, Bertini, and Macaulay2. Cygwin is required for each of the above for Windows users. See INSTALL file for details.
Packaged: 2014-12-06 01:17:27 UTC; david_kahle
Author: David Kahle [aut, cre], Luis Garcia-Puente [aut]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-06 02:23:38

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Fri, 05 Dec 2014

New package NISTunits with initial version 1.0.0
Package: NISTunits
Type: Package
Title: Fundamental Physical Constants and Unit Conversions from NIST
Version: 1.0.0
Encoding: UTF-8
Authors@R: c(person(given = "Jose", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"))
Description: Fundamental physical constants (Quantity, Value, Uncertainty, Unit) for SI (International System of Units) and non-SI, plus unit conversions Based on the data from NIST (National Institute of Standards and Technology)
License: GPL (>= 3)
Depends: R (>= 2.7.0)
Packaged: 2014-12-05 22:45:28.711 UTC; poky
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-06 00:00:05

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New package EpiResTest with initial version 1.0
Package: EpiResTest
Type: Package
Title: Latent Residuals Test for Epidemiology and Ecology Models
Version: 1.0
Date: 2014-07-07
Author: Max S. Y. Lau; Jeffrey Pollock
Maintainer: Max S. Y. Lau
Description: Latent residual tests recently developed (Lau et al. 2014) which are specifically designed to measure the goodness-of-fit of different model components of a general spatial S-E-I-R model commonly used in epidemiology and ecology studies. More restrictive model classes such as S-I-R can be accommodated. Note that although each test is specifically designed to be sensitive to one particular component of a spatio-temporal model, they are not theoretically restricted to only testing these specific aspects and can be used as a general model assessment tool like any other conventional model selection techniques. The underlying functions are coded in C++ so they should be generally quick.
Note: Under the null hypothesis that the model is correct, the residuals follow distribution U(0,1). The examples only compute a single set of residuals given actual values of most of the model components which are typically required to be imputed in data augmentation schemes such as MCMC in which multiple sets of residuals can be imputed. Only the raw residuals are outputted, a natural summary statistics of the residual samples is the p-value which may be computed using Kolmogorov-Smirnov or Anderson-Darling test.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp, RcppArmadillo
Suggests: RUnit, ADGofTest
Packaged: 2014-12-05 14:12:57 UTC; sl451
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-05 15:29:39

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New package archiDART with initial version 1.0
Package: archiDART
Type: Package
Title: Plant Root System Architecture Analysis Using DART Output Files
Version: 1.0
Date: 2014-12-05
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory
Description: Analysis of complex plant root system architectures using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, 326, 261--273).
License: GPL-2
Imports: stats, utils, graphics, grDevices
Packaged: 2014-12-05 09:14:22 UTC; Benjamin Delory
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-05 11:00:19

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Thu, 04 Dec 2014

New package rstackdeque with initial version 1.1
Package: rstackdeque
Type: Package
Title: Persistent Fast Amortized Stack and Queue Data Structures
Version: 1.1
Date: 2014-12-01
URL: https://github.com/oneilsh/rstackdeque
BugReports: https://github.com/oneilsh/rstackdeque/issues
Author: Shawn T. O'Neil
Maintainer: Shawn T. O'Neil
Description: Provides fast, persistent (side-effect-free) stack, queue and deque (double-ended-queue) data structures. While deques include a superset of functionality provided by queues, in these implementations queues are more efficient in some specialized situations. See the documentation for rstack, rdeque, and rpqueue for details.
License: MIT + file LICENSE
Suggests: testthat
Depends: utils
Packaged: 2014-12-04 20:03:38 UTC; soneil
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-05 01:31:28

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New package acid with initial version 1.0
Package: acid
Type: Package
Title: Analysing Conditional Distributions of Income
Version: 1.0
Date: 2014-11-18
Author: Alexander Sohn
Maintainer: Alexander Sohn
Description: Functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture distribution as well as functions for moments, inequality measures and entropy measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.
Depends: gamlss,gamlss.dist,Hmisc
Suggests: ineq
License: GPL-3
Packaged: 2014-12-04 10:03:30 UTC; admin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-05 01:30:20

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New package textreg with initial version 0.1
Package: textreg
Type: Package
Title: n-gram Text Regression, aka Concise Comparative Summarization
Version: 0.1
Date: 2014-01-16
Author: Luke Miratrix
Maintainer: Luke Miratrix
Description: Function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.
License: GPL (>= 2)
Depends: R (>= 2.10),
Imports: tm (>= 0.6), NLP (>= 0.1-3), Rcpp (>= 0.10.6)
Suggests: corrplot
LinkingTo: Rcpp
Packaged: 2014-12-04 15:36:01 UTC; lmiratrix
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-04 17:52:34

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New package RStars with initial version 1.0
Package: RStars
Type: Package
Title: Access to the Digital Universe Data set API
Version: 1.0
Date: 2014-12-03
Author: William Kyle Hamilton
Maintainer: William Kyle Hamilton
Description: Access to the Digital Universe Data set API pulls data on exoplants, stars, and galaxies.
Depends: R (>= 3.0.3), RJSONIO, RCurl
License: GPL-3
URL: https://github.com/kylehamilton/RStars
BugReports: https://github.com/kylehamilton/RStars/issues
Packaged: 2014-12-04 01:38:06 UTC; whamilton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-04 08:29:55

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Wed, 03 Dec 2014

New package sensitivityPStrat with initial version 1.0-6
Package: sensitivityPStrat
Type: Package
Title: Principal Stratification Sensitivity Analysis Functions
Version: 1.0-6
Date: 2014-11-04
Author: Charles Dupont, Bryan Shepherd
Maintainer: Charles Dupont
Description: This package provides functions to perform principal stratification sensitivity analyses on datasets.
Imports: stats, survival
License: GPL
LazyLoad: yes
Packaged: 2014-12-03 15:40:49 UTC; dupontct
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-04 00:14:37

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New package panelaggregation with initial version 0.1
Package: panelaggregation
Title: Aggregate Longitudinal Survey Data
Description: Aggregate Business Tendency Survey Data (and other qualitative surveys) to time series at various aggregation levels. Run aggregation of survey data in a speedy, re-traceable and a easily deployable way. Aggregation is substantially accelerated by use of data.table. Panelaggregation aims at providing an interface that is more geared towards survey researchers.
Version: 0.1
Authors@R: as.person(c('Matthias Bannert [aut, cre]','Gabriel Bucur [aut]'))
Author: Matthias Bannert [aut, cre], Gabriel Bucur [aut]
Maintainer: Matthias Bannert
Depends: R (>= 3.0.0), data.table (>= 1.9.4)
License: GPL-2
LazyData: true
Packaged: 2014-12-03 14:04:09 UTC; mbannert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-03 17:25:49

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New package ClimClass with initial version 1.0
Package: ClimClass
Type: Package
Title: Climate Classification According To Several Indices
Version: 1.0
Date: 2014-11-27
Author: Emanuele Eccel, Emanuele Cordano, Giambattista Toller
Maintainer: Emanuele Eccel
Description: Classification of climate according to Koeppen - Geiger, of aridity indices, of continentality indices, and of water balance after Thornthwaite. Drawing climographs: Thornthwaite, Peguy, Bagnouls-Gaussen.
License: GPL (>= 2)
Depends: R(>= 2.10.0),geosphere,ggplot2,reshape2
Suggests: stringr
URL: https://github.com/ecor/ClimClass
Packaged: 2014-12-03 12:36:13 UTC; ecor
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-03 17:01:22

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Tue, 02 Dec 2014

New package retistruct with initial version 0.5.9
Package: retistruct
License: CC BY-NC-SA 4.0
Title: Retistruct - Retinal Reconstruction Program
Authors@R: c(person("David C.", "Sterratt", role=c("aut", "cre", "cph"), email="david.c.sterratt@ed.ac.uk"), person("Daniel", "Lyngholm", role=c("aut", "cph")))
Description: Program to reconstruct retinae from flattened retinae in which there are incisions and tears
Version: 0.5.9
URL: http://retistruct.r-forge.r-project.org/
BugReports: https://github.com/davidcsterratt/retistruct/issues
Date: 2014-12-02
Depends: R (>= 3.1.0)
Imports: foreign, RImageJROI, png, ttutils, sp, geometry (>= 0.2-1), RTriangle (>= 1.6-0.4), rgl, R.matlab
Suggests: testthat, gWidgetsRGtk2, gWidgets, cairoDevice
Packaged: 2014-12-02 16:59:26 UTC; sterratt
Author: David C. Sterratt [aut, cre, cph], Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 20:19:11

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New package hnp with initial version 1.0
Package: hnp
Type: Package
Title: Half-Normal Plots with Simulation Envelopes
Version: 1.0
Date: 2014-11-27
Authors@R: c(person("Rafael", "de Andrade Moral", role = c("aut", "cre"), email = "rafael_moral@yahoo.com.br"), person("John", "Hinde", role = "aut"), person("Clarice", "Garcia Borges Demetrio", role = "aut"))
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral
Depends: R (>= 3.0.0), MASS (>= 7.3-35)
Suggests: lme4, gamlss, gamlss.dist, pscl, nnet, aods3, VGAM, glmmADMB, latticeExtra
Additional_repositories: http://www.hafro.is/~arnima/repos
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
License: GPL (>= 2)
Packaged: 2014-12-02 18:49:32 UTC; Rafael
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 20:22:29

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New package rncl with initial version 0.2.0
Package: rncl
Title: An interface to the Nexus Class Library
Version: 0.2.0
Date: 2014-12-01
Authors@R: c(person("Francois", "Michonneau", role=c("aut", "cre"), email="francois.michonneau@gmail.com"), person("Ben", "Bolker", role=c("aut")), person("Mark", "Holder", role=c("aut", "cre")), person("Paul", "Lewis", role=c("aut", "cre")), person("Brian", "O'Meara", role=c("aut", "cre")))
Maintainer: Francois Michonneau
Description: An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's phylo or phylobase's phylo4(d).
Imports: Rcpp (>= 0.11.0), ape
Suggests: testthat
LinkingTo: Rcpp
Depends: R (>= 3.1.1)
License: BSD_2_clause + file LICENSE
URL: https://github.com/fmichonneau/rncl
BugReports: https://github.com/fmichonneau/rncl/issues
LazyData: true
Packaged: 2014-12-02 16:52:49 UTC; francois
Author: Francois Michonneau [aut, cre], Ben Bolker [aut], Mark Holder [aut, cre], Paul Lewis [aut, cre], Brian O'Meara [aut, cre]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 18:23:19

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New package radar with initial version 1.0.0
Package: radar
Type: Package
Title: Fundamental Formulas for Radar
Version: 1.0.0
Encoding: UTF-8
Authors@R: c(person(given = "Jose'", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"), person(given = "Nick", family = "Guy", role = c("aut")))
Description: Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet
License: GPL (>= 3)
Depends: R (>= 2.7.0)
Packaged: 2014-12-02 15:31:46.027 UTC; poky
Author: Jose' Gama [aut, cre], Nick Guy [aut]
Maintainer: Jose' Gama
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 17:04:26

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New package RPANDA with initial version 1.0
Package: RPANDA
Version: 1.0
Date: 2014-02-04
Type: Package
Title: Phylogenetic ANalyses of DiversificAtion
Depends: R (>= 2.14.2), ape, picante, pspline, deSolve
Suggests: testthat
Encoding: UTF-8
Author: Hélène Morlon [aut, cre, cph]
Authors@R: c(person("Hélène", "Morlon", role = c("aut", "cre", "cph"), email = "morlon@biologie.ens.fr"))
Maintainer: Hélène Morlon
Description: Implements fits of diversification models to phylogenetic data. See Morlon et al. PLoSB (2010), Morlon et al. PNAS (2011), Condamine et al. Eco Lett (2013), Morlon et al. Eco Lett (2014) and Manceau et al. (in prep).
License: GPL-2
URL: https://github.com/hmorlon/PANDA
Packaged: 2014-12-02 11:24:04 UTC; helenemorlon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 14:36:08

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New package choroplethrAdmin1 with initial version 1.0.0
Package: choroplethrAdmin1
Type: Package
Title: Contains an Administrative-Level-1 Map of the World
Version: 1.0.0
Date: 2014-12-02
Author: Ari Lamstein
Maintainer: Ari Lamstein
Description: Contains an administrative-level-1 map of the world. Administrative-level-1 is the generic term for the largest sub-national subdivision of a country. This package was created for use with the choroplethr package.
License: BSD_3_clause + file LICENSE
URL: https://groups.google.com/forum/#!forum/choroplethr
Imports: ggplot2
Packaged: 2014-12-02 11:47:09 UTC; arilamstein
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 14:30:53

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New package ASPBay with initial version 1.0
Package: ASPBay
Type: Package
Title: Bayesian Inference on Causal Genetic Variants using Affected Sib-Pairs Data
Depends: hexbin, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Version: 1.0
Date: 2014-11-18
Author: Claire Dandine-Roulland
Maintainer: Claire Dandine-Roulland
Description: This package allows to make inference on the properties of causal genetic variants in linkage disequilibrium with genotyped markers. In a first step, we select a subset of variants using a score statistic for affected sib-pairs. In a second step, on the selected subset, we make inference on causal genetic variants in the considered region.
License: GPL-2
Packaged: 2014-12-02 11:25:15 UTC; dandine
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 14:28:23

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New package ARTool with initial version 0.9.3
Package: ARTool
Title: Aligned Rank Transform
Version: 0.9.3
Date: 2014-11-20
Authors@R: c(person("Matthew", "Kay", role = c("aut", "cre"), email = "mjskay@uw.edu"), person("Jacob O.", "Wobbrock", role = "aut", email = "wobbrock@uw.edu"))
Maintainer: Matthew Kay
Description: Aligned Rank Transform for nonparametric factorial ANOVAs
Depends: lme4, car
Imports: plyr, pbkrtest
Suggests: testthat, lsmeans
License: GPL (>= 2)
BugReports: https://github.com/mjskay/ARTool/issues/new
URL: https://github.com/mjskay/ARTool
Packaged: 2014-12-02 09:30:57 UTC; Matthew
Author: Matthew Kay [aut, cre], Jacob O. Wobbrock [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 12:24:50

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New package secrlinear with initial version 1.0.3
Package: secrlinear
Type: Package
Title: Spatially Explicit Capture-Recapture for Linear Habitats
Version: 1.0.3
Depends: R (>= 3.0.0), secr(>= 2.9.1), sp, igraph
Imports: parallel, maptools, rgeos, MASS
Suggests: knitr, secrdesign
VignetteBuilder: knitr
Date: 2014-12-02
Author: Murray Efford
Maintainer: Murray Efford
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'
License: GPL (>= 2)
LazyData: yes
URL: http://www.otago.ac.nz/density
Packaged: 2014-12-02 07:18:35 UTC; Murray
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 09:45:03

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New package netgsa with initial version 1.0
Package: netgsa
Type: Package
Title: Network-based Gene Set Analysis
Version: 1.0
Date: 2014-12-01
Author: Ali Shojaie and Jing Ma
Maintainer: Jing Ma
Description: Functions for carrying out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data
Depends: cvTools, corpcor, glasso, glmnet, igraph
Suggests: MASS
License: GPL (>= 2)
LazyLoad: yes
URL: http://arxiv.org/abs/1411.7919
Packaged: 2014-12-02 02:14:06 UTC; jingma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 07:29:28

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New package MOrder with initial version 0.1
Package: MOrder
Title: Check Time Homogeneity and Markov Chain Order
Description: MOrder provide functions to check time homogeneity and order of markov chain by using chi-squared test, AIC value and BIC value.
Version: 0.1
Date: 2014-03-04
Author: Akshay Chougule , Dr Robert Canales
Maintainer: Dr Robert Canales
License: GPL-2
LazyData: true
Packaged: 2014-12-01 22:49:02 UTC; akshaychougule
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 07:23:02

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Mon, 01 Dec 2014

New package wrassp with initial version 0.1.3
Package: wrassp
Version: 0.1.3
Title: Interface to the ASSP Library
Authors@R: as.person(c( "Raphael Winkelmann [aut, cre]", "Lasse Bombien [aut]", "Michel Scheffers [aut]"))
Description: wrassp is a wrapper around Michel Scheffers's libassp (Advanced Speech Signal Processor). The libassp library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.
Depends: R (>= 3.1.1)
VignetteBuilder: knitr
Suggests: compare(>= 0.2.4), knitr(>= 1.7), testthat(>= 0.7.1.99)
License: GPL (>= 3)
URL: https://github.com/IPS-LMU/wrassp
BugReports: https://github.com/IPS-LMU/wrassp/issues
Packaged: 2014-12-01 17:13:26 UTC; raphaelwinkelmann
Author: Raphael Winkelmann [aut, cre], Lasse Bombien [aut], Michel Scheffers [aut]
Maintainer: Raphael Winkelmann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 00:17:08

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New package RegressionFactory with initial version 0.7
Package: RegressionFactory
Type: Package
Title: Expander Functions for Generating Full Gradient and Hessian from Single- and Multi-Slot Base Distributions
Version: 0.7
Date: 2014-12-01
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansion framework is of conceptual value by offering new opportunities to generate novel regression problems.
License: GPL (>= 2)
Suggests: sns
Packaged: 2014-12-01 17:23:57 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 22:00:48

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New package paleofire with initial version 1.1.5
Package: paleofire
Type: Package
Title: Analysis of Charcoal Records from the Global Charcoal Database
Version: 1.1.5
Date: 2014-11-24
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
URL: http://gpwg.org
License: GPL (>= 2)
Imports: locfit, raster, ggplot2, plyr, rgdal, lattice
Suggests: gtools,caTools,pscl,agricolae,Imap,sp,rworldmap,RColorBrewer
Depends: R(>= 2.10.0), methods, GCD
LazyLoad: yes
LazyData: no
Encoding: UTF-8
Packaged: 2014-11-30 18:41:01 UTC; Olivier
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 18:09:29

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New package GCPM with initial version 1.1.1
Package: GCPM
Type: Package
Title: Generalized Credit Portfolio Model
Version: 1.1.1
Date: 2014-12-01
Author: Kevin Jakob
Maintainer: Kevin Jakob
Description: The package helps to analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
License: GPL-2
Imports: Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1)
LinkingTo: Rcpp, RcppProgress
SystemRequirements: Windows, Linux, OS X
Packaged: 2014-12-01 09:43:48 UTC; Kevin_Jakob
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-01 18:13:42

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New package ssd with initial version 0.3
Package: ssd
Type: Package
Title: Sample Size Determination (SSD) for Unordered Categorical Data
Version: 0.3
Date: 2014-11-30
Author: Junheng Ma and Jiayang Sun
Maintainer: Junheng Ma
Description: ssd calculates the sample size needed to detect the differences between two sets of unordered categorical data.
License: GPL-2
Packaged: 2014-12-01 05:48:18 UTC; Junheng Ma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:28:44

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New package rngSetSeed with initial version 0.3-1
Package: rngSetSeed
Type: Package
Title: Seeding the Default RNG With a Numeric Vector
Version: 0.3-1
Date: 2014-12-01
Author: Petr Savicky
Maintainer: Petr Savicky
Description: A function setVectorSeed() is provided. Its argument is a numeric vector of an arbitrary nonzero length, whose components have integer values from [0, 2^32-1]. The input vector is transformed using AES (Advanced Encryption Standard) algorithm into an initial state of Mersenne-Twister random number generator. The function provides a better alternative to the R base function set.seed() if the input vector is a single integer. Initializing a stream of random numbers with a vector is a convenient way to obtain several streams, each of which is identified by several integer indices.
License: GPL-3
Packaged: 2014-12-01 08:01:26 UTC; petr
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-01 11:07:13

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New package mipfp with initial version 1.0
Package: mipfp
Type: Package
Title: Multidimensional Iterative Proportional Fitting
Version: 1.0
Date: 2014-11-26
Authors@R: c(person("Johan", "Barthelemy", role = c("aut", "cre"),email = "johan@uow.edu.au"),person("Thomas", "Suesse", role = "aut"),person("Mohammad", "Namazi-Rad", role = "ctb"))
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy
Description: An implementation of the iterative proportional fitting procedure for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional)
License: GPL-2
URL: www.r-project.org
Packaged: 2014-12-01 00:10:22 UTC; johan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:10:27

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New package lintr with initial version 0.2.0
Package: lintr
Title: Static R Code Analysis
Version: 0.2.0
Authors@R: "Jim Hester [aut, cre]"
URL: https://github.com/jimhester/lintr
BugReports: https://github.com/jimhester/lintr/issues
Description: Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with Emacs, Vim and Sublime Text.
Depends: R (>= 3.1.1)
Imports: rex, crayon, codetools, stringdist, testthat, digest, igraph
License: MIT + file LICENSE
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-01 02:53:22 UTC; james.hester
Author: "Jim Hester" [aut, cre]
Maintainer: "Jim Hester"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:09:24

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