Fri, 09 Oct 2015

Package sequenza updated to version 2.1.2 with previous version 2.1.1 dated 2015-01-27

Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero <favero@cbs.dtu.dk>

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Package rmarkdown updated to version 0.8.1 with previous version 0.8 dated 2015-08-30

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between rmarkdown versions 0.8 dated 2015-08-30 and 0.8.1 dated 2015-10-09

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Package paco updated to version 0.2.2 with previous version 0.2.1 dated 2015-07-18

Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot <tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>, Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>

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New package dtwSat with initial version 0.1.0
Package: dtwSat
Type: Package
Title: Time-Weighted Dynamic Time Warping for Remote Sensing Time Series Analysis
Version: 0.1.0
Date: 2015-10-01
Authors@R: c(person("Victor", "Maus", role = c("aut", "cre"), email = "vwmaus1@gmail.com") )
Description: Provides a Time-Weighted Dynamic Time Warping (TWDTW) algorithm to measure similarity between two temporal sequences. This adaptation of the classical Dynamic Time Warping (DTW) algorithm is flexible to compare events that have a strong time dependency, such as phenological stages of cropland systems and tropical forests. This package provides methods for visualization of minimum cost paths, time series alignment, and time intervals classification.
Depends: R (>= 3.0.0), methods, dtw, zoo
Imports: proxy, waveslim, graphics, ggplot2, scales, reshape2, grDevices, utils
Suggests: testthat
License: GPL (>= 2) | file LICENSE
Author: Victor Maus [aut, cre]
Maintainer: Victor Maus <vwmaus1@gmail.com>
LazyData: true
NeedsCompilation: no
Packaged: 2015-10-08 23:37:13 UTC; mausv
Repository: CRAN
Date/Publication: 2015-10-10 01:21:00

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New package deformula with initial version 0.1.0
Package: deformula
Version: 0.1.0
Date: 2015-10-8
Title: Integration of One-Dimensional Functions with Double Exponential Formulas
Type: Package
Author: Hiroyuki Okamura
Maintainer: Hiroyuki Okamura <okamu@rel.hiroshima-u.ac.jp>
Description: Numerical quadrature of functions of one variable over a finite or infinite interval with double exponential formulas.
Encoding: UTF-8
License: GPL (>= 2)
Packaged: 2015-10-09 12:03:06 UTC; okamu
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-10-10 01:23:42

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Package Surrogate updated to version 0.1-63 with previous version 0.1-62 dated 2015-08-24

Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package rerddap updated to version 0.3.0 with previous version 0.2.0 dated 2015-07-01

Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes functions to search for 'datasets', get summary information on 'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format. 'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rerddap versions 0.2.0 dated 2015-07-01 and 0.3.0 dated 2015-10-09

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Package pedgene updated to version 2.9 with previous version 2.7 dated 2015-08-03

Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut], Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>

Diff between pedgene versions 2.7 dated 2015-08-03 and 2.9 dated 2015-10-09

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New package HDGLM with initial version 0.1
Package: HDGLM
Title: Tests for High Dimensional Generalized Linear Models
Version: 0.1
Author: Bin Guo
Maintainer: Bin Guo <guobinscu@scu.edu.cn>
Description: Test the significance of coefficients in high dimensional generalized linear models.
Depends: R (>= 3.1.1)
License: GPL-2
LazyData: true
Packaged: 2015-10-09 12:57:53 UTC; bin
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-10-10 00:54:38

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Package gistr updated to version 0.3.4 with previous version 0.3.0 dated 2015-07-03

Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g., http://en.wikipedia.org/wiki/GitHub#Gist, https://help.github.com/articles/about-gists/). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut], Karthik Ram [aut], Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between gistr versions 0.3.0 dated 2015-07-03 and 0.3.4 dated 2015-10-09

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Package fishmethods updated to version 1.9-0 with previous version 1.8-0 dated 2015-05-28

Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>

Diff between fishmethods versions 1.8-0 dated 2015-05-28 and 1.9-0 dated 2015-10-09

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Package FactoMineR updated to version 1.31.4 with previous version 1.31.3 dated 2015-07-09

Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>

Diff between FactoMineR versions 1.31.3 dated 2015-07-09 and 1.31.4 dated 2015-10-09

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Package ChannelAttribution updated to version 1.2 with previous version 1.1 dated 2015-09-16

Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare and David Loris
Maintainer: Davide Altomare <davide.altomare@gmail.com>

Diff between ChannelAttribution versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-09

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New package Barnard with initial version 1.4
Package: Barnard
Type: Package
Title: Barnard's Unconditional Test
Version: 1.4
Date: 2015-10-09
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Description: Barnard's unconditional test for 2x2 contingency tables.
License: GPL-2
LazyLoad: yes
Packaged: 2015-10-09 13:11:42 UTC; kamil
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-10-09 23:18:28

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Package aprof updated to version 0.3.1 with previous version 0.2.5 dated 2015-07-20

Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and where to focus code optimization, using Amdahl's law and visual aids based on line profiling. Amdahl's profiler organises profiling output files (including memory profiling) in a visually appealing way. It is meant to help to balance development vs. execution time by helping to identify the most promising sections of code to optimize and projecting potential gains. The package is an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>

Diff between aprof versions 0.2.5 dated 2015-07-20 and 0.3.1 dated 2015-10-09

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 7 files changed, 283 insertions(+), 223 deletions(-)

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Package gitter updated to version 1.1 with previous version 1.0.4 dated 2014-01-23

Title: An R Package for Quantification of Pinned Microbial Culture
Description: The goal of this package is to allow users to robustly and quickly grid and quantify sizes of pinned colonies in plate images. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. It includes several image pre-processing techniques, such as autorotation of plates, noise removal, contrast adjustment and image resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>

Diff between gitter versions 1.0.4 dated 2014-01-23 and 1.1 dated 2015-10-09

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 20 files changed, 205 insertions(+), 378 deletions(-)

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Package gimms updated to version 0.1.1 with previous version 0.1 dated 2015-10-08

Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download and re-arrange the bi-monthly datasets according to creation time; import downloaded files from native binary (ENVI) format directly into R based on the widely applied 'raster' package; and calculate monthly value composites (e.g. maximum value composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>

Diff between gimms versions 0.1 dated 2015-10-08 and 0.1.1 dated 2015-10-09

 DESCRIPTION      |    8 ++++----
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 R/createHdr.R    |    2 ++
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 4 files changed, 11 insertions(+), 7 deletions(-)

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New package AdaptGauss with initial version 1.0
Package: AdaptGauss
Type: Package
Title: Gaussian Mixture Models (GMM)
Version: 1.0
Date: 2015-10-09
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot and Chi-squared test.
Imports: shiny, caTools, mclust, methods
Depends: R (>= 2.10)
License: GPL-3
LazyLoad: yes
NeedsCompilation: no
Packaged: 2015-10-09 09:25:00 UTC; MT
Repository: CRAN
Date/Publication: 2015-10-09 11:36:40

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New package water with initial version 0.3
Package: water
Title: Actual Evapotranspiration with Energy Balance Models
Version: 0.3
Date: 2015-10-8
Author: Guillermo Federico Olmedo [aut, cre], Samuel Ortega-Farias [aut], David Fonseca-Luengo [aut], Daniel de la Fuente-Saiz [aut], Fernando Fuentes Pe<c3><b1>ailillo [aut]
Maintainer: Guillermo Federico Olmedo <guillermo.olmedo@gmail.com>
Description: Tools and functions to calculate actual evapotranspiration using surface energy balance models.
Depends: R (>= 3.0), raster (>= 2.4-18), sp (>= 1.1-1), rgdal (>= 1.0-4)
Imports:
License: GPL (>= 2)
URL: https://github.com/midraed/water
BugReports: https://github.com/midraed/water/issues
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-10-08 23:55:19 UTC; guillermo
Repository: CRAN
Date/Publication: 2015-10-09 10:29:19

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New package TauStar with initial version 1.0.0
Package: TauStar
Type: Package
Title: Efficient Computation of the t* Statistic of Bergsma and Dassios (2014)
Version: 1.0.0
Date: 2015-9-30
Authors@R: c(person("Luca", "Weihs", email="lucaw@uw.edu", role=c("aut", "cre")), person("Emin", "Martinian", role=c("ctb"), comment="Created the red-black tree library included in package."))
Maintainer: Luca Weihs <lucaw@uw.edu>
Description: Computes the t* statistic corresponding to the tau star population coefficient introduced by Bergsma and Dassios (Bernoulli 20(2), 2014, 1006-1028) and does so in O(n^2*log(n)) time. Can provide both the V-statistic and U-statistic related to the tau star measure depending on user preference.
License: GPL (>= 3)
Imports: Rcpp (>= 0.11.4)
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat
NeedsCompilation: yes
Packaged: 2015-10-08 22:38:50 UTC; lucaweihs
Author: Luca Weihs [aut, cre], Emin Martinian [ctb] (Created the red-black tree library included in package.)
Repository: CRAN
Date/Publication: 2015-10-09 10:28:56

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Package qlcMatrix updated to version 0.9.5 with previous version 0.9.4 dated 2015-04-27

Title: Utility Sparse Matrix Functions for Quantitative Language Comparison
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>

Diff between qlcMatrix versions 0.9.4 dated 2015-04-27 and 0.9.5 dated 2015-10-09

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Package qdap updated to version 2.2.4 with previous version 2.2.2 dated 2015-07-05

Title: Bridging the Gap Between Qualitative Data and Quantitative Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb], Dason Kurkiewicz [ctb], Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between qdap versions 2.2.2 dated 2015-07-05 and 2.2.4 dated 2015-10-09

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 NAMESPACE                             |    1 
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 24 files changed, 313 insertions(+), 220 deletions(-)

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New package optigrab with initial version 0.7.3
Package: optigrab
Type: Package
Title: Command-Line Parsing for an R World
Version: 0.7.3
Date: 2015-10-08
Author: Christopher Brown
URL: https://github.com/decisionpatterns/optigrab
BugReports: https://github.com/decisionpatterns/optigrab/issues
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Description: Parse options from the command-line using a simple, clean syntax. It requires little or no specification and supports short and long options, GNU-, Java- or Microsoft- style syntaxes, verb commands and more.
Depends: R (>= 3.0.0), methods
Imports: stringi (>= 0.4.1), magrittr (>= 1.5)
Suggests: testthat (>= 0.9.1), knitr (>= 1.9), rmarkdown
License: GPL (>= 2) | file LICENSE
LazyLoad: no
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-10-09 02:02:55 UTC; cbrown
Repository: CRAN
Date/Publication: 2015-10-09 10:28:58

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Package OpenStreetMap updated to version 0.3.2 with previous version 0.3.1 dated 2013-04-14

Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported, including CloudMade, Mapnik, Bing, stamen, and MapQuest. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Author: Ian Fellows, using the JMapViewer library by Jan Peter Stotz
Maintainer: Ian Fellows <ian@fellstat.com>

Diff between OpenStreetMap versions 0.3.1 dated 2013-04-14 and 0.3.2 dated 2015-10-09

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Package HelpersMG updated to version 1.2.3 with previous version 1.2 dated 2015-06-29

Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 1.2 dated 2015-06-29 and 1.2.3 dated 2015-10-09

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Package FIACH updated to version 0.1.2 with previous version 0.1.1 dated 2015-10-01

Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>

Diff between FIACH versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-09

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 32 files changed, 827 insertions(+), 1073 deletions(-)

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