Tue, 28 Apr 2015

Package urltools updated to version 1.1.0 with previous version 0.6 dated 2014-12-22

Title: Vectorised Tools for URL Handling and Parsing
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.
Author: Oliver Keyes [aut, cre], Mark Greenaway [ctb]
Maintainer: Oliver Keyes

Diff between urltools versions 0.6 dated 2014-12-22 and 1.1.0 dated 2015-04-28

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New package uniqtag with initial version 1.0
Package: uniqtag
Type: Package
Version: 1.0
Title: Abbreviate Strings to Short, Unique Identifiers
Description: For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the "UniqTag" of that string.
Authors@R: person("Shaun", "Jackman", , "sjackman@gmail.com", c("cre"))
URL: https://github.com/sjackman/uniqtag
BugReports: https://github.com/sjackman/uniqtag/issues
Suggests: testthat
License: MIT + file LICENSE
Packaged: 2015-04-28 19:20:22 UTC; sjackman
Author: Shaun Jackman [cre]
Maintainer: Shaun Jackman
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-29 01:17:59

More information about uniqtag at CRAN
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Package RSEIS updated to version 3.4-5 with previous version 3.3-3 dated 2014-01-05

Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between RSEIS versions 3.3-3 dated 2014-01-05 and 3.4-5 dated 2015-04-28

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More information about RSEIS at CRAN
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Package Quandl updated to version 2.6.0 with previous version 2.4.0 dated 2014-11-04

Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, as well as the ability to search.
Author: Raymond McTaggart [aut, cre], Gergely Daroczi [aut], Quandl Inc. [cph]
Maintainer: Raymond McTaggart

Diff between Quandl versions 2.4.0 dated 2014-11-04 and 2.6.0 dated 2015-04-28

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More information about Quandl at CRAN
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Package mixOmics updated to version 5.0-4 with previous version 5.0-3 dated 2014-09-01

Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and variants to analyse highly dimensional data sets: regularized Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS') to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao

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More information about mixOmics at CRAN
Permanent link

Package icenReg updated to version 1.1 with previous version 1.0 dated 2015-04-28

Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and an imputation Cox-PH model which imputes the interval censored times based on Cox-PH model with an parametric baseline and then analyzes each imputed data set with the semi-parametric model.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman

Diff between icenReg versions 1.0 dated 2015-04-28 and 1.1 dated 2015-04-28

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
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Package glmm updated to version 1.0.3 with previous version 1.0.2 dated 2015-03-19

Title: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson

Diff between glmm versions 1.0.2 dated 2015-03-19 and 1.0.3 dated 2015-04-28

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 MD5                 |   15 ++++++++-------
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More information about glmm at CRAN
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Package dunn.test updated to version 1.2.4 with previous version 1.2.3 dated 2015-02-25

Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno

Diff between dunn.test versions 1.2.3 dated 2015-02-25 and 1.2.4 dated 2015-04-28

 DESCRIPTION   |   10 +++++-----
 MD5           |    4 ++--
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Package fastclime updated to version 1.2.5 with previous version 1.2.4 dated 2014-04-29

Title: A Fast Solver for Parameterized Linear Programming Problems and Constrained L1 Minimization Approach to Sparse Precision Matrix Estimation
Description: An efficient method of recovering precision matrices by applying the parametric simplex method is provided in this package. The computation is based on a linear optimization solver. It also contains a generic Linear Programming solver and a parameterized Linear Programming solver based on the parametric simplex method.
Author: Haotian Pang, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang

Diff between fastclime versions 1.2.4 dated 2014-04-29 and 1.2.5 dated 2015-04-28

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New package simpleNeural with initial version 0.1.1
Package: simpleNeural
Version: 0.1.1
Date: 2015-04-27
Title: An Easy to Use Multilayer Perceptron
Description: Trains neural networks (multilayer perceptrons with one hidden layer) for bi- or multi-class classification.
Authors@R: person(given="David",family="Dernoncourt",email="me@daviddernoncourt.com",role=c("aut","cre"),comment="LUNAM Universite, Universite Angers, Laboratoire d'ergonomie et d'epidemiologie en sante au travail (LEEST), w/ support from the French National Research Program for Environmental and Occupational Health of Anses (2012/18)")
Depends: R (>= 3.1)
Suggests: verification
License: MIT + file LICENSE
LazyData: true
URL: https://bitbucket.org/patheticcockroach/simpleneural
BugReports: me@daviddernoncourt.com
NeedsCompilation: no
Packaged: 2015-04-28 08:41:30 UTC; Admin
Author: David Dernoncourt [aut, cre] (LUNAM Universite, Universite Angers, Laboratoire d'ergonomie et d'epidemiologie en sante au travail (LEEST), w/ support from the French National Research Program for Environmental and Occupational Health of Anses (2012/18))
Maintainer: David Dernoncourt
Repository: CRAN
Date/Publication: 2015-04-28 20:24:29

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Package Renext updated to version 2.1-10 with previous version 2.1-0 dated 2013-10-04

Title: Renewal Method for Extreme Values Extrapolation
Description: Extreme value analysis using the Peaks Over Threshold (POT) method also called 'methode du renouvellement' by some French-speaking hydrologists.
Author: Yves Deville , IRSN
Maintainer: Lise Bardet

Diff between Renext versions 2.1-0 dated 2013-10-04 and 2.1-10 dated 2015-04-28

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Package PopVar updated to version 1.1 with previous version 1.0 dated 2015-04-01

Title: Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede

Diff between PopVar versions 1.0 dated 2015-04-01 and 1.1 dated 2015-04-28

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Package LambertW updated to version 0.5.1 with previous version 0.5 dated 2014-11-21

Title: Analyze and Gaussianize Heavy-Tailed, Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. They are based on an input/output system, where the input random variable (RV) X ~ F, and the output Y is a non-linearly transformed version of X with similar properties, but slightly skewed and/or heavy-tailed. This transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/print results nicely. Probably the most important function is 'Gaussianize', which works similarly to 'scale', but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg

Diff between LambertW versions 0.5 dated 2014-11-21 and 0.5.1 dated 2015-04-28

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Package causaleffect updated to version 1.1.1 with previous version 1.1 dated 2015-04-21

Title: Deriving Expressions of Joint Interventional Distributions in Causal Models
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka

Diff between causaleffect versions 1.1 dated 2015-04-21 and 1.1.1 dated 2015-04-28

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New package DIFtree with initial version 1.0.0
Package: DIFtree
Type: Package
Title: Item Focused Trees for the Identification of Items in Differential Item Functioning
Version: 1.0.0
Date: 2015-04-23
Author: Moritz Berger
Depends: penalized, plotrix
Maintainer: Moritz Berger
Description: Item focused recursive partitioning for simultaneous selection of items and variables that induce Differential Item Functioning (DIF) in Item Response models.
License: GPL-2
LazyLoad: yes
Packaged: 2015-04-28 08:04:43 UTC; bergerm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-28 10:24:11

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New package timetree with initial version 1.0
Package: timetree
Type: Package
Title: Interface to the TimeTree of Life Webpage
Description: A interface to the TimeTree of Life Webpage (www.timetree.org). TimeTree is a public database for information on the evolutionary timescale of life. This package includes functions for searching divergence time for taxa or all nodes of a phylogeny.
URL: http://www.timetree.org
Version: 1.0
Imports: XML, phangorn
Date: 2015-04-11
Author: Franz-Sebastian Krah
Maintainer: Franz-Sebastian Krah
License: GPL (>= 2)
Repository: CRAN
Packaged: 2015-04-27 17:37:03 UTC; test
NeedsCompilation: no
Date/Publication: 2015-04-28 07:32:02

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Package tfplot updated to version 2015.4-1 with previous version 2014.2-2 dated 2014-02-10

Title: Time Frame User Utilities
Description: Utilities for simple manipulation and quick plotting of time series data. These utilities use the tframe package which provides a programming kernel for time series. Extensions to tframe provided in tframePlus can also be used. See the Guide vignette for examples.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between tfplot versions 2014.2-2 dated 2014-02-10 and 2015.4-1 dated 2015-04-28

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Package R.filesets updated to version 2.7.1 with previous version 2.7.0 dated 2015-02-23

Title: Easy Handling of and Access to Files Organized in Structured Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.filesets versions 2.7.0 dated 2015-02-23 and 2.7.1 dated 2015-04-28

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New package randNames with initial version 0.2
Package: randNames
Title: Package Provides Access to Fake User Data
Version: 0.2
Authors@R: person("Karthik", "Ram", email = "karthik.ram@gmail.com", role = c("aut", "cre"))
Description: Generates random names with additional information including fake SSNs, gender, location, zip, age, address, and nationality.
Depends: R (>= 3.1.2)
URL: https://github.com/karthik/randNames
BugReports: https://github.com/karthik/randNames/issues
License: MIT + file LICENSE
LazyData: true
Imports: dplyr, httr, jsonlite
Suggests: gender, testthat
NeedsCompilation: no
Packaged: 2015-04-28 06:21:14 UTC; karthik
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
Repository: CRAN
Date/Publication: 2015-04-28 09:03:47

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Package multicool updated to version 0.1-6 with previous version 0.1-5 dated 2015-02-26

Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran

Diff between multicool versions 0.1-5 dated 2015-02-26 and 0.1-6 dated 2015-04-28

 DESCRIPTION         |    8 ++--
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Package lessR updated to version 3.3.1 with previous version 3.3 dated 2015-03-19

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing

Diff between lessR versions 3.3 dated 2015-03-19 and 3.3.1 dated 2015-04-28

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Package texreg updated to version 1.35 with previous version 1.34 dated 2014-10-31

Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

Diff between texreg versions 1.34 dated 2014-10-31 and 1.35 dated 2015-04-28

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Package pgmm updated to version 1.2 with previous version 1.1 dated 2014-07-13

Title: Parsimonious Gaussian Mixture Models
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models.
Author: Paul D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F. McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]
Maintainer: Paul D. McNicholas

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Package pairsD3 updated to version 0.1.0 with previous version 0.0.6 dated 2015-04-08

Title: D3 Scatterplot Matrices
Description: Creates an interactive scatterplot matrix using the D3 JavaScript library. See for more information on D3.
Author: Garth Tarr [aut, cre]
Maintainer: Garth Tarr

Diff between pairsD3 versions 0.0.6 dated 2015-04-08 and 0.1.0 dated 2015-04-28

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Package emplik updated to version 1.0-1 with previous version 0.9-9-6 dated 2014-08-26

Title: Empirical Likelihood Ratio for Censored/Truncated Data
Description: Empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. Now does regression too. This version contains some C code.
Author: Mai Zhou. (Art Owen for el.test(). Yifan Yang for C code.)
Maintainer: Mai Zhou

Diff between emplik versions 0.9-9-6 dated 2014-08-26 and 1.0-1 dated 2015-04-28

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New package icenReg with initial version 1.0
Package: icenReg
Type: Package
Title: Regression Models for Interval Censored Data
Version: 1.0
Date: 2015-04-21
Author: Clifford Anderson-Bergman
Depends: survival, foreach
Maintainer: Clifford Anderson-Bergman
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and an imputation Cox-PH model which imputes the interval censored times based on Cox-PH model with an parametric baseline and then analyzes each imputed data set with the semi-parametric model.
License: GPL-2
Packaged: 2015-04-27 23:37:31 UTC; cliffandersonbergman
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-28 06:58:00

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New package Claddis with initial version 0.1
Package: Claddis
Type: Package
Title: Measuring Morphological Diversity and Evolutionary Tempo
Version: 0.1
Date: 2015-04-27
Author: Graeme T. Lloyd
Maintainer: Graeme T. Lloyd
Depends: gdata,ape,phytools,strap
Description: Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.
License: GPL (>= 2)
LazyData: yes
ByteCompile: yes
Packaged: 2015-04-27 22:21:44 UTC; gral
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-28 06:57:55

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