Sat, 25 Jun 2016

Package proxy updated to version 0.4-16 with previous version 0.4-15 dated 2015-07-08

Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre], Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>

Diff between proxy versions 0.4-15 dated 2015-07-08 and 0.4-16 dated 2016-06-25

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Package MALDIquant updated to version 1.15 with previous version 1.14 dated 2015-11-18

Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

Diff between MALDIquant versions 1.14 dated 2015-11-18 and 1.15 dated 2016-06-25

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Package Gmedian updated to version 1.2.1 with previous version 1.2 dated 2016-04-20

Title: Geometric Median, k-Median Clustering and Robust Median PCA
Description: Fast algorithms for robust estimation with large samples of multivariate observations. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.
Author: Herve Cardot
Maintainer: Herve Cardot <herve.cardot@u-bourgogne.fr>

Diff between Gmedian versions 1.2 dated 2016-04-20 and 1.2.1 dated 2016-06-25

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New package doFuture with initial version 0.2.0
Package: doFuture
Version: 0.2.0
Title: Foreach Parallel Adaptor using the Future API of the 'future' Package
Depends: future (>= 1.0.0), foreach (>= 1.4.3), iterators (>= 1.0.8)
Suggests: doRNG (>= 1.6), markdown, R.rsp
VignetteBuilder: R.rsp
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Provides a '%dopar%' adaptor such that any type of futures can be used as backends for the 'foreach' framework.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/doFuture
BugReports: https://github.com/HenrikBengtsson/doFuture/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-25 17:25:07 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-06-25 19:53:58

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Package tidytext updated to version 0.1.1 with previous version 0.1.0 dated 2016-04-28

Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using 'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb], David Robinson [aut], Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>

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Package statar updated to version 0.6.2 with previous version 0.6.1 dated 2016-05-20

Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize', 'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>

Diff between statar versions 0.6.1 dated 2016-05-20 and 0.6.2 dated 2016-06-25

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New package SPEDInstabR with initial version 1.0
Package: SPEDInstabR
Version: 1.0
Date: 2016-06-23
Title: Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Description: From output files obtained from the software ModestR, the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
License: GPL (>= 2)
Encoding: latin1
Depends: R (>= 3.1.1), beanplot, raster, plotrix, TeachingDemos
Repository: CRAN
Packaged: 2016-06-23 20:23:34 UTC; castor
NeedsCompilation: no
Date/Publication: 2016-06-25 19:07:30

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Package simLife updated to version 0.2.1 with previous version 0.2 dated 2016-05-31

Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

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Package rstanarm updated to version 2.10.1 with previous version 2.9.0-4 dated 2016-05-24

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Trustees of Columbia University [cph], R Core Deveopment Team [cph] (R/pp_data.R, R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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New package MixSIAR with initial version 3.1.6
Package: MixSIAR
Title: Bayesian Mixing Models in R
Version: 3.1.6
Authors@R: c( person("Brian", "Stock", email = "b1stock@ucsd.edu", role = c("cre","aut")), person("Brice", "Semmens", email = "semmens@ucsd.edu", role = "aut"), person("Eric", "Ward", role = "ctb"), person("Andrew", "Parnell", role = "ctb"), person("Andrew", "Jackson", role = "ctb"), person("Donald", "Phillips", role = "ctb"), person("Jon", "Moore", role = "ctb"), person("Stuart", "Bearhop", role = "ctb"), person("Richard", "Inger", role = "ctb"))
Description: Creates and runs Bayesian mixing models to analyze biotracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR', and includes both GUI (graphical user interface) and script versions.
Depends: R (>= 3.2.3)
Imports: ggplot2 (>= 1.0.1), rjags (>= 4-4), R2jags (>= 0.5-7), MASS (>= 7.3), RColorBrewer (>= 1.1), reshape (>= 0.8), reshape2 (>= 1.4.1), lattice (>= 0.20), compositions (>= 1.40), ggmcmc (>= 0.7.2), coda (>= 0.18-1)
Suggests: gWidgets (>= 0.0-54), gWidgetsRGtk2 (>= 0.0-83), splancs (>= 2.01-38), knitr, rmarkdown, testthat
SystemRequirements: JAGS (>= 4.1) for the script version, both JAGS and GTK+ for the GUI version. For install instructions, see manual at <https://github.com/brianstock/MixSIAR/blob/master/inst/mixsiar_manual_3.1_small.pdf>
URL: https://github.com/brianstock/MixSIAR
BugReports: https://github.com/brianstock/MixSIAR/issues
License: GPL-3
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-25 00:38:37 UTC; brian
Author: Brian Stock [cre, aut], Brice Semmens [aut], Eric Ward [ctb], Andrew Parnell [ctb], Andrew Jackson [ctb], Donald Phillips [ctb], Jon Moore [ctb], Stuart Bearhop [ctb], Richard Inger [ctb]
Maintainer: Brian Stock <b1stock@ucsd.edu>
Repository: CRAN
Date/Publication: 2016-06-25 19:07:27

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Package metricTester updated to version 1.2.2 with previous version 1.0.2 dated 2016-05-10

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and performance of phylogenetic metrics and null models.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

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Package ks updated to version 1.10.4 with previous version 1.10.3 dated 2016-04-04

Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>

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Package GSIF updated to version 0.5-2 with previous version 0.5-1 dated 2016-05-03

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [ctb], Gerard Heuvelink [ctb], Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>

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Package googleAuthR updated to version 0.3.1 with previous version 0.3.0 dated 2016-05-09

Title: Easy Authentication with Google OAuth2 API
Description: Create R functions that interact with OAuth2 Google APIs easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre], Jennifer Bryan [ctb], Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

Diff between googleAuthR versions 0.3.0 dated 2016-05-09 and 0.3.1 dated 2016-06-25

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 googleAuthR-0.3.1/googleAuthR/R/googleAuthR_generator.R  |   38 +-
 googleAuthR-0.3.1/googleAuthR/README.md                  |   78 ++--
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 15 files changed, 298 insertions(+), 588 deletions(-)

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Package ddpcr updated to version 1.4 with previous version 1.3 dated 2016-06-05

Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between ddpcr versions 1.3 dated 2016-06-05 and 1.4 dated 2016-06-25

 DESCRIPTION                     |    8 ++++----
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 12 files changed, 43 insertions(+), 35 deletions(-)

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Package benchmarkme updated to version 0.3.0 with previous version 0.2.3 dated 2016-02-26

Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>

Diff between benchmarkme versions 0.2.3 dated 2016-02-26 and 0.3.0 dated 2016-06-25

 DESCRIPTION                            |   12 +--
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 NEWS.md                                |    9 ++
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New package BACCT with initial version 1.0
Package: BACCT
Type: Package
Title: Bayesian Augmented Control for Clinical Trials
Version: 1.0
Date: 2016-06-24
Authors@R: c( person("Hongtao", "Zhang", role = c("aut", "cre"), email = "hongtao.zhang@abbvie.com"), person("Qi", "Tang", role = "aut", email = "qi.tang@abbvie.com") )
Description: Implements the Bayesian Augmented Control (BAC, a.k.a. Bayesian historical data borrowing) method under clinical trial setting by calling 'Just Another Gibbs Sampler' ('JAGS') software. In addition, the 'BACCT' package evaluates user-specified decision rules by computing the type-I error/power, or probability of correct go/no-go decision at interim look. The evaluation can be presented numerically or graphically. Users need to have 'JAGS' 4.0.0 or newer installed due to a compatibility issue with 'rjags' package. Currently, the package implements the BAC method for binary outcome only. Support for continuous and survival endpoints will be added in future releases. We would like to thank AbbVie's Statistical Innovation group and Clinical Statistics group for their support in developing the 'BACCT' package.
Depends: R (>= 2.10)
Imports: rjags, ggplot2, reshape2
License: GPL (>= 3)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-24 19:05:19 UTC; zhanghx5
Author: Hongtao Zhang [aut, cre], Qi Tang [aut]
Maintainer: Hongtao Zhang <hongtao.zhang@abbvie.com>
Repository: CRAN
Date/Publication: 2016-06-25 19:07:22

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Package asymmetry updated to version 1.1 with previous version 1.0 dated 2016-04-26

Title: The Slide-Vector Model for Multidimensional Scaling of Asymmetric Data
Description: The slide-vector model is provided in this package together with functions for the analysis and graphical display of asymmetry. The slide vector model is a scaling model for asymmetric data. A distance model is fitted to the symmetric part of the data whereas the asymmetric part of the data is represented by projections of the coordinates onto the slide-vector. The slide-vector points in the direction of large asymmetries in the data. The distance is modified in such a way that the distance between two points that are parallel to the slide-vector is larger in the direction of this vector. The distance is smaller in the opposite direction. If the line connecting two points is perpendicular to the slide-vector the difference between the two projections is zero. In this case the distance between the two points is symmetric. The algorithm for fitting this model is derived from the majorization approach to multidimensional scaling.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>

Diff between asymmetry versions 1.0 dated 2016-04-26 and 1.1 dated 2016-06-25

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Package AnalyzeTS updated to version 2.0 with previous version 1.9 dated 2016-05-26

Title: Analyze (Fuzzy) Time Series
Description: Analyze (fuzzy) time series, calculate AIC value of common time series models and propose the best model. Fuzzy time series can be analyzed by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models. The Abbasov-Mamedova model and an improved version of the Abbasov-Mamedova model is included as well.
Author: Tran Thi Ngoc Han, Doan Hai Nghi, Mai Thi Hong Diem, Nguyen Thi Diem My, Hong Viet Minh, Vo Van Tai.
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>

Diff between AnalyzeTS versions 1.9 dated 2016-05-26 and 2.0 dated 2016-06-25

 DESCRIPTION              |   14 
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 34 files changed, 3184 insertions(+), 2875 deletions(-)

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