Sat, 28 Mar 2015

New package spgs with initial version 1.0
Package: spgs
Type: Package
Encoding: latin1
Title: Statistical Patterns in Genomic Sequences
Version: 1.0
Date: 2015-03-27
Authors@R: c(person("Andrew", "Hart", role = c("aut", "cre"), email = "ahart@dim.uchile.cl"), person("Servet", "Martínez", role = "aut"), person("Universidad de Chile", role = "cph"), person("INRIA-Chile", role = "cph"))
Author: Andrew Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
Maintainer: Andrew Hart
Copyright: Universidad de Chile, INRIA-Chile
Depends: R (>= 3.0)
Enhances: seqinr
Description: A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
License: GPL (>= 2)
NeedsCompilation: yes
Classification/MSC: 62F03, 62G10, 62M07, 62P10, 92D20
Packaged: 2015-03-28 01:05:50 UTC; ahart
Repository: CRAN
Date/Publication: 2015-03-28 07:40:29

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Fri, 27 Mar 2015

New package StatMeasures with initial version 1.0
Package: StatMeasures
Type: Package
Title: Easy Data Manipulation, Data Quality and Statistical Checks
Version: 1.0
Date: 2015-03-24
Author: Akash Jain
Maintainer: Akash Jain
Description: Offers useful functions to perform day-to-day data manipulation operations, data quality checks and post modelling statistical checks. One can effortlessly change class of a number of variables to factor, remove duplicate observations from the data, create deciles of a variable, perform data quality checks for continuous (integer or numeric), categorical (factor) and date variables, and compute goodness of fit measures such as auc for statistical models. The functions are consistent for objects of class 'data.frame' and 'data.table', which is an enhanced 'data.frame' implemented in the package 'data.table'.
Depends: R (>= 3.1.3)
Imports: data.table (>= 1.9.4)
License: GPL-2
Packaged: 2015-03-27 19:59:01 UTC; akash.jain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-27 23:46:22

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New package SOMbrero with initial version 1.0
Package: SOMbrero
Title: SOM Bound to Realize Euclidean and Relational Outputs
Version: 1.0
Date: 2015-03-27
Authors@R: c(person("Laura", "Bendhaiba", role = "aut", email="laurabendhaiba@gmail.com"), person("Julien", "Boelaert", role= "aut", email="julien.boelaert@gmail.com"), person("Madalina", "Olteanu", role = "aut", email="madalina.olteanu@univ-paris1.fr"), person("Nathalie", "Villa-Vialaneix", role = c("aut", "cre"), email="nathalie.villa@toulouse.inra.fr"))
Maintainer: Nathalie Villa-Vialaneix
Description: The stochastic (also called on-line) version of the Self-Organising Map (SOM) algorithm is provided. Different versions of the algorithm are implemented, for numeric and relational data and for contingency tables. The package also contains many plotting features (to help the user interpret the results) and a graphical user interface based on shiny (which is also available on-line at http://shiny.nathalievilla.org/sombrero).
Depends: R (>= 3.0), knitr, igraph (>= 0.6)
Imports: wordcloud, scatterplot3d, RColorBrewer, shiny
License: GPL (>= 2)
Repository: CRAN
VignetteBuilder: knitr
Packaged: 2015-03-27 20:51:28 UTC; nathalie
Author: Laura Bendhaiba [aut], Julien Boelaert [aut], Madalina Olteanu [aut], Nathalie Villa-Vialaneix [aut, cre]
NeedsCompilation: no
Date/Publication: 2015-03-27 23:44:41

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New package gdm with initial version 1.0
Package: gdm
Type: Package
Title: Functions for Generalized Dissimilarity Modeling
Version: 1.0
Date: 2015-03-27
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
License: GPL-2
Depends: R (>= 2.15.2), Rcpp (>= 0.10.4), raster, reshape2, vegan
LinkingTo: Rcpp
Imports: plyr
Packaged: 2015-03-27 18:56:55 UTC; mlisk
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-27 20:58:26

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New package PAFit with initial version 0.7.2
Package: PAFit
Type: Package
Title: Nonparametric Estimation of Preferential Attachment and Node Fitness in Temporal Complex Networks
Version: 0.7.2
Date: 2015-03-28
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham
Description: A statistically sound method for estimating jointly the attachment function and node fitness in a temporal complex network by maximizing a suitable penalized log-likelihood function is implemented in this package.
URL: www.thongpham.net
License: GPL-3
Depends: R(>= 2.10.0)
Imports: Rcpp (>= 0.11.3)
LinkingTo: Rcpp
LazyData: True
NeedsCompilation: yes
Suggests: R.rsp
VignetteBuilder: R.rsp
Packaged: 2015-03-27 06:49:35 UTC; pham
Repository: CRAN
Date/Publication: 2015-03-27 08:31:40

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New package ELYP with initial version 0.7-1
Package: ELYP
Maintainer: Mai Zhou
Version: 0.7-1
Depends: R (>= 2.15.0), survival
Suggests: emplik
Author: Mai Zhou
Description: Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazard ratio) models. Empirical likelihood tests within a Cox model, for parameters defined via both baseline hazard function and regression parameters.
Title: Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model
License: GPL (>= 2)
URL: http://www.ms.uky.edu/~mai/EmpLik.html
NeedsCompilation: yes
Packaged: 2015-03-27 06:41:46 UTC; mai
Repository: CRAN
Date/Publication: 2015-03-27 08:31:37

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New package SAMUR with initial version 0.6
Package: SAMUR
Type: Package
Title: Stochastic Augmentation of Matched Data Using Restriction Methods
Version: 0.6
Date: 2015-03-26
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: Augmenting a matched data set by generating multiple stochastic, matched samples from the data using a multi-dimensional histogram constructed from dropping the input matched data into a multi-dimensional grid built on the full data set. The resulting stochastic, matched sets will likely provide a collectively higher coverage of the full data set compared to the single matched set. Each stochastic match is without duplication, thus allowing downstream validation techniques such as cross-validation to be applied to each set without concern for overfitting.
License: GPL (>= 2)
Imports: Matching
Packaged: 2015-03-27 02:20:08 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-27 07:15:54

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New package hgm with initial version 1.10
Package: hgm
Type: Package
Depends: R (>= 2.6.0), deSolve
Title: Holonomic Gradient Method and Gradient Descent
Version: 1.10
Date: 2015-03-26
Author: Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta Nishiyama
Maintainer: Nobuki Takayama
Description: The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization constants of unnormalized probability distributions by utilizing holonomic systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method to find maximal likelihood estimates by utilizing the HGM.
License: GPL-2
LazyLoad: yes
URL: http://www.openxm.org
Packaged: 2015-03-27 02:38:17 UTC; taka
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-27 07:16:52

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Thu, 26 Mar 2015

New package reval with initial version 1.0
Package: reval
Title: Repeated Function Evaluation for Sensitivity Analysis
Version: 1.0
Date: 2015-03-25
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan
Description: Simplified scenario testing and sensitivity analysis with R via a generalized function for one-factor-at-a-time (OFAT) sensitivity analysis, evaluation of parameter sets and (sampled) parameter permutations. Options for formatting output and parallel processing are also provided.
URL: https://github.com/mkoohafkan/reval
BugReports: https://github.com/mkoohafkan/reval/issues
License: GPL (>= 3)
Depends: R (>= 3.1.3)
Imports: doParallel (>= 1.0.8), foreach (>= 1.4.2)
Suggests: knitr, ggplot2, dplyr, rivr
VignetteBuilder: knitr
Packaged: 2015-03-26 17:09:50 UTC; Michael
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-27 00:47:32

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New package ggExtra with initial version 0.1.0
Package: ggExtra
Title: Collection of Functions and Layers to Enhance ggplot2
Version: 0.1.0
Authors@R: c( person("Dean", "Attali", , "daattali@gmail.com", role = c("aut", "cre")) )
Description: Collection of functions and layers to enhance ggplot2.
URL: https://github.com/daattali/ggExtra
Depends: R (>= 3.1.0)
Imports: ggplot2 (>= 1.0.0)
Suggests: grid (>= 3.1.3), gridExtra (>= 0.9.1), knitr (>= 1.7)
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Packaged: 2015-03-26 20:22:53 UTC; Dean
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-27 00:46:19

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New package chopthin with initial version 0.1
Package: chopthin
Type: Package
Title: The Chopthin Resampler
Version: 0.1
Date: 2015-03-26
Author: Axel Gandy and F. Din-Houn Lau
Maintainer: Axel Gandy
Description: Resampling is a standard step in particle filtering and in sequential Monte Carlo. This package implements the chopthin resampler, which keeps a bound on the ratio between the largest and the smallest weights after resampling.
License: GPL-3
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp
Suggests: testthat
Packaged: 2015-03-26 16:41:22 UTC; agandy
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-26 18:06:09

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New package kmodR with initial version 0.1.0
Package: kmodR
Type: Package
Title: K-Means with Simultaneous Outlier Detection
Version: 0.1.0
Date: 2015-03-26
Authors@R: c(person("David Charles", "Howe", role = c("aut", "cre"), email = "kmodR@edgecondition.com"))
Author: David Charles Howe [aut, cre]
Maintainer: David Charles Howe
Description: An implementation of the 'k-means--' algorithm proposed by Chawla and Gionis, 2013 in their paper, "k-means-- : A unified approach to clustering and outlier detection. SIAM International Conference on Data Mining (SDM13)", and using 'ordering' described by Howe, 2013 in the thesis, "Clustering and anomaly detection in tropical cyclones". Useful for creating (potentially) tighter clusters than standard k-means and simultaneously finding outliers inexpensively in multidimensional space.
License: GPL-3
LazyData: TRUE
Suggests: testthat
Packaged: 2015-03-26 08:09:09 UTC; David
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-26 10:51:13

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Wed, 25 Mar 2015

New package hsdar with initial version 0.1.1
Package: hsdar
Type: Package
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Version: 0.1.1
Date: 2015-03-23
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [ctb], Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert
Depends: R (>= 2.10.0), sp, raster, rgdal, rootSolve, signal, methods
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using PROSPECT and PROSAIL.
License: GPL
LazyLoad: yes
BuildVignettes: yes
Copyright: see file COPYRIGHTS
URL: http://lcrs.geographie.uni-marburg.de, http://teledetection.ipgp.jussieu.fr/prosail/
Packaged: 2015-03-23 09:32:58 UTC; lehnert
NeedsCompilation: yes
X-CRAN-History: Archived on 2015-03-06 as had memory-access errors and failed with parallel makes.
Repository: CRAN
Date/Publication: 2015-03-25 08:54:00

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Tue, 24 Mar 2015

New package searchable with initial version 0.1.2
Package: searchable
Type: Package
Title: Make R Objects Searchable by Matching Names Based on Case (in)Sensitivity, Regular Expressions, ...
Version: 0.1.2
Date: 2015-03-23
Author: "DecisionPatterns [aut, cre]"
Maintainer: Christopher Brown
Description: Provides functionality for searching named vectors and lists more configurable. The packages uses 'stringr'-style match modifiers to allow for matching by case (in)sensitivity, regular expressions or fixed expression. It also allows searching through values rather than names. This functionality facilitates creating dictionary and thesaurus like structures.
Depends: R (>= 3.0.2)
Imports: methods, stringr (>= 0.6.2)
Suggests: testthat, magrittr
License: GPL-2
URL: https://github.com/decisionpatterns/searchable
BugReports: https://github.com/decisionpatterns/searchable/issues
Collate: 'Class-searchable.R' 'extract.R' 'invert.R' 'is.string.R' 'match-modifiers.R' 'reverse.lookup.R' 'searchable-package.R' 'zzz.R'
Packaged: 2015-03-24 09:48:59 UTC; cbrown
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-25 00:16:06

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New package radiant with initial version 0.1.83
Package: radiant
Title: Business Analytics using R and Shiny
Version: 0.1.83
Date: 2015-3-24
Authors@R: person("Vincent", "Nijs", , "radiant@rady.ucsd.edu", c("aut", "cre"))
Description: A platform-independent browser-based interface for business analytics in R, based on the Shiny package.
Depends: R (>= 3.1.0), lubridate (>= 1.3.3), ggplot2 (>= 1.0.0), dplyr (>= 0.4.1), magrittr (>= 1.5)
Imports: car (>= 2.0.22), MASS (>= 7.3), gridExtra (>= 0.9.1), AlgDesign (>= 1.1.7.3), GPArotation (>= 2014.11.1), psych (>= 1.4.8.11), wordcloud (>= 2.5), markdown (>= 0.7.4), knitr (>= 1.8), ggdendro (>= 0.1.15), broom (>= 0.3.6), tidyr (>= 0.2.0), pryr (>= 0.1), shiny (>= 0.11.1), shinyAce (>= 0.1.0)
Suggests: rmarkdown (>= 0.4.2), ggvis (>= 0.4), testthat (>= 0.9.1)
URL: https://github.com/vnijs/radiant, http://vnijs.github.io/radiant/
BugReports: https://github.com/vnijs/radiant/issues
License: AGPL-3 | file LICENSE
LazyData: true
Packaged: 2015-03-24 18:22:29 UTC; vnijs
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs
NeedsCompilation: no
X-CRAN-Comment: Archived on 2015-03-24 for policy violation.
Repository: CRAN
Date/Publication: 2015-03-25 00:18:56

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New package internetarchive with initial version 0.1.2
Package: internetarchive
Type: Package
Title: An API Client for the Internet Archive
Description: Search the Internet Archive, retrieve metadata, and download files.
Version: 0.1.2
Authors@R: c(person("Lincoln", "Mullen", role = c("aut", "cre"), email = "lincoln@lincolnmullen.com"))
License: MIT + file LICENSE
LazyData: TRUE
URL: https://github.com/ropensci/internetarchive
BugReports: https://github.com/ropensci/internetarchive/issues
Depends: R (>= 3.1.0)
Imports: httr (>= 0.6.1), jsonlite (>= 0.9.14), dplyr (>= 0.4.1)
Suggests: knitr, testthat
VignetteBuilder: knitr
Packaged: 2015-03-24 22:17:51 UTC; lmullen
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-25 00:19:59

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New package trend with initial version 0.0.1
Package: trend
Version: 0.0.1
Date: 2015-03-23
Title: Non-Parametric Trend Tests and Change-Point Detection
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert
Depends: R (>= 2.12.0)
Description: The analysis of environmental data often requires the detection of trends and change-points. This package provides the Mann-Kendall Trend Test, seasonal Mann-Kendall Test, correlated seasonal Mann-Kendall Test, partial Mann-Kendall Trend test, (Seasonal) Sen's slope, partial correlation trend test and change-point test after Pettitt.
License: GPL-3
ZipData: yes
NeedsCompilation: yes
Suggests: Kendall, zyp
Packaged: 2015-03-24 13:04:34 UTC; thorpohl
Repository: CRAN
Date/Publication: 2015-03-24 18:20:23

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New package rgexf with initial version 0.15.3
Package: rgexf
Type: Package
Encoding: UTF-8
Title: Build, Import and Export GEXF Graph Files
Version: 0.15.3
Date: 2015-03-24
Author: George Vega Yon [aut], Jorge Fábrega Lacoa [ctb], Joshua B. Kunst [ctb]
Maintainer: George Vega Yon
Description: Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). Using the XML package, it allows the user to easily build/read graph files including attributes, GEXF viz attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through "sigmajs" (a javascript library) and interact with the igraph package.
URL: http://bitbucket.org/gvegayon/rgexf, http://www.ggvega.com
Depends: XML, Rook, igraph
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2015-03-24 15:40:34 UTC; george
NeedsCompilation: yes
X-CRAN-History: Archived on 2014-12-22 as maintainer address bounced.
Repository: CRAN
Date/Publication: 2015-03-24 18:27:01

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New package sspse with initial version 0.5
Package: sspse
Type: Package
Version: 0.5
Date: 2015-03-20
Title: Estimating Hidden Population Size using Respondent Driven Sampling Data
Authors@R: c( person("Mark S.", "Handcock", role=c("aut","cre","cph"), email="handcock@stat.ucla.edu"), person("Krista J.", "Gile", role=c("aut","cph"), email="gile@math.umass.edu"))
Maintainer: Mark S. Handcock
Depends: parallel
Suggests: network, testthat
Description: An integrated set of tools to estimate the size of a networked population based on respondent-driven sampling data. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data.
License: GPL-3 + file LICENSE
URL: http://www.hpmrg.org
Imports: coda
Packaged: 2015-03-23 23:47:40 UTC; handcock
Author: Mark S. Handcock [aut, cre, cph], Krista J. Gile [aut, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-24 07:25:05

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New package rtable with initial version 0.1.0
Package: rtable
Type: Package
Title: Tabular Reporting Functions
Description: Provides tabular reporting functionalities to work with 'ReporteRs' package: 'as.FlexTable' methods are available for 'ftable' and 'xtable' objects, function 'FlexPivot' is producing a pivot table and 'freqtable' a percentage table, a 'knitr' print method and a 'shiny' render function are provided for 'FlexTable' objects.
Version: 0.1.0
Date: 2015-03-23
Authors@R: c( person("David", "Gohel", role = c("aut", "cre"), email = "david.gohel@lysis-consultants.fr") )
Author: David Gohel [aut, cre]
Maintainer: David Gohel
License: GPL-3
Depends: xtable, ReporteRs (>= 0.7.8)
Imports: knitr, tidyr, shiny
Suggests: dplyr
URL: http://davidgohel.github.io/tabular/index.html
BugReports: https://github.com/davidgohel/rtable/issues
Packaged: 2015-03-23 20:42:08 UTC; davidgohel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-24 07:21:47

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Mon, 23 Mar 2015

New package NPBayesImpute with initial version 0.5
Package: NPBayesImpute
Type: Package
Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Version: 0.5
Date: 2015-03-22
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
License: GPL (>= 3)
Depends: methods, Rcpp (>= 0.10.2)
LinkingTo: Rcpp
RcppModules: clcm
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-03-23 12:52:42 UTC; quanli
X-CRAN-History: Archived on 2015-03-13 as misuse of \donttest was not corrected.
Date/Publication: 2015-03-23 21:17:06

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New package ramify with initial version 0.1.0
Package: ramify
Type: Package
Title: Additional Matrix Functionality
Version: 0.1.0
Date: 2015-03-22
Authors@R: person("Brandon", "Greenwell", email = "greenwell.brandon@gmail.com", role = c("aut", "cre"))
Description: Additional matrix functionality for R. Includes a wrapper to the base matrix function that extends its functionality by allowing matrices to be created from character strings and lists. A number of convenience functions have also been added for users more familiar with other scientific languages like Julia, MATLAB/Octave, or Python.
Suggests: testthat
License: GPL (>= 2)
URL: https://github.com/w108bmg/ramify
BugReports: https://github.com/w108bmg/ramify/issues
Packaged: 2015-03-22 16:31:20 UTC; w108bmg
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-23 16:46:24

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New package MixAll with initial version 1.0
Package: MixAll
Version: 1.0
Date: 2015-02-20
Title: Clustering using Mixture Models
Authors@R: c(person("Serge", "Iovleff", role = c("aut","cre"), email = "Serge.Iovleff@stkpp.org"))
Copyright: inria 2013-2015
Depends: R (>= 3.0.2), rtkpp
Imports: methods
Description: Algorithms and methods for estimating parametric mixture models with missing data.
License: GPL (>= 2)
LinkingTo: Rcpp, rtkpp
SystemRequirements: GNU make
Collate: 'global.R' 'ClusterAlgo.R' 'ClusterInit.R' 'ClusterStrategy.R' 'IClusterModel.R' 'ClusterCategorical.R' 'ClusterPoisson.R' 'ClusterDiagGaussian.R' 'ClusterHeterogeneous.R' 'ClusterGamma.R' 'ClusterModelNames.R' 'ClusterPlot.R' 'missingValues.R' 'MixAll.R'
Packaged: 2015-03-23 09:45:27 UTC; iovleff
Author: Serge Iovleff [aut, cre]
Maintainer: Serge Iovleff
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-23 13:29:03

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New package rTableICC with initial version 1.0.2
Package: rTableICC
Type: Package
Title: Random Generation of Contingency Tables
Version: 1.0.2
Date: 2015-03-12
Author: Haydar Demirhan
Maintainer: Haydar Demirhan
Description: Contains functions for random generation of R x C and 2 x 2 x K contingency tables. In addition to the generation of contingency tables over predetermined intraclass-correlated clusters, it is possible to generate contingency tables without intraclass correlations under product multinomial, multinomial, and Poisson sampling plans. It also consists of a function for generation of random data from a given discrete probability distribution function.
Depends: partitions, aster
License: GPL-3
Packaged: 2015-03-23 08:46:57 UTC; Stat
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-23 10:50:29

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New package Copula.Markov with initial version 1.0
Package: Copula.Markov
Type: Package
Title: Estimation and Statistical Process Control Under Copula-Based Time Series Models
Version: 1.0
Date: 2015-03-23
Author: Takeshi Emura and Ting-Hsuan Long
Maintainer: Takeshi Emura
Description: Estimation and statistical process control are performed under copula-based time-series models.
License: GPL-2
Packaged: 2015-03-23 07:09:22 UTC; user
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-23 10:49:06

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New package bootsPLS with initial version 1.0.2
Package: bootsPLS
Type: Package
Title: Bootstrap Subsamplings of Sparse Partial Least Squares - Discriminant Analysis for Classification and Signature Identification
Version: 1.0.2
Author: Florian Rohart [aut, cre], Kim-Anh Le Cao [boss], Christine Wells [boss]
Maintainer: Florian Rohart
Description: Bootstrap Subsamplings of sparse Partial Least Squares - Discriminant Analysis (sPLS-DA) for Classification and Signature Identification. The method is applicable to any classification problem with more than 2 classes. It relies on bootstrap subsamplings of sPLS-DA and provides tools to select the most stable variables (defined as the ones consistently selected over the bootstrap subsamplings) and to predict the class of test samples.
License: GPL-3
Depends: mixOmics
Packaged: 2015-03-21 08:35:38 UTC; florian
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-23 07:32:59

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Sun, 22 Mar 2015

New package waffle with initial version 0.3
Package: waffle
Type: Package
Title: Create Waffle Chart Visualizations in R
Version: 0.3
Date: 2015-03-20
Author: Bob Rudis
Maintainer: Bob Rudis
Description: Square pie charts (a.k.a. waffle charts) can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used with each square representing 1% of the total. Modern uses of waffle charts do not necessarily adhere to this rule and can be created with a grid of any rectangular shape. Best practices suggest keeping the number of categories small, just as should be done when creating pie charts.
URL: http://github.com/hrbrmstr/waffle
BugReports: https://github.com/hrbrmstr/waffle/issues
Suggests: testthat
Depends: R (>= 3.0.0), ggplot2
License: GPL (>= 2)
Imports: RColorBrewer, grid, gridExtra, gtable
Packaged: 2015-03-21 18:40:12 UTC; bob
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-22 08:07:57

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New package sjmisc with initial version 1.0.0
Package: sjmisc
Type: Package
Encoding: UTF-8
Title: Miscellaneous Data Management Tools
Version: 1.0.0
Date: 2015-03-21
Author: Daniel LĂĽdecke
Maintainer: Daniel LĂĽdecke
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
License: GPL-3
Imports: MASS
Suggests: coin, foreign, haven, lme4, stringdist
URL: https://github.com/sjPlot/sjmisc
BugReports: https://github.com/sjPlot/sjmisc/issues
Packaged: 2015-03-21 07:45:15 UTC; Luedeke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-22 08:07:48

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New package assertr with initial version 0.4
Package: assertr
Type: Package
Title: Assertive Programming for R Analysis Pipelines
Version: 0.4
Authors@R: person("Tony", "Fischetti", email="tony.fischetti@gmail.com", role = c("aut", "cre"))
Maintainer: Tony Fischetti
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
URL: https://github.com/tonyfischetti/assertr
BugReports: https://github.com/tonyfischetti/assertr/issues
License: MIT + file LICENSE
LazyData: TRUE
Imports: dplyr,
Suggests: knitr, testthat, magrittr
VignetteBuilder: knitr
Packaged: 2015-03-21 19:02:19 UTC; tonyfischetti
Author: Tony Fischetti [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-22 08:03:30

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Sat, 21 Mar 2015

New package UNF with initial version 2.0
Package: UNF
Version: 2.0
Title: Tools for Creating Universal Numeric Fingerprints for Data
Date: 2015-03-21
Authors@R: c(person("Thomas", "Leeper", role = c("aut","cre"), email = "thosjleeper@gmail.com"), person("Micah", "Altman", role = c("aut")))
Description: Computes a universal numeric fingerprint (UNF) for an R data object. UNF is a cryptographic hash or signature that can be used to uniquely identify (a version of) a rectangular dataset, or a subset thereof. UNF can be used, in tandem with a DOI, to form a persistent citation to a versioned dataset.
Depends: R (>= 2.0)
Imports: base64enc, digest, tools
Suggests: knitr, testthat
License: GPL-2
URL: https://github.com/leeper/UNF
BugReports: https://github.com/leeper/UNF/issues
VignetteBuilder: knitr
Packaged: 2015-03-21 12:48:26 UTC; Thomas
Author: Thomas Leeper [aut, cre], Micah Altman [aut]
Maintainer: Thomas Leeper
NeedsCompilation: no
X-CRAN-History: Archived and orphaned long ago (last update was in 2009). The original maintainer was Micah Altman.
Repository: CRAN
Date/Publication: 2015-03-21 14:23:31

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Fri, 20 Mar 2015

New package hierDiversity with initial version 0.1
Package: hierDiversity
Version: 0.1
Date: 2015-03-11
Title: Hierarchical Multiplicative Partitioning of Complex Phenotypes
Author: Zachary Marion, James Fordyce, and Benjamin Fitzpatrick
Maintainer: Zachary Marion
Description: Hierarchical group-wise partitioning of phenotypic diversity into within-group (alpha), among-group (beta), and pooled-total (gamma) components using Hill numbers. Turnover and overlap are also calculated as standardized alternatives to beta diversity. Hierarchical bootstrapping is used to approximate uncertainty around each diversity component.
License: GPL (>= 2)
Packaged: 2015-03-20 15:33:23 UTC; Squeakums
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-20 18:05:19

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New package eurostat with initial version 1.0.15
Package: eurostat
Type: Package
Title: Tools for Eurostat Open Data
Version: 1.0.15
Date: 2015-03-20
Authors@R: c( person("Lahti", "Leo", email = "louhos@googlegroups.com", role = c("aut", "cre")), person("Biecek", "Przemyslaw" , role = "aut"), person("Kainu", "Markus", role = "aut"), person("Huovari", "Janne", role = "aut"))
MailingList: rOpenGov
Description: Tools to download data from the Eurostat database http://ec.europa.eu/eurostat/ together with search and manipulation utilities.
License: BSD_2_clause + file LICENSE
Depends: R (>= 3.0.2)
Imports: plyr, tidyr
Suggests: knitr, mapproj, plotrix, reshape2, rmarkdown, ggplot2, testthat
URL: https://github.com/ropengov/eurostat
BugReports: https://github.com/ropengov/eurostat/issues
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-03-20 08:38:31 UTC; lei
Author: Lahti Leo [aut, cre], Biecek Przemyslaw [aut], Kainu Markus [aut], Huovari Janne [aut]
Maintainer: Lahti Leo
Date/Publication: 2015-03-20 14:32:57

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New package biosignalEMG with initial version 1.0
Package: biosignalEMG
Type: Package
Title: Standard Processing Tools for Electromyogram Signals
Version: 1.0
Date: 2015-03-07
Author: Jose Antonio Guerrero Diaz de Leon, Jorge Eduardo Macias Diaz
Maintainer: Antonio Guerrero
Description: Data processing tools for electromyogram (EMG) signals to compute the rectified, integrated and averaged EMG. Tools to plot the ensembled average EMG.
License: GPL (>= 2)
Suggests: signal
Packaged: 2015-03-19 23:17:27 UTC; antoniog
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-20 10:17:24

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Thu, 19 Mar 2015

New package GAR with initial version 1.0
Package: GAR
Type: Package
Title: Authorize and Request Google Analytics Data
Version: 1.0
Date: 2015-03-18
Author: Andrew Geisler
Maintainer: Andrew Geisler
BugReports: https://github.com/andrewgeisler/GAR/issues
Description: The functions included are used to obtain initial authentication with Google Analytics as well as simple and organized data retrieval from the API. Allows for retrieval from multiple profiles at once.
License: GPL-2
Depends: httr, jsonlite
NeedsCompilation: no
Packaged: 2015-03-19 16:27:52 UTC; andrewgeisler
Repository: CRAN
Date/Publication: 2015-03-20 00:12:53

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New package VarSelLCM with initial version 1.0
Package: VarSelLCM
Type: Package
Version: 1.0
Date: 2015-03-19
Author: Matthieu Marbac and Mohammed Sedki
Title: Variable Selection for Model-Based Clustering using the Integrated Complete-Data Likelihood of a Latent Class Model
Description: Variable Selection for model-based clustering by using a mixture model of Gaussian distributions assuming conditional independence between variables. The algorithm carries out the model selection by optimizing the MICL criterion which has a closed form for such a distribution.
Maintainer: Mohammed Sedki
Imports: methods, Rcpp (>= 0.11.1), parallel, mclust
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2)
ByteCompile: true
LazyLoad: yes
Collate: 'ICLexact.R' 'RcppExports.R' 'VSLCM_Classes.R' 'VSLCM_initialization.R' 'VarSelLCM.R' 'Print.R' 'Summary.R' 'onAttach.R'
Packaged: 2015-03-19 13:58:52 UTC; sedki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-19 23:47:39

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New package systemicrisk with initial version 0.2
Package: systemicrisk
Type: Package
Title: A Toolbox for Systemic Risk
Version: 0.2
Date: 2015-03-19
Author: Axel Gandy and Luitgard A.M. Veraart
Maintainer: Axel Gandy
Description: A toolbox for systemic risk based on liabilities matrices. Contains a Gibbs sampler for liabilities matrices where only row and column sums of the liabilities matrix are observed.
License: GPL-3
Imports: Rcpp (>= 0.11.2), lpSolve
LinkingTo: Rcpp
Suggests: testthat, knitr
VignetteBuilder: knitr
Packaged: 2015-03-19 20:59:36 UTC; agandy
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-20 00:02:28

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New package prais with initial version 0.1.1
Package: prais
Type: Package
Title: Prais-Winsten Estimation Procedure for AR(1) Serial Correlation
Version: 0.1.1
Date: 2015-03-18
Author: Franz Mohr
Maintainer: Franz Mohr
Description: The Prais-Winsten estimation procedure takes into account serial correlation of type AR(1) in a linear model. The procedure is an iterative method that recursively estimates the beta coefficients and the error autocorrelation of the specified model until convergence of rho, i.e. the AR(1) coefficient, is attained. All estimates are obtained by OLS.
Depends: base, stats
License: GPL-2
Packaged: 2015-03-19 23:04:23 UTC; franz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-20 00:08:02

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New package phylocurve with initial version 1.0.0
Package: phylocurve
Version: 1.0.0
Date: 2015-03-19
Title: Phylogenetic Comparative Methods for Function-Valued and Other High-Dimensional Traits
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
License: GPL (>= 2)
URL: http://www.phylocurve.org
Imports: ape, geiger, phytools, abind, phylolm
Packaged: 2015-03-19 17:43:48 UTC; Eric
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-19 23:52:49

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New package mapfit with initial version 0.9.6
Package: mapfit
Version: 0.9.6
Date: 2015-03-19
Title: A Tool for PH/MAP Parameter Estimation
Type: Package
Author: Hiroyuki OKAMURA
Maintainer: Hiroyuki OKAMURA
Description: Estimation methods for phase-type distribution (PH) and Markovian arrival process (MAP) from empirical data (point and grouped data) and density function.
Depends: methods, Matrix
Encoding: UTF-8
License: GPL (>= 2)
Packaged: 2015-03-19 16:28:05 UTC; okamu
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-19 20:39:55

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New package james.analysis with initial version 1.0.0
Package: james.analysis
Type: Package
Title: Analysis Tools for the 'JAMES' Framework
Version: 1.0.0
Date: 2015-03-19
Author: Herman De Beukelaer
Maintainer: Herman De Beukelaer
Description: Analyze and visualize results of studies performed with the analysis tools in 'JAMES', a modern object-oriented Java framework for discrete optimization using local search metaheuristics (see http://www.jamesframework.org).
License: MIT + file LICENSE
Depends: R (>= 2.10), graphics (>= 2.15.3)
Imports: rjson (>= 0.2.14), naturalsort (>= 0.1.2)
Suggests: testthat (>= 0.9.1)
LazyData: true
Packaged: 2015-03-19 16:24:20 UTC; hdbeukel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-20 00:04:39

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New package Interatrix with initial version 1.0
Package: Interatrix
Type: Package
Title: Compute Chi-Square Measures with Corrections
Version: 1.0
Date: 2015-03-19
Author: Aurélie Siberchicot, Eléonore Hellard, Dominique Pontier, David Fouchet and Franck Sauvage
Maintainer: Aurélie Siberchicot
Description: Chi-square tests are computed with corrections.
Depends: R (>= 2.14)
Imports: MASS, tcltk, tkrplot, tools
Suggests: doParallel, foreach
License: GPL (>= 2)
Encoding: UTF-8
Packaged: 2015-03-19 09:33:31 UTC; aurelie
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-19 11:19:39

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New package eco with initial version 3.1-7
Package: eco
Version: 3.1-7
Date: 2015-3-4
Title: Ecological Inference in 2x2 Tables
Author: Kosuke Imai , Ying Lu , Aaron B Strauss .
Maintainer: Ying Lu
Depends: R (>= 2.0), MASS, utils
Description: We implement the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008, 2011) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
URL: http://imai.princeton.edu/software/eco.html
Packaged: 2015-03-05 04:04:38 UTC; kimai
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-19 09:46:08

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New package pipe.design with initial version 0.1
Package: pipe.design
Type: Package
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE Design
Version: 0.1
Date: 2015-03-18
Author: Michael Sweeting
Maintainer: Michael Sweeting
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
License: GPL (>= 2)
LazyLoad: yes
Depends: ggplot2 (>= 0.9.2), gtools
Packaged: 2015-03-18 22:14:41 UTC; michaels
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-19 06:52:07

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Wed, 18 Mar 2015

New package CARLIT with initial version 1.0
Package: CARLIT
Type: Package
Title: Ecological Quality Ratios Calculation and Plot
Version: 1.0
Date: 2015-03-17
Author: Danilo Pecorino, Gina de la Fuente Mancebo, Xavier Torras
Maintainer: Danilo Pecorino
Description: Functions to calculate and plot ecological quality ratios (EQR) as specified by Ballesteros et al. 2007.
License: GPL-2
Packaged: 2015-03-18 13:33:54 UTC; danilo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-18 18:01:26

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Tue, 17 Mar 2015

New package staTools with initial version 0.1.0
Package: staTools
Title: Statistical Tools for Social Network Analysis
Version: 0.1.0
Author: Alessandro Bessi
Maintainer: Alessandro Bessi
Description: A collection of statistical tools for social network analysis, with strong emphasis on the analysis of discrete powerlaw distributions and statistical hypothesis tests.
Depends: R (>= 3.1.1)
License: GPL (>= 2)
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, VGAM, magicaxis
Packaged: 2015-03-17 18:46:20 UTC; alessandro
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-17 21:00:02

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New package gapminder with initial version 0.1.0
Package: gapminder
Title: Gapminder Data
Version: 0.1.0
Authors@R: person("Jennifer", "Bryan", email = "jenny@stat.ubc.ca", role = c('aut', 'cre'))
Description: An excerpt of the data available at Gapminder.org. For each of 142 countries, the package provides values for life expectancy, GDP per capita, and population, every five years, from 1952 to 2007.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
URL: https://github.com/jennybc/gapminder, http://www.gapminder.org/data/
BugReports: https://github.com/jennybc/gapminder/issues
Suggests: dplyr, gdata, ggplot2, tidyr, testthat
Packaged: 2015-03-17 17:33:44 UTC; jenny
Author: Jennifer Bryan [aut, cre]
Maintainer: Jennifer Bryan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 20:59:55

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New package EntropyExplorer with initial version 1.0
Package: EntropyExplorer
Type: Package
Title: Tools for Exploring Differential Shannon Entropy, Differential Coefficient of Variation and Differential Expression
Version: 1.0
Date: 2015-3-16
Author: Kai Wang, Charles A. Phillips, Arnold M. Saxton and Michael A. Langston
Maintainer: Kai Wang
Depends: R (>= 3.0)
Description: Rows of two matrices are compared for Shannon entropy, coefficient of variation, and expression. P-values can be requested for all metrics.
License: GPL-3
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 20:45:35

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New package atsd with initial version 1.0.8441
Package: atsd
Title: Support Querying Axibase Time-Series Database
Version: 1.0.8441
Date: 2015-03-16
Author: Axibase Corporation
Maintainer: Mikhail Zvagelsky
URL: https://github.com/axibase/atsd-api-r/
Description: Provides functions for retrieving time-series and related meta-data such as entities, metrics, and tags from the Axibase Time-Series Database (ATSD). ATSD is a non-relational clustered database used for storing performance measurements from IT infrastructure resources: servers, network devices, storage systems, and applications.
Depends: R (>= 3.1.2)
License: Apache License 2.0
Imports: RCurl (>= 1.95.4.5), httr (>= 0.6.1)
Suggests: zoo, knitr, pander
VignetteBuilder: knitr
Packaged: 2015-03-17 07:47:35 UTC; mikhail
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 10:29:33

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New package tsallisqexp with initial version 0.9-1
Package: tsallisqexp
Type: Package
Title: Tsallis q-Exp Distribution
Version: 0.9-1
Author: Cosma Shalizi [aut] (original R code), Christophe Dutang [cre] (R code packaging)
Maintainer: Christophe Dutang
Description: Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Depends: R (>= 3.0.0)
License: GPL (>= 2)
Packaged: 2015-03-17 06:41:38 UTC; dutangc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 07:53:46

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New package Coxnet with initial version 0.1
Package: Coxnet
Type: Package
Title: Regularized Cox Model
Version: 0.1
Date: 2015-03-16
Author: Xiang Li, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li
Description: Cox model regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty. In addition, it efficiently solves an approximate L0 variable selection based on truncated likelihood function. Moreover, it can also handle the adaptive version of these regularization forms, such as adaptive lasso and net adjusting for signs of linked coefficients. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.5)
LinkingTo: Rcpp, RcppEigen
Depends: Matrix (>= 1.1-5)
Packaged: 2015-03-16 22:20:34 UTC; Li Xiang
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-17 07:36:38

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Mon, 16 Mar 2015

New package kfigr with initial version 1.1.0
Package: kfigr
Title: Integrated Code Chunk Anchoring and Referencing for R Markdown Documents
Version: 1.1.0
Date: 2015-03-16
Author: Michael Koohafkan
Maintainer: Michael Koohafkan
Description: A streamlined cross-referencing system for R Markdown documents generated with 'knitr'. R Markdown is an authoring format for generating dynamic content from R. 'kfigr' provides a hook for anchoring code chunks and a function to cross-reference document elements generated from said chunks, e.g. figures and tables.
Depends: R (>= 3.1.0)
Imports: knitr (>= 1.6)
Suggests: ggplot2
LazyData: true
VignetteBuilder: knitr
License: GPL (>= 3)
URL: https://github.com/mkoohafkan/kfigr
BugReports: https://github.com/mkoohafkan/kfigr/issues
Packaged: 2015-03-16 17:04:31 UTC; Michael
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 00:20:06

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New package radiant with initial version 0.1.71
Package: radiant
Title: Business Analytics using R and Shiny
Version: 0.1.71
Date: 2015-3-16
Authors@R: person("Vincent", "Nijs", , "radiant@rady.ucsd.edu", c("aut", "cre"))
Description: A platform-independent browser-based interface for business analytics in R, based on the Shiny package.
Depends: R (>= 3.1.0), lubridate (>= 1.3.3), ggplot2 (>= 1.0.0), dplyr (>= 0.4.1), magrittr (>= 1.5)
Imports: car (>= 2.0.22), MASS (>= 7.3), gridExtra (>= 0.9.1), AlgDesign (>= 1.1.7.3), GPArotation (>= 2014.11.1), psych (>= 1.4.8.11), wordcloud (>= 2.5), markdown (>= 0.7.4), knitr (>= 1.8), ggdendro (>= 0.1.15), broom (>= 0.3.6), tidyr (>= 0.2.0), pryr (>= 0.1), shiny (>= 0.11.1), shinyAce (>= 0.1.0)
Suggests: rmarkdown (>= 0.4.2), ggvis (>= 0.4), testthat (>= 0.9.1)
URL: https://github.com/mostly-harmless/radiant, http://mostly-harmless.github.io/radiant/
BugReports: https://github.com/mostly-harmless/radiant/issues
License: AGPL-3 | CC BY-NC-SA 4.0
LazyData: true
Packaged: 2015-03-16 18:18:05 UTC; vnijs
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-17 00:11:12

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New package ROCS with initial version 1.2
Package: ROCS
Type: Package
Title: Receiver Operating Characteristics Surface
Version: 1.2
Date: 2015-03-08
Author: Tianwei Yu
Maintainer: Tianwei Yu
Description: Plots the Receiver Operating Characteristics Surface for high-throughput class-skewed data, calculates the Volume under the Surface (VUS) and the FDR-Controlled Area Under the Curve (FCAUC), and conducts tests to compare two ROC surfaces.
License: GPL-2
Depends: rgl
Packaged: 2015-03-16 15:08:05 UTC; tianwei
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-16 17:15:15

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New package VCA with initial version 1.1
Package: VCA
Version: 1.1
Date: 2015-03-16
Title: Variance Component Analysis
Author: Andre Schuetzenmeister
Maintainer: Andre Schuetzenmeister
Depends: R (>= 3.0.0), stats
Imports: Matrix, numDeriv
Description: ANOVA-type estimation (prediction) of random effects and variance components in linear mixed models, is implemented. Random models, a sub-set of mixed models, can be fit applying a Variance Component Analysis (VCA). This is a special type of analysis frequently used in verifying the precision performance of diagnostics. The Satterthwaite approximation of the total degrees of freedom is implemented. There are several functions for extracting, random effects, fixed effects, variance-covariance matrices of random and fixed effects. Residuals can be extracted as raw, standardized and studentized residuals. Additionally, a variability chart is implemented for visualizing the variability in sub-classes emerging from an experimental design ('varPlot').
License: GPL (>= 3)
Collate: 'plot.R' 'vca.R'
Packaged: 2015-03-16 07:51:45 UTC; schueta6
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-16 10:29:47

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New package nnlasso with initial version 0.1
Package: nnlasso
Type: Package
Title: Non-Negative Lasso and Elastic Net Penalized Generalized Linear Models
Version: 0.1
Date: 2015-03-13
Author: B N Mandal and Jun Ma
Maintainer: B N Mandal
Depends: R (>= 3.1.3)
Description: Estimates of coefficients of lasso penalized linear regression and generalized linear models subject to non-negativity constraints on the parameters using multiplicative iterative algorithm. Entire regularization path for a sequence of lambda values can be obtained. Functions are available for creating plots of regularization path, cross validation and estimating coefficients at a given lambda value. There is also provision for obtaining standard error of coefficient estimates.
License: GPL (>= 2)
Packaged: 2015-03-16 06:56:45 UTC; Lenovo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-16 08:46:31

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Sun, 15 Mar 2015

New package jmetrik with initial version 1.0
Package: jmetrik
Type: Package
Title: Tools for Interacting with 'jMetrik'
Version: 1.0
Date: 2015-03-13
Author: J. Patrick Meyer
Maintainer: J. Patrick Meyer
Description: The main purpose of this package is to make it easy for userR's to interact with 'jMetrik' an open source application for psychometric analysis. For example it allows useR's to write data frames to file in a format that can be used by 'jMetrik'. It also allows useR's to read *.jmetrik files (e.g. output from an analysis) for follow-up analysis in R. The *.jmetrik format is a flat file that includes a multiline header and the data as comma separated values. The header includes metadata about the file and one row per variable with the following information in each row: variable name, data type, item scoring, special data codes, and variable label.
License: GPL (>= 3)
Packaged: 2015-03-14 22:55:58 UTC; Patrick
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-15 06:16:16

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New package glmgraph with initial version 1.0.0
Package: glmgraph
Type: Package
Title: Graph-Constrained Regularization for Sparse Generalized Linear Models
Version: 1.0.0
Date: 2015-03-14
Author: Li Chen, Jun Chen
Maintainer: Li Chen
Description: We propose to use sparse regression model to achieve variable selection while accounting for graph-constraints among coefficients. Different linear combination of a sparsity penalty(L1) and a smoothness(MCP) penalty has been used, which induces both sparsity of the solution and certain smoothness on the linear coefficients.
License: GPL-2
Depends: Rcpp (>= 0.11.0)
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2015-03-15 00:55:00 UTC; lichen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-15 06:16:18

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Sat, 14 Mar 2015

New package dmm with initial version 1.5-1
Package: dmm
Type: Package
Title: Dyadic Mixed Model for Pedigree Data
Version: 1.5-1
Date: 2015-03-12
Author: Neville Jackson
Maintainer: Neville Jackson
Description: Dyadic mixed model analysis with multi-trait responses and pedigree-based partitioning of individual variation into a range of environmental and genetic variance components for individual and maternal effects.
Depends: MASS, Matrix, nadiv, robustbase, pls
License: GPL-2 | GPL (>= 2) | GPL-3
NeedsCompilation: no
Packaged: 2015-03-14 09:56:14 UTC; nevj
Repository: CRAN
Date/Publication: 2015-03-14 14:25:11

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Thu, 12 Mar 2015

New package CFC with initial version 0.7.0
Package: CFC
Type: Package
Title: Cause-Specific Framework for Competing-Risk Analysis
Version: 0.7.0
Date: 2015-03-11
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: Functions for combining survival curves of competing risks to produce cumulative incidence and event-free probability functions, and for summarizing and plotting the results. Survival curves can be either time-denominated or probability-denominated. Point estimates as well as Bayesian, sample-based representations of survival can utilize this framework.
License: GPL (>= 2)
Suggests: survival, BSGW, BayesMixSurv
Imports: abind
Packaged: 2015-03-12 21:53:51 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-12 23:16:34

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New package RxnSim with initial version 1.0
Package: RxnSim
Type: Package
Title: Functions to Compute Chemical Reaction Similarity
Version: 1.0
Date: 2015-03-12
Authors@R: person("Varun", "Giri", role=c("aut", "cre"), email="varungiri@gmail.com")
Maintainer: Varun Giri
Description: RxnSim provides methods to compute chemical similarity between two or more reactions and molecules. Molecular similarity is computed based on structural features. Reaction similarity is a function of similarities of participating molecules. The package additionally provides functionality to mask chemical substructures for weighted similarity computations. It uses rCDK and fingerprint packages for cheminformatics functionality.
License: GPL
Depends: R (>= 2.5.0)
Imports: rJava, fingerprint, rcdk (>= 3.3.2)
Packaged: 2015-03-12 07:21:27 UTC; varungiri
Author: Varun Giri [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-12 09:37:28

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Wed, 11 Mar 2015

New package NORRRM with initial version 1.0.0
Package: NORRRM
Type: Package
Title: Geochemical Toolkit for R
Version: 1.0.0
Date: 2015-01-29
Author: Renee Gonzalez Guzman
Maintainer: Renee Gonzalez Guzman
Imports: ggplot2,SDMTools
Description: CIPW Norm (acronym from the surnames of the authors: Cross, Iddings, Pirrson and Washington) is the most commonly used calculation algorithm to estimate the standard mineral assemblages for igneous rocks from its geochemical composition. NORRRM (acronym from noRm, R language and Renee) is the highly consistent program to calculate the CIPW Norm.
Depends: R (>= 3.1.1)
License: GPL (>= 3)
Packaged: 2015-03-11 03:18:51 UTC; linus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-11 21:49:49

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New package texmexseq with initial version 0.1
Package: texmexseq
Type: Package
Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Version: 0.1
Date: 2015-03-11
Author: Scott Olesen
Maintainer: Scott Olesen
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
License: GPL-3
URL: http://almlab.mit.edu/texmex.html
NeedsCompilation: yes
Packaged: 2015-03-11 16:21:01 UTC; scott
Repository: CRAN
Date/Publication: 2015-03-11 17:59:11

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New package seismicRoll with initial version 1.0.1
Type: Package
Package: seismicRoll
Version: 1.0.1
Title: Fast Rolling Functions for Seismology using Rcpp
Authors@R: c( person("Jonathan", "Callahan", email="jonathan.s.callahan@gmail.com", role=c("aut","cre")), person("Rob", "Casey", email="rob@iris.washington.edu", role=c("aut")), person("Mary", "Templeton", email="met@iris.washington.edu", role=c("aut")) )
Author: Jonathan Callahan [aut, cre], Rob Casey [aut], Mary Templeton [aut]
Maintainer: Jonathan Callahan
Depends: R (>= 2.14.1), Rcpp (>= 0.10.4)
Suggests: microbenchmark
LinkingTo: Rcpp
Description: Fast versions of seismic analysis functions that 'roll' over a vector of values. See the RcppRoll package for alternative versions of basic statistical functions such as rolling mean, median, etc.
Collate: seismicRoll.R RcppExports.R findOutliers.R roll_hampel.R roll_mean.R roll_median.R roll_sd.R roll_stalta.R
License: GPL-2
Repository: CRAN
Packaged: 2015-03-11 15:44:41 UTC; jonathan
NeedsCompilation: yes
Date/Publication: 2015-03-11 17:59:03

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New package rgrass7 with initial version 0.1-0
Package: rgrass7
Version: 0.1-0
Date: 2015-03-11
Title: Interface Between GRASS 7 Geographical Information System and R
Authors@R: c( person("Roger", "Bivand", role = c("cre", "aut"), email = "Roger.Bivand@nhh.no"), person("Rainer", "Krug", role = "ctb", email="Rainer@krugs.de"), person("Markus", "Neteler", role = "ctb"))
Description: Interpreted interface between GRASS 7 geographical information system and R, based on starting R from within the GRASS environment, or running free-standing R in a temporary GRASS location; the package provides facilities for using all GRASS commands from the R command line. This package may not be used for GRASS 6, for which spgrass6 should be used.
Depends: R (>= 2.12), sp (>= 0.9), XML
Suggests: rgdal (>= 0.8-8)
SystemRequirements: GRASS (>= 7)
License: GPL (>= 2)
URL: http://grass.osgeo.org/
Collate: AAA.R options.R rgrass.R bin_link.R vect_link.R initGRASS.R xml1.R
Packaged: 2015-03-10 20:15:06 UTC; rsb
Author: Roger Bivand [cre, aut], Rainer Krug [ctb], Markus Neteler [ctb]
Maintainer: Roger Bivand
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-11 11:04:53

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New package graphicalVAR with initial version 0.1.1
Package: graphicalVAR
Type: Package
Title: Graphical VAR for Experience Sampling Data
Version: 0.1.1
Date: 2015-03-05
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical VAR model in combination with LASSO and EBIC.
License: GPL (>= 2)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp (>= 0.11.3), Matrix, glasso, glmnet, mvtnorm, qgraph (>= 1.3.1)
Depends: R (>= 3.1.0)
NeedsCompilation: yes
Packaged: 2015-03-11 10:07:43 UTC; sacha
Repository: CRAN
Date/Publication: 2015-03-11 11:26:08

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New package MCL with initial version 1.0
Package: MCL
Type: Package
Title: Markov Cluster Algorithm
Version: 1.0
Date: 2015-03-11
Author: Martin L. Jäger
Maintainer: Ronja Foraita
Description: Contains the Markov cluster algorithm (MCL) for identifying clusters in networks and graphs. The algorithm simulates random walks on a (n x n) matrix as the adjacency matrix of a graph. It alternates an expansion step and an inflation step until an equilibrium state is reached.
License: GPL (>= 2)
Depends: R (>= 2.10.0)
Imports: expm
Encoding: UTF-8
Packaged: 2015-03-11 08:27:50 UTC; foraita
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-11 09:56:32

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Tue, 10 Mar 2015

New package gsheet with initial version 0.1.0
Package: gsheet
Type: Package
Title: Download Google Sheets Using Just the URL
Version: 0.1.0
Date: 2015-03-09
Authors@R: person("Max", "Conway", email = "conway.max1@gmail.com", role = c("aut", "cre"))
Description: Simple package to download Google Sheets using just the sharing link. Spreadsheets can be downloaded as a data frame, or as plain text to parse manually. Google Sheets is the new name for Google Docs Spreadsheets.
License: GPL-3
URL: https://github.com/maxconway/gsheet
BugReports: https://github.com/maxconway/gsheet/issues
Imports: dplyr, rvest, stringr
Suggests: testthat
Packaged: 2015-03-10 12:18:03 UTC; mjc233
Author: Max Conway [aut, cre]
Maintainer: Max Conway
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 23:13:49

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New package lmfor with initial version 1.1
Package: lmfor
Type: Package
Title: Functions for Forest Biometrics
Version: 1.1
Date: 2015-03-10
Author: Lauri Mehtatalo
Maintainer: Lauri Mehtatalo
Depends: stats4, nlme, MASS
Description: Functions related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, and recovery of tree diameter distributions. Datasets on tree height-diameter relationship and light response of moss photosynthesis are included.
License: GPL-2
Packaged: 2015-03-10 14:50:03 UTC; lamehtat
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 17:47:31

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New package import with initial version 1.0.1
Package: import
Type: Package
Title: An Import Mechanism for R
Version: 1.0.1
Date: 2015-03-10
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache
Description: This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import package bridges some of the gap between using library (or require) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment.
License: MIT + file LICENSE
ByteCompile: TRUE
Packaged: 2015-03-10 14:53:33 UTC; shb
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 17:51:42

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New package histmdl with initial version 0.3-2
Package: histmdl
Type: Package
Title: A Most Informative Histogram-Like Model
Version: 0.3-2
Date: 2015-03-10
Author: Jouke Witteveen
Maintainer: Jouke Witteveen
Description: Using the MDL principle, it is possible to estimate parameters for a histogram-like model. The package contains the implementation of such an estimation method.
License: GPL (>= 2)
ByteCompile: yes
Packaged: 2015-03-10 08:37:08 UTC; jouke
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-10 11:14:10

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New package blatr with initial version 1.0
Package: blatr
Type: Package
Title: Send Emails Using "Blat" for Windows
Version: 1.0
Date: 2014-03-17
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache
Description: A wrapper around the Blat command line SMTP mailer for Windows. Blat is public domain software, but be sure to read the license before use. It can be found at the Blat website http://www.blat.net.
License: MIT + file LICENSE
OS_type: windows
ByteCompile: Yes
Packaged: 2015-03-10 08:58:26 UTC; shb
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 11:22:37

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New package vmsbase with initial version 2.0
Package: vmsbase
Version: 2.0
License: GPL (>= 2)
Description: The tools you need to process, analyze, combine, integrate and plot your fishery data: the georeferenced dataset from the Vessel Monitoring System (VMS), from the Automatic Information System (AIS) or other tracking devices, as well as the catches or landings dataset from the Logbook or Vessel Register. Package 'vmsbase' is equipped by Viewer Tools to visually inspect data at different steps of the analyses and to produce effective outputs for reports and scientific publications. Viewers are conceived to show the VMS pings, to visualize single or multiple tracks for fishing vessels, or to represent the VMS data on Google Viewer, so that the user can produce easy to interpret and more realistic visualization of both fishing effort and effort behaviour. Package 'vmsbase' represents the implementation of several R routines which have been developed by the "Tor Vergata" University of Rome Team involved in the Italian National Program for the Data Collection Framework for Fisheries Data between 2009-2012.
Title: GUI Tools to Process, Analyze and Plot Fisheries Data
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea
Date: 2015-03-10
Depends: sqldf, ggmap, mapdata, maps
Imports: marmap, intervals, methods, plotrix, sp, foreign, cluster, cairoDevice, ggplot2, DBI, RSQLite, fields, gsubfn, AMORE, ecodist, gWidgets, gWidgetsRGtk2, chron, maptools, outliers, PBSmapping, R6, grid, VennDiagram, gmt
URL: http://www.vmsbase.org/
Packaged: 2015-03-10 08:12:22 UTC; fish_team
ByteCompile: yes
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 09:25:05

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New package MRIaggr with initial version 1.0
Package: MRIaggr
Type: Package
Title: Management, Display, and Processing of Medical Imaging Data
Version: 1.0
Date: 2015-02-27
Author: Brice Ozenne
Maintainer: Brice Ozenne
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
License: GPL-3
Depends: R (>= 2.10), Rcpp
Imports: methods, stats4, RANN, spam, Matrix, ROCR, fields, mritc, oro.dicom, oro.nifti
Suggests: rgl
LazyLoad: yes
LinkingTo: Rcpp, RcppArmadillo
Collate: 'Generic_functions.R' 'RcppExports.R' 'Associated_functions.R' 'GR_functions.R' 'Class_Carto3D.R' 'Class_MRIaggr.R'
Packaged: 2015-03-09 07:46:39 UTC; ozennebr
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-10 09:24:57

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New package showtextdb with initial version 1.0
Package: showtextdb
Type: Package
Title: Font Files for the 'showtext' Package
Version: 1.0
Date: 2015-03-09
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu
Description: Providing font files that are needed by the 'showtext' package.
Depends: sysfonts
License: Apache License (>= 2.0)
Copyright: see file COPYRIGHTS
Packaged: 2015-03-10 01:08:39 UTC; qyx
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-10 07:01:27

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Mon, 09 Mar 2015

New package SensusR with initial version 1.0
Package: SensusR
Type: Package
Title: Sensus Analytics
Version: 1.0
Date: 2015-03-05
Author: Matthew S. Gerber
Maintainer: Matthew S. Gerber
Description: Provides access and analytic functions for Sensus data.
License: GPL-3
Copyright: The Rector and Visitors of the University of Virginia
URL: https://github.com/MatthewGerber/sensus/wiki
Imports: jsonlite (>= 0.9.14), lubridate (>= 1.3.3), rworldmap (>= 1.3-1), plyr (>= 1.8.1), sp (>= 1.0-16)
NeedsCompilation: no
Packaged: 2015-03-09 19:12:21 UTC; matt
Repository: CRAN
Date/Publication: 2015-03-09 20:43:37

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New package histmdl with initial version 0.3-1
Package: histmdl
Type: Package
Title: A Most Informative Histogram-Like Model
Version: 0.3-1
Date: 2015-02-19
Author: Jouke Witteveen
Maintainer: Jouke Witteveen
Description: Using the MDL principle, it is possible to estimate parameters for a histogram-like model. The package contains the implementation of such an estimation method.
License: GPL (>= 2)
ByteCompile: yes
Packaged: 2015-03-09 14:04:34 UTC; jouke
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-09 16:24:03

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New package cOde with initial version 0.1
Package: cOde
Type: Package
Title: Automated C Code Generation for Use with the "deSolve" and "bvpSolve"" Packages
Version: 0.1
Depends: R (>= 3.0)
Suggests: deSolve, bvpSolve
Date: 2015-03-05
Author: Daniel Kaschek
Maintainer: Daniel Kaschek
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". The package also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
License: GPL (>= 2)
Packaged: 2015-03-09 11:50:27 UTC; kaschek
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-09 14:21:45

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New package inferference with initial version 0.4.61
Package: inferference
Type: Package
Title: Methods for Causal Inference with Interference
Version: 0.4.61
Date: 2015-03-08
Author: Bradley Saul
Maintainer: Bradley Saul
Description: Provides methods for estimating causal effects in the presence of interference. Currently it implements the IPW estimators proposed by EJ Tchetgen Tchetgen and TJ Vanderweele in "On causal inference in the presence of interference" (Statistical Methods in Medical Research, 21(1) 55-75).
Depends: R (>= 3.1)
Imports: numDeriv (>= 2012.9-1), lme4 (>= 1.1-6), Formula (>= 1.1-2)
License: GPL (>= 2)
Suggests: testthat, knitr
VignetteBuilder: knitr
LazyData: true
Packaged: 2015-03-08 21:23:57 UTC; bradley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-09 07:39:44

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Sun, 08 Mar 2015

New package GameTheory with initial version 1.0
Package: GameTheory
Type: Package
Title: Cooperative Game Theory
Version: 1.0
Date: 2015-02-04
Author: Sebastian Cano-Berlanga
Maintainer: Sebastian Cano-Berlanga
Depends: lpSolveAPI, combinat, gtools, ineq, kappalab
Description: Implementation of a common set of punctual solutions for Cooperative Game Theory.
License: GPL (>= 2)
URL: http://canoberlanga.com
Suggests: R.rsp
VignetteBuilder: R.rsp
Repository: CRAN
Packaged: 2015-03-07 22:32:12 UTC; sebastian
NeedsCompilation: no
Date/Publication: 2015-03-08 07:18:06

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Sat, 07 Mar 2015

New package SID with initial version 1.0
Package: SID
Type: Package
Title: Structural Intervention Distance
Version: 1.0
Date: 2015-03-07
Author: Jonas Peters
Encoding: UTF-8
Imports: pcalg, igraph, RBGL, Matrix
Maintainer: Jonas Peters
Description: The code computes the structural intervention distance (SID) between a true directed acyclic graph (DAG) and an estimated DAG. Definition and details about the implementation can be found in J. Peters and P. BĂĽhlmann: "Structural intervention distance (SID) for evaluating causal graphs", Neural Computation 27, pages 771-799, 2015.
License: FreeBSD
Packaged: 2015-03-07 14:35:03 UTC; jopeters
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-07 17:35:02

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Fri, 06 Mar 2015

New package webchem with initial version 0.0.1
Package: webchem
Type: Package
Title: Chemical Information from the Web
Version: 0.0.1
Date: 2015-03-05
Author: Eduard Szoecs
Maintainer: Eduard Szoecs
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
URL: https://github.com/EDiLD/webchem
BugReports: https://github.com/EDiLD/webchem/issues
License: MIT + file LICENSE
LazyLoad: yes
LazyData: yes
Imports: XML, RCurl, RJSONIO
Packaged: 2015-03-06 11:33:33 UTC; edisz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-06 17:50:54

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New package SDDE with initial version 1.0.0
Package: SDDE
Type: Package
Depends: R (>= 3.0), igraph, doParallel, foreach, iterators, parallel
Title: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
Version: 1.0.0
Date: 2015-03-01
Author: Etienne Lord, Margaux Le Cam, Eric Bapteste, Vladimir Makarenkov and Francois-Joseph Lapointe
Maintainer: Etienne Lord
Description: Compares the evolution of an original network X to an augmented network Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal paths and disconnected nodes.
License: GPL-3
LazyLoad: yes
Packaged: 2015-03-06 13:06:01 UTC; Etienne
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-06 17:41:51

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New package httk with initial version 1.1
Title: High-Throughput Toxicokinetics
Package: httk
Version: 1.1
Date: 3/5/2015
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Suggests: ggplot2
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics (TK) using data obtained from relatively high throughput, in vitro studies. Both physiologically-based (PBTK) and empirical (e.g., one compartment) TK models can be parameterized for sevral hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurment limitations. Functions are also provided for exporting PBTK models to SBML and JARNAC for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation (IVIVE) of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Maintainer: John Wambaugh
License: GPL-3
Packaged: 2015-03-06 15:46:56 UTC; jwambaug
LazyData: true
Imports: deSolve, msm
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-06 17:47:38

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New package pointRes with initial version 1.0.1
Package: pointRes
Type: Package
Title: Analyzing Pointer Years and Components of Resilience
Version: 1.0.1
Date: 2015-03-06
Author: Marieke van der Maaten-Theunissen and Ernst van der Maaten
Maintainer: Marieke van der Maaten-Theunissen
Description: Functions to calculate and plot event and pointer years as well as components of resilience. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.
License: GPL (>= 2)
Depends: R (>= 3.1.0), stats, ggplot2
Imports: gridExtra, plyr, TripleR
Suggests: dplR
Encoding: UTF-8
Repository: CRAN
Packaged: 2015-03-06 09:13:09 UTC; Marieke
NeedsCompilation: no
Date/Publication: 2015-03-06 12:33:33

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New package rscala with initial version 1.0.1
Package: rscala
Type: Package
Title: Bi-Directional Interface Between R and Scala with Callbacks
Version: 1.0.1
Date: 2015-03-05
Authors@R: c(person(given="David B.",family="Dahl",role=c("aut","cre"),email="dahl@stat.byu.edu"), person(family="Scala developers",role="ctb",comment="see http://scala-lang.org/"))
SystemRequirements: Java (>= 1.6)
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
License: GPL (>= 2) | BSD_3_clause + file LICENSE
NeedsCompilation: no
Packaged: 2015-03-06 06:42:38 UTC; dahl
Author: David B. Dahl [aut, cre], Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl
Repository: CRAN
Date/Publication: 2015-03-06 08:26:48

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New package RESS with initial version 1.0
Package: RESS
Type: Package
Title: Integrates R and Essentia
Version: 1.0
Date: 2015-03-03
Author: Ben Waxer
Maintainer: Ben Waxer
Description: Contains two functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.udb' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install.html.
License: LGPL-3
Packaged: 2015-03-06 00:33:03 UTC; ec2-user
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-06 08:20:41

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New package climwin with initial version 0.0.1
Package: climwin
Type: Package
Title: Climate Window Analysis
Version: 0.0.1
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Depends: R (>= 2.10), ggplot2, gridExtra
Imports: evd, lme4, lubridate, MuMIn, reshape
Suggests: testthat
License: GPL-2
Repository: CRAN
LazyData: True
Packaged: 2015-03-06 04:25:51 UTC; u5307828
NeedsCompilation: no
Date/Publication: 2015-03-06 08:27:13

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Thu, 05 Mar 2015

New package biogas with initial version 1.0
Package: biogas
Type: Package
Title: Analyze Biogas Data and Predict Biogas Production
Version: 1.0
Date: 2015-03-05
Author: Sasha D. Hafner, Charlotte Rennuit, Jin Mi Triolo, and Ali Heidarzadeh Vazifehkhoran.
Maintainer: Sasha D. Hafner
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
License: GPL-2
Packaged: 2015-03-05 21:25:54 UTC; sasha
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-06 00:44:06

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New package sadists with initial version 0.1.0
Package: sadists
Maintainer: Steven E. Pav
Authors@R: c(person(c("Steven", "E."), "Pav", role=c("aut","cre"), email="shabbychef@gmail.com"))
Version: 0.1.0
Date: 2015-03-05
License: LGPL-3
Title: Some Additional Distributions
BugReports: https://github.com/shabbychef/sadists/issues
Description: Provides the density, distribution, quantile and generation functions of some obscure probability distributions, including the doubly non-central t and F distributions; Lecoutre's lambda-prime and K-prime; the upsilon distribution; the (weighted) sum of non-central chi-squares to a power.
Depends: R (>= 3.0.2)
Imports: PDQutils (>= 0.1.1), hypergeo, orthopolynom
Suggests: testthat, ggplot2, knitr
URL: https://github.com/shabbychef/sadists
VignetteBuilder: knitr
Collate: 'cumulants.r' 'dnf.r' 'dnt.r' 'kprime.r' 'lambdap.r' 'moments.r' 'sadists.r' 'sumchisqpow.r' 'upsilon.r' 'utils.r'
Packaged: 2015-03-05 16:41:39 UTC; spav
Author: Steven E. Pav [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 22:18:18

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New package CAM with initial version 1.0
Package: CAM
Type: Package
Title: Causal Additive Model (CAM)
Version: 1.0
Date: 2015-03-03
Author: Jonas Peters and Jan Ernest
Encoding: UTF-8
Depends: glmnet, mboost, Matrix, parallel, mgcv
Maintainer: Jonas Peters
Description: The code takes an n x p data matrix and fits a Causal Additive Model (CAM) for estimating the causal structure of the underlying process. The output is a p x p adjacency matrix (a one in entry (i,j) indicates an edge from i to j). Details of the algorithm can be found in: P. BĂĽhlmann, J. Peters, J. Ernest: "CAM: Causal Additive Models, high-dimensional order search and penalized regression", Annals of Statistics 42:2526-2556, 2014.
License: FreeBSD
Packaged: 2015-03-05 17:14:16 UTC; jopeters
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 22:01:05

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New package Binarize with initial version 1.0
Package: Binarize
Type: Package
Title: Binarization of One-Dimensional Data
Version: 1.0
Date: 2015-03-05
Author: Stefan Mundus, Christoph Müssel, Ludwig Lausser, Tamara J. Blätte, Martin Hopfensitz, Hans A. Kestler
Maintainer: Hans Kestler
Description: Provides methods for the binarization of one-dimensional data and some visualization functions.
License: Artistic-2.0
LazyLoad: yes
Depends: methods, diptest
Encoding: UTF-8
Packaged: 2015-03-05 16:07:18 UTC; muessel
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-03-05 22:03:50

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New package KOGMWU with initial version 1.0
Package: KOGMWU
Type: Package
Title: Functional Summary and Meta-Analysis of Gene Expression Data
Version: 1.0
Date: 2015-03-02
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
Description: Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
License: GPL-3
Depends: R (>= 2.10), pheatmap
Packaged: 2015-03-05 07:12:15 UTC; c-monster
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 08:49:58

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New package gtop with initial version 0.2.0
Package: gtop
Type: Package
Title: Game-Theoretically OPtimal (GTOP) Reconciliation Method
Version: 0.2.0
Date: 2015-01-23
Author: Jairo Cugliari, Tim van Erven
Maintainer: Jairo Cugliari
Description: In hierarchical time series (HTS) forecasting, the hierarchical relation between multiple time series is exploited to make better forecasts. This hierarchical relation implies one or more aggregate consistency constraints that the series are known to satisfy. Many existing approaches, like for example bottom-up or top-down forecasting, therefore attempt to achieve this goal in a way that guarantees that the forecasts will also be aggregate consistent. This package provides with an implementation of the Game-Theoretically OPtimal (GTOP) reconciliation method proposed in van Erven and Cugliari (2015), which is guaranteed to only improve any given set of forecasts. This opens up new possibilities for constructing the forecasts. For example, it is not necessary to assume that bottom-level forecasts are unbiased, and aggregate forecasts may be constructed by regressing both on bottom-level forecasts and on other covariates that may only be available at the aggregate level.
License: GPL-2 | GPL-3
Depends: hts, quadprog, lassoshooting
Packaged: 2015-03-05 06:33:35 UTC; jairo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 07:40:24

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New package GLDreg with initial version 1.0.2
Package: GLDreg
Type: Package
Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Version: 1.0.2
Date: 2015-03-04
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su
Depends: GLDEX (>= 2.0.0.1)
Suggests: MASS, quantreg
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
License: GPL (>= 3)
Packaged: 2015-03-04 23:29:16 UTC; Steve
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 07:40:58

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Wed, 04 Mar 2015

New package clifro with initial version 2.4-0
Package: clifro
Type: Package
Title: Easily Download and Visualise Climate Data from CliFlo
Version: 2.4-0
Date: 2015-03-05
Authors@R: person("Blake", "Seers", role = c("aut", "cre"), email = "blake.seers@gmail.com")
VignetteBuilder: knitr
Imports: methods, lubridate, XML, selectr, RCurl, utils, ggplot2, scales, RColorBrewer, reshape2
Suggests: knitr, ggmap
Description: CliFlo is a web portal to the New Zealand National Climate Database and provides public access (via subscription) to around 6,500 various climate stations. Collating and manipulating data from CliFlo (hence clifro) and importing into R for further analysis, exploration and visualisation is now straightforward and coherent. The user is required to have an internet connection, and a current CliFlo subscription (free) if data from stations, other than the public Reefton electronic weather station, is sought.
URL: http://cliflo.niwa.co.nz/ https://github.com/ropensci/clifro
BugReports: https://github.com/ropensci/clifro/issues
License: GPL-2
Collate: 'dataFrame.R' 'cfStation.R' 'cfData.R' 'cfDataList.R' 'cfData-plotMethods.R' 'cfDatatype.R' 'cfQuery.R' 'cfUser.R' 'findStations.R'
Packaged: 2015-03-04 21:31:08 UTC; bsee002
Author: Blake Seers [aut, cre]
Maintainer: Blake Seers
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-04 23:47:33

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New package TR8 with initial version 0.9.12
Package: TR8
Type: Package
Title: A Tool for Downloading Functional Traits Data for Plant Species
Version: 0.9.12
Date: 2014-02-27
Author: Gionata Bocci
Maintainer: Gionata Bocci
Description: Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from publicly available databases (Biolflor, The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity databases). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
URL: https://github.com/GioBo/TR8
BugReports: https://github.com/GioBo/TR8/issues
Depends: R (>= 2.10), methods
Imports: RCurl, XML, taxize, plyr, rappdirs, gWidgets, gWidgetstcltk
NeedsCompilation: no
Packaged: 2015-03-04 16:22:37 UTC; gionata
Repository: CRAN
Date/Publication: 2015-03-04 18:34:07

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New package ncappc with initial version 0.1
Package: ncappc
Title: NCA Calculation and Population PK Model Diagnosis
Version: 0.1
Authors@R: c(person("Chayan", "Acharya", role = c("aut", "cre"), email = "chayan.acharya@farmbio.uu.se"), person("Andrew C.", "Hooker", role = "aut"), person("Siv", "Jonsson", role = "aut"), person("Mats O.", "Karlsson", role = "aut"))
Description: A flexible tool is presented here that can perform (i) traditional non-compartmental analysis (NCA) and (ii) simulation-based posterior predictive checks for a population pharmacokinetic (PK) model using NCA metrics.
Depends: R (>= 3.0.2)
Imports: ggplot2, grid, gridExtra, scales, gtable, PerformanceAnalytics, lattice, knitr, xtable, reshape2
Suggests: testthat
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Packaged: 2015-03-04 12:02:05 UTC; chaac446
Author: Chayan Acharya [aut, cre], Andrew C. Hooker [aut], Siv Jonsson [aut], Mats O. Karlsson [aut]
Maintainer: Chayan Acharya
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-04 16:14:48

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New package gvcm.cat with initial version 1.8
Package: gvcm.cat
Type: Package
Title: Regularized Categorical Effects/Categorical Effect Modifiers/Continuous/Smooth Effects in GLMs
Version: 1.8
Date: 2015-03-03
Author: Margret Oelker
Maintainer: Margret Oelker
Description: Generalized structured regression models with regularized categorical effects, categorical effect modifiers, continuous effects and smooth effects.
Depends: R (>= 2.10.0), Matrix, MASS, splines
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-03-04 13:36:48 UTC; oelker
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-04 16:05:24

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New package geocodeHERE with initial version 0.1.2
Package: geocodeHERE
Title: Wrapper for Nokia's HERE Geocoding API
Version: 0.1.2
Author: Cory Nissen [aut, cre]
Maintainer: Cory Nissen
Description: Wrapper for Nokia's HERE geocoding API. See http://here.com/ for more information on HERE and https://developer.here.com/geocoder for more information on the HERE geocoding API.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
Imports: httr
URL: https://github.com/corynissen/geocodeHERE
Packaged: 2015-03-04 13:36:11 UTC; c
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-04 16:05:22

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