Sat, 01 Oct 2016

Package sommer updated to version 2.2 with previous version 2.1 dated 2016-08-31

Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

Diff between sommer versions 2.1 dated 2016-08-31 and 2.2 dated 2016-10-01

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Package RSelenium updated to version 1.4.5 with previous version 1.4.0 dated 2016-07-30

Title: R Bindings for Selenium WebDriver
Description: The RSelenium package provides a set of R bindings for the Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
Author: John Harrison <johndharrison0@gmail.com>
Maintainer: John Harrison <johndharrison0@gmail.com>

Diff between RSelenium versions 1.4.0 dated 2016-07-30 and 1.4.5 dated 2016-10-01

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Package colorscience updated to version 1.0.4 with previous version 1.0.2 dated 2016-02-28

Title: Color Science Methods and Data
Description: Methods and data for color science - color conversions by observer, illuminant and gamma. Color matching functions and chromaticity diagrams. Color indices, color differences and spectral data conversion/analysis.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>

Diff between colorscience versions 1.0.2 dated 2016-02-28 and 1.0.4 dated 2016-10-01

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Package RcppAnnoy updated to version 0.0.8 with previous version 0.0.7 dated 2015-11-15

Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppAnnoy versions 0.0.7 dated 2015-11-15 and 0.0.8 dated 2016-10-01

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Package linkR updated to version 1.1.1 with previous version 1.0.1 dated 2015-06-19

Title: 3D Lever and Linkage Mechanism Modeling
Description: Creates kinematic and static force models of 3D levers and linkage mechanisms, with particular application to the fields of engineering and biomechanics.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between linkR versions 1.0.1 dated 2015-06-19 and 1.1.1 dated 2016-10-01

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Package HelpersMG updated to version 1.7 with previous version 1.6 dated 2016-07-18

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 1.6 dated 2016-07-18 and 1.7 dated 2016-10-01

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Package Surrogate updated to version 0.1-77 with previous version 0.1-76 dated 2016-09-24

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 (bio)marker 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 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

Diff between Surrogate versions 0.1-76 dated 2016-09-24 and 0.1-77 dated 2016-10-01

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Package supervisedPRIM updated to version 2.0.0 with previous version 1.0.1 dated 2016-08-22

Title: Supervised Classification Learning and Prediction using Patient Rule Induction Method (PRIM)
Description: The Patient Rule Induction Method (PRIM) is typically used for "bump hunting" data mining to identify regions with abnormally high concentrations of data with large or small values. This package extends this methodology so that it can be applied to binary classification problems and used for prediction.
Author: David Shaub [aut, cre]
Maintainer: David Shaub <davidshaub@gmx.com>

Diff between supervisedPRIM versions 1.0.1 dated 2016-08-22 and 2.0.0 dated 2016-10-01

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Package stringi updated to version 1.1.2 with previous version 1.1.1 dated 2016-05-27

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 1.1.1 dated 2016-05-27 and 1.1.2 dated 2016-10-01

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Package smam updated to version 0.3-0 with previous version 0.2-2 dated 2013-11-04

Title: Statistical Modeling of Animal Movements
Description: Animal movement models including moving-resting process with embedded Brownian motion, Brownian motion with measurement error.
Author: Jun Yan <jun.yan@uconn.edu> and Vladimir Pozdnyakov <vladimir.pozdnyakov@uconn.edu>
Maintainer: Jun Yan <jun.yan@uconn.edu>

Diff between smam versions 0.2-2 dated 2013-11-04 and 0.3-0 dated 2016-10-01

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New package stremr with initial version 0.1
Package: stremr
Title: Streamlined Estimation of Survival for Static, Dynamic and Stochastic Treatment and Monitoring Regimes
Version: 0.1
Authors@R: c( person("Oleg", "Sofrygin", role=c("aut", "cre"), email="oleg.sofrygin@gmail.com"), person(c("Mark", "J."), "van der Laan", role="aut", email="laan@berkeley.edu"), person("Romain", "Neugebauer", role="aut", email="Romain.S.Neugebauer@kp.org"))
Description: Analysis of longitudinal time-to-event or time-to-failure data. Estimates the counterfactual discrete survival curve under static, dynamic and stochastic interventions on treatment (exposure) and monitoring events over time. Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying confounding and informative right-censoring. Model fitting can be performed either with GLM or H2O-3 machine learning libraries, including the ensemble-based SuperLearner ("h2oEnsemble"). The exposure, monitoring and censoring variables can be coded as either binary, categorical or continuous. Each can be multivariate (e.g., can use more than one column of dummy indicators for different censoring events). The input data needs to be in long format.
URL: https://github.com/osofr/stremr
BugReports: https://github.com/osofr/stremr/issues
Depends: R (>= 3.2.1)
Imports: assertthat, data.table, methods, R6, Rcpp, rmarkdown, pander, speedglm, stats, stringr, zoo
LinkingTo: Rcpp
Suggests: devtools, h2o, h2oEnsemble, knitr, magrittr, RUnit, foreach, doParallel
Additional_repositories: https://osofr.github.io/drat/
License: GPL (>= 2)
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-10-01 01:10:15 UTC; olegsofrygin
Author: Oleg Sofrygin [aut, cre], Mark J. van der Laan [aut], Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Repository: CRAN
Date/Publication: 2016-10-01 14:36:45

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Package SCBmeanfd updated to version 1.2.1 with previous version 1.2 dated 2016-09-24

Title: Simultaneous Confidence Bands for the Mean of Functional Data
Description: Statistical methods for estimating and inferring the mean of functional data. The methods include simultaneous confidence bands, local polynomial fitting, bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for parametric models, equality tests for two-sample problems, and plotting functions.
Author: David Degras
Maintainer: David Degras <ddegrasv@gmail.com>

Diff between SCBmeanfd versions 1.2 dated 2016-09-24 and 1.2.1 dated 2016-10-01

 DESCRIPTION              |    8 ++++----
 MD5                      |    8 ++++----
 R/plot.SCBand.R          |   14 +++++++-------
 R/scb.model.R            |   27 +++++++++++++--------------
 man/SCBmeanfd-package.Rd |   11 +++++------
 5 files changed, 33 insertions(+), 35 deletions(-)

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New package sBIC with initial version 0.2.0
Package: sBIC
Type: Package
Title: Computing the Singular BIC for Multiple Models
Version: 0.2.0
Date: 2016-09-20
Authors@R: c(person("Luca", "Weihs", role=c("aut","cre"), email="lucaw@uw.edu"), person("Martyn", "Plummer", role="ctb"))
Description: Computes the sBIC for various singular model collections including: binomial mixtures, factor analysis models, Gaussian mixtures, latent forests, latent class analyses, and reduced rank regressions.
License: GPL (>= 3)
URL: https://github.com/Lucaweihs/sBIC
BugReports: https://github.com/Lucaweihs/sBIC/issues
Imports: poLCA, R.oo (>= 1.20.0), R.methodsS3, mclust, igraph (>= 1.0.1), Rcpp (>= 0.12.3), combinat, flexmix, hash
LinkingTo: Rcpp
Suggests: testthat, mvtnorm, knitr, MASS
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Collate: 'ModelPoset.R' 'MixtureModels.R' 'BinomialMixtures.R' 'FactorAnalyses.R' 'GaussianMixtures.R' 'LCAs.R' 'LatentForests-Helpers.R' 'LatentForests.R' 'RcppExports.R' 'ReducedRankRegressions.R' 'sBIC-Function.R' 'sbic.R'
NeedsCompilation: yes
Packaged: 2016-09-30 23:20:04 UTC; lucaweihs
Author: Luca Weihs [aut, cre], Martyn Plummer [ctb]
Maintainer: Luca Weihs <lucaw@uw.edu>
Repository: CRAN
Date/Publication: 2016-10-01 14:31:14

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Package phenology updated to version 5.3 with previous version 5.2 dated 2016-07-18

Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between phenology versions 5.2 dated 2016-07-18 and 5.3 dated 2016-10-01

 DESCRIPTION                    |    8 
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 NEWS                           |   17 +
 R/add_phenology.R              |    2 
 R/phenology-package.R          |    4 
 R/phenology.R                  |    3 
 R/plot.phenology.R             |   17 +
 inst/shiny/babel.Rdata         |only
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 man/phenology-package.Rd       |    4 
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 19 files changed, 507 insertions(+), 150 deletions(-)

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New package expandFunctions with initial version 0.1.0
Package: expandFunctions
Type: Package
Date: 2016-09-19
Title: Feature Matrix Builder
Version: 0.1.0
Authors@R: person("Scott", "Miller", email = "sam3CRAN@gmail.com", role = c("aut", "cre"))
Imports: utils, stats, graphics, plyr, orthopolynom, polynom, glmnet
Description: Generates feature matrix outputs from R object inputs using a variety of expansion functions. The generated feature matrices have applications as inputs for a variety of machine learning algorithms. The expansion functions are based on coercing the input to a matrix, treating the columns as features and converting individual columns or combinations into blocks of columns. Currently these include expansion of columns by efficient sparse embedding by vectors of lags, quadratic expansion into squares and unique products, powers by vectors of degree, vectors of orthogonal polynomials functions, and block random affine projection transformations (RAPTs). The transformations are magrittr- and cbind-friendly, and can be used in a building block fashion. For instance, taking the cos() of the output of the RAPT transformation generates a stationary kernel expansion via Bochner's theorem, and this expansion can then be cbind-ed with other features. Additionally, there are utilities for replacing features, removing rows with NAs, creating matrix samples of a given distribution, a simple wrapper for LASSO with CV, a Freeman-Tukey transform, generalizations of the outer function, matrix size-preserving discrete difference by row, plotting, etc.
License: GPL-2
NeedsCompilation: no
LazyData: TRUE
RoxygenNote: 5.0.1
Packaged: 2016-10-01 02:05:07 UTC; scott
Author: Scott Miller [aut, cre]
Maintainer: Scott Miller <sam3CRAN@gmail.com>
Repository: CRAN
Date/Publication: 2016-10-01 15:05:50

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New package D3partitionR with initial version 0.1
Package: D3partitionR
Title: Plotting D3 Hierarchical Plots in R and Shiny
Version: 0.1
Authors@R: c(person("Antoine", "GUILLOT", email = "antoine.guil@outlook.fr", role ="cre"), person( "Mike", "Bostock" , role = c("aut", "cph") , comment = "d3.js library in htmlwidgets/lib, http://d3js.org. The partitionChart, sunburst, the treemap, and the zoomable circlePackig are all derived from his works." ))
Description: Plotting hierarchical plots in R such as Sunburst, Treemap, Circle Treemap and Partition Chart.
Depends: R (>= 3.3.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
Imports: htmlwidgets, stats
NeedsCompilation: no
Packaged: 2016-10-01 09:06:11 UTC; Antoi
Author: Antoine GUILLOT [cre], Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org. The partitionChart, sunburst, the treemap, and the zoomable circlePackig are all derived from his works.)
Maintainer: Antoine GUILLOT <antoine.guil@outlook.fr>
Repository: CRAN
Date/Publication: 2016-10-01 15:08:35

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