Fri, 05 Aug 2016

Package betareg updated to version 3.1-0 with previous version 3.0-5 dated 2014-09-24

Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of a beta-distributed response), bias-corrected and bias-reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre], Francisco Cribari-Neto [aut], Bettina Gruen [aut], Ioannis Kosmidis [aut], Alexandre B. Simas [ctb] (earlier version by), Andrea V. Rocha [ctb] (earlier version by)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between betareg versions 3.0-5 dated 2014-09-24 and 3.1-0 dated 2016-08-05

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Package shazam updated to version 0.1.4 with previous version 0.1.3 dated 2016-07-31

Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires.
Author: Mohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>

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Package ontologySimilarity updated to version 2.0 with previous version 1.0 dated 2016-01-13

Title: Functions for Calculating Ontological Similarities
Description: Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>

Diff between ontologySimilarity versions 1.0 dated 2016-01-13 and 2.0 dated 2016-08-05

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Package dynlm updated to version 0.3-5 with previous version 0.3-3 dated 2014-02-20

Title: Dynamic Linear Regression
Description: Dynamic linear models and time series regression.
Author: Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between dynlm versions 0.3-3 dated 2014-02-20 and 0.3-5 dated 2016-08-05

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Package dbscan updated to version 0.9-8 with previous version 0.9-7 dated 2016-04-14

Title: Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph], Matthew Piekenbrock [ctb, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package alakazam updated to version 0.2.5 with previous version 0.2.4 dated 2016-07-28

Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction, diversity profiling, and amino acid property analysis. Also provides core functionality for other tools in the Change-O suite.
Author: Jason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Roy Jiang [ctb], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>

Diff between alakazam versions 0.2.4 dated 2016-07-28 and 0.2.5 dated 2016-08-05

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New package wtest with initial version 1.0
Package: wtest
Type: Package
Title: The W-Test on Genetic Interactions Testing
Version: 1.0
Author: Rui Sun, Maggie Haitian Wang
Maintainer: Rui Sun <rsunzju@gmail.com>
Description: Perform the calculation of W-test, diagnostic checking, calculate minor allele frequency (MAF) and odds ratio.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-08-05 20:50:58 UTC; rui
Repository: CRAN
Date/Publication: 2016-08-05 23:02:36

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Package sparsebnUtils updated to version 0.0.2 with previous version 0.0.1 dated 2016-04-29

Title: Utilities for Learning Sparse Bayesian Networks
Description: A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data.
Author: Bryon Aragam [aut, cre], Jiaying Gu [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>

Diff between sparsebnUtils versions 0.0.1 dated 2016-04-29 and 0.0.2 dated 2016-08-05

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Package MVLM updated to version 0.0.1 with previous version 0.0.0 dated 2016-06-16

Title: Multivariate Linear Model with Analytic p-Values
Description: Allows a user to conduct multivariate multiple regression using analytic p-values rather than classic approximate F-tests.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>

Diff between MVLM versions 0.0.0 dated 2016-06-16 and 0.0.1 dated 2016-08-05

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Package MDMR updated to version 0.4.1 with previous version 0.4.0 dated 2016-03-31

Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>

Diff between MDMR versions 0.4.0 dated 2016-03-31 and 0.4.1 dated 2016-08-05

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Package APtools updated to version 3.0 with previous version 2.0 dated 2016-06-22

Title: Average Positive Predictive Values (AP) for Binary Outcomes and Censored Event Times
Description: We provide tools to estimate two prediction performance metrics, the average positive predictive values (AP) as well as the well-known AUC (the area under the receiver operator characteristic curve) for risk scores or marker. The outcome of interest is either binary or censored event time. Note that for censored event time, our functions estimate the AP and the AUC are time-dependent for pre-specified time interval(s). A function that compares the APs of two risk scores/markers is also included. Optional outputs include positive predictive values and true positive fractions at the specified marker cut-off values, and a plot of the time-dependent AP versus time (available for event time data).
Author: Hengrui Cai <hengruicai@gmail.com>, Yan Yuan <yyuan@ualberta.ca>, Qian Michelle Zhou <qz70@msstate.edu>, Bingying Li<dorisli1120@gmail.com>
Maintainer: Hengrui Cai <hengruicai@gmail.com>

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New package GESE with initial version 1.0
Package: GESE
Type: Package
Title: Gene-Based Segregation Test
Version: 1.0
Date: 2016-08-03
Author: Dandi Qiao
Maintainer: Dandi Qiao <redaq@channing.harvard.edu>
Description: Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hobbs, B., et al. 2016. Gene-based segregation method for identifying rare variants for family-based sequencing studies. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Depends: kinship2
License: GPL-2
NeedsCompilation: yes
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2016-08-05 14:41:57 UTC; redaq
Repository: CRAN
Date/Publication: 2016-08-05 17:20:55

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Package slam updated to version 0.1-37 with previous version 0.1-35 dated 2016-06-14

Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre], David Meyer [aut], Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between slam versions 0.1-35 dated 2016-06-14 and 0.1-37 dated 2016-08-05

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Package Fragman updated to version 1.0.6 with previous version 1.0.5 dated 2016-06-24

Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

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Package tmod updated to version 0.30 with previous version 0.27 dated 2016-06-04

Title: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
Description: Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between tmod versions 0.27 dated 2016-06-04 and 0.30 dated 2016-08-05

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Package RcppStreams updated to version 0.1.1 with previous version 0.1.0 dated 2015-01-31

Title: 'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream Processing
Description: The 'Streamulus' (template, header-only) library by Irit Katriel (at <https://github.com/iritkatriel/streamulus>) provides a very powerful yet convenient framework for stream processing. This package connects 'Streamulus' to R by providing both the header files and all examples.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package Compositional updated to version 1.8 with previous version 1.6 dated 2016-08-01

Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 1.6 dated 2016-08-01 and 1.8 dated 2016-08-05

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Package survey updated to version 3.31 with previous version 3.30-3 dated 2014-08-15

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

Diff between survey versions 3.30-3 dated 2014-08-15 and 3.31 dated 2016-08-05

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New package uaparserjs with initial version 0.1.0
Package: uaparserjs
Type: Package
Title: Parse Browser 'User-Agent' Strings into Data Frames
Version: 0.1.0
Date: 2016-08-04
Authors@R: c( person("Bob", "Rudis", , "bob@rud.is", c("aut", "cre")), person("Lindsey", "Simon", role = "aut", comment = "uap-core"), person("Tobie", "Langel", role = "aut", comment = "uap-core"))
Maintainer: Bob Rudis <bob@rud.is>
Description: Despite there being a section in RFC 7231 <https://tools.ietf.org/html/rfc7231#section-5.5.3> defining a suggested structure for 'User-Agent' headers this data is notoriously difficult to parse consistently. A function is provided that will take in user agent strings and return structured R objects. This is a 'V8'-backed package based on the 'ua-parser' project <https://github.com/ua-parser>.
URL: http://github.com/hrbrmstr/uaparserjs
BugReports: https://github.com/hrbrmstr/uaparserjs/issues
License: Apache License
Suggests: testthat
Depends: R (>= 3.0.0)
Imports: purrr, dplyr, V8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-05 02:53:40 UTC; bob
Author: Bob Rudis [aut, cre], Lindsey Simon [aut] (uap-core), Tobie Langel [aut] (uap-core)
Repository: CRAN
Date/Publication: 2016-08-05 11:53:30

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Package statmod updated to version 1.4.25 with previous version 1.4.24 dated 2016-02-02

Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>

Diff between statmod versions 1.4.24 dated 2016-02-02 and 1.4.25 dated 2016-08-05

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Package MXM updated to version 0.9.4 with previous version 0.9.3 dated 2016-07-10

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>

Diff between MXM versions 0.9.3 dated 2016-07-10 and 0.9.4 dated 2016-08-05

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Package mombf updated to version 1.8.0 with previous version 1.7.1 dated 2016-05-17

Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local and Zellner priors. Bayes factors, marginal densities and variable selection in regression setups. Routines to sample, evaluate prior densities, distribution functions and quantiles are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>

Diff between mombf versions 1.7.1 dated 2016-05-17 and 1.8.0 dated 2016-08-05

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New package MetaIntegrator with initial version 1.0.0
Package: MetaIntegrator
Type: Package
Title: MetaIntegrator- Meta-Analysis of Gene Expression Data
Version: 1.0.0
Date: 2016-07-28
Author: Winston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Maintainer: Winston A. Haynes <hayneswa@stanford.edu>
Description: A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis).
License: LGPL
Imports: rmeta, multtest, ggplot2, parallel, Rmisc, reshape, gplots, Biobase, RMySQL, DBI, stringr, preprocessCore, GEOquery, GEOmetadb, RSQLite
Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-04 23:58:44 UTC; hayneswa
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2016-08-05 11:53:08

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Package liftr updated to version 0.4 with previous version 0.3 dated 2015-10-11

Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb], Tengfei Yin [ctb], Nan Xiao [aut, cre]
Maintainer: Nan Xiao <me@nanx.me>

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Package l0ara updated to version 0.1.3 with previous version 0.1.2 dated 2016-07-26

Title: Sparse Generalized Linear Model with L0 Approximation for Feature Selection
Description: An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
Author: Wenchuan Guo, Zhenqiu Liu, Fengzhu Sun, Dermot P McGovern, Sandra Orsulic
Maintainer: Wenchuan Guo <wguo007@ucr.edu>

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Package hdnom updated to version 4.1 with previous version 4.0 dated 2016-07-05

Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for reproducible model validation, calibration, and comparison.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <me@nanx.me>
Maintainer: Nan Xiao <me@nanx.me>

Diff between hdnom versions 4.0 dated 2016-07-05 and 4.1 dated 2016-08-05

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Package grex updated to version 1.2 with previous version 1.1 dated 2016-06-13

Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description: Convert the 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
Author: Nan Xiao <me@nanx.me>, Gao Wang <gaow@uchicago.edu>, Lei Sun <sunl@uchicago.edu>
Maintainer: Nan Xiao <me@nanx.me>

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Package ggsci updated to version 1.5 with previous version 1.1 dated 2016-04-04

Title: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by scientific journals and science fiction TV shows.
Author: Nan Xiao <me@nanx.me>, Miaozhu Li <miaozhu.li@duke.edu>
Maintainer: Nan Xiao <me@nanx.me>

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Package formattable updated to version 0.2.0.1 with previous version 0.2 dated 2016-07-28

Title: Create 'Formattable' Data Structures
Description: Provides functions to create formattable vectors and data frames. 'Formattable' vectors are printed with text formatting, and formattable data frames are printed with multiple types of formatting in HTML to improve the readability of data presented in tabular form rendered in web pages.
Author: Kun Ren [aut, cre], Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>

Diff between formattable versions 0.2 dated 2016-07-28 and 0.2.0.1 dated 2016-08-05

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Package caret updated to version 6.0-71 with previous version 6.0-70 dated 2016-06-13

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau, Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>

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