Tue, 23 May 2017

Package tsiR updated to version 0.2.0 with previous version 0.1.0 dated 2017-02-17

Title: An Implementation of the TSIR Model
Description: An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The method implemented here is described by Finkenstadt and Grenfell (2000) <DOI:10.1111/1467-9876.00187>.
Author: Alexander D. Becker [aut, cre], Sinead E. Morris [ctb]
Maintainer: Alexander D. Becker <adbecker@princeton.edu>

Diff between tsiR versions 0.1.0 dated 2017-02-17 and 0.2.0 dated 2017-05-23

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Package simEd updated to version 1.0.1 with previous version 1.0.0 dated 2017-05-10

Title: Simulation Education
Description: Contains various functions to be used for simulation education, including queueing simulation functions, variate generation functions capable of producing independent streams and antithetic variates, functions for illustrating random variate generation for various discrete and continuous distributions, and functions to compute time-persistent statistics. Also contains two queueing data sets (one fabricated, one real-world) to facilitate input modeling.
Author: Barry Lawson, Larry Leemis
Maintainer: Barry Lawson <blawson@richmond.edu>

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Package regnet updated to version 0.1.1 with previous version 0.1.0 dated 2017-05-21

Title: Network-Based Regularization for Generalized Linear Models
Description: Network-based regularization has achieved success in variable selections for high-dimensional biological data, due to its ability to incorporate the correlations among genomic features. This package provides procedures for fitting network-based regularization, minimax concave penalty (MCP) and lasso penalty for generalized linear models. This first version, regnet0.1.1, focuses on binary outcomes. Functions for continuous, survival outcomes and other regularization methods will be included in the forthcoming upgraded version.
Author: Jie Ren, Luann C. Jung, Yinhao Du, Cen Wu, Yu Jiang, Junhao Liu
Maintainer: Jie Ren <jieren@ksu.edu>

Diff between regnet versions 0.1.0 dated 2017-05-21 and 0.1.1 dated 2017-05-23

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Package HTSSIP updated to version 1.1.1 with previous version 1.0.3 dated 2016-11-01

Title: High Throughput Sequencing of Stable Isotope Probing Data Analysis
Description: Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).
Author: Nicholas Youngblut [aut, cre], Samuel Barnett [ctb]
Maintainer: Nicholas Youngblut <nyoungb2@gmail.com>

Diff between HTSSIP versions 1.0.3 dated 2016-11-01 and 1.1.1 dated 2017-05-23

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Package corpus updated to version 0.5.0 with previous version 0.4.0 dated 2017-05-16

Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, and for computing term occurrence frequencies.
Author: Patrick O. Perry [aut, cre], Martin Porter and Richard Boulton [ctb, cph] (Snowball), Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

Diff between corpus versions 0.4.0 dated 2017-05-16 and 0.5.0 dated 2017-05-23

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Package QNB updated to version 1.1.8 with previous version 1.1.7 dated 2017-01-11

Title: Differential RNA Methylation Analysis for Count-Based Small-Sample Sequencing Data with a Quad-Negative Binomial Model
Description: As a newly emerged research area, RNA epigenetics has drawn increasing attention recently for the participation of RNA methylation and other modifications in a number of crucial biological processes. Thanks to high throughput sequencing techniques, such as m6A-Seq, transcriptome-wide RNA methylation profile is now available in the form of count-based data, with which it is often of interests to study the dynamics in epitranscriptomic layer. However, the sample size of RNA methylation experiment is usually very small due to its costs; and additionally, there usually exist a large number of genes whose methylation level cannot be accurately estimated due to their low expression level, making differential RNA methylation analysis a difficult task. We present QNB, a statistical approach for differential RNA methylation analysis with count-based small-sample sequencing data. The method is based on 4 independent negative binomial dis-tributions with their variances and means linked by local regressions. QNB showed improved performance on simulated and real m6A-Seq datasets when compared with competing algorithms. And the QNB model is also applicable to other datasets related RNA modifications, including but not limited to RNA bisulfite sequencing, m1A-Seq, Par-CLIP, RIP-Seq, etc.Please don't hesitate to contact <liulian19860905@163.com> if you have any questions.
Author: Lian Liu <liulian19860905@163.com>
Maintainer: Lian Liu <liulian19860905@163.com>

Diff between QNB versions 1.1.7 dated 2017-01-11 and 1.1.8 dated 2017-05-23

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Package multisom updated to version 1.3 with previous version 1.2 dated 2016-11-06

Title: Clustering a Data Set using Multi-SOM Algorithm
Description: Implements two versions of the algorithm namely: stochastic and batch. The package determines also the best number of clusters and offers to the user the best clustering scheme from different results.
Author: Sarra Chair and Malika Charrad
Maintainer: Sarra Chair <sarra.chair@gmail.com>

Diff between multisom versions 1.2 dated 2016-11-06 and 1.3 dated 2017-05-23

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Package JOUSBoost updated to version 2.0.0 with previous version 1.0.0 dated 2016-09-12

Title: Implements Under/Oversampling for Probability Estimation
Description: Implements under/oversampling for probability estimation. To be used with machine learning methods such as adaBoost, random forests, etc.
Author: Matthew Olson [aut, cre]
Maintainer: Matthew Olson <maolson@wharton.upenn.edu>

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Package IRISMustangMetrics updated to version 2.0.8 with previous version 2.0.4 dated 2017-02-11

Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the 'IRIS DMC MUSTANG' project. The functionality in this package builds upon the base classes of the 'IRISSeismic' package. Metrics include basic statistics as well as higher level 'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut], Rob Casey [aut], Mary Templeton [aut], Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>

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Package hBayesDM updated to version 0.4.0 with previous version 0.3.0 dated 2017-01-22

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

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Package GenomicMating updated to version 1.2 with previous version 1.1 dated 2017-05-22

Title: Efficient Breeding by Genomic Mating
Description: Implements the genomic mating approach in the recently published article: Akdemir, D., & Sanchez, J. I. (2016). Efficient Breeding by Genomic Mating. Frontiers in Genetics, 7. <DOI:10.3389/fgene.2016.00210>.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>

Diff between GenomicMating versions 1.1 dated 2017-05-22 and 1.2 dated 2017-05-23

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Package BTLLasso updated to version 0.1-6 with previous version 0.1-5 dated 2017-01-16

Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' (Schauberger and Tutz, 2017: Subject-Specific Modelling of Paired Comparison Data - a Lasso-Type Penalty Approach), a method to include different types of variables in paired comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>

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Package brms updated to version 1.7.0 with previous version 1.6.1 dated 2017-04-17

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models using Stan for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package BacArena updated to version 1.6 with previous version 1.5.1 dated 2016-07-25

Title: Modeling Framework for Cellular Communities in their Environments
Description: Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.
Author: Eugen Bauer [aut], Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>

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Package Tmisc updated to version 0.1.16 with previous version 0.1.15 dated 2017-05-16

Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation, data tidying, and working with gene expression data.
Author: Stephen Turner [aut, cre]
Maintainer: Stephen Turner <vustephen@gmail.com>

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Package rpatrec updated to version 1.0.1 with previous version 0.9.1 dated 2017-04-20

Title: Recognising Visual Charting Patterns in Time Series Data
Description: Generating visual charting patterns and noise, smoothing to find a signal in noisy time series and enabling users to apply their findings to real life data.
Author: Stephan Maier [aut, cre]
Maintainer: Stephan Maier <sm297@st-andrews.ac.uk>

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Package itcSegment updated to version 0.5 with previous version 0.4 dated 2017-04-13

Title: Individual Tree Crowns Segmentation
Description: Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>

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Package xLLiM updated to version 2.1 with previous version 2.0 dated 2017-05-16

Title: High Dimensional Locally-Linear Mapping
Description: Provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <https://hal.archives-ouvertes.fr/hal-01347455>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <https://arxiv.org/abs/1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).
Author: Emeline Perthame (emeline.perthame@inria.fr), Florence Forbes (florence.forbes@inria.fr), Antoine Deleforge (antoine.deleforge@inria.fr), Emilie Devijver (emilie.devijver@kuleuven.be), Melina Gallopin (melina.gallopin@u-psud.fr)
Maintainer: Emeline Perthame <emeline.perthame@pasteur.fr>

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Package glm.predict updated to version 2.5-1 with previous version 2.5-0 dated 2017-05-16

Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between the two cases with confidence interval for glm(), glm.nb(), polr() and multinom().
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>

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Package flan updated to version 0.5 with previous version 0.4 dated 2017-03-02

Title: FLuctuation ANalysis on Mutation Models
Description: Tools for fluctuations analysis of mutant cells counts.
Author: Adrien Mazoyer [aut, cre], Remy Drouilhet [aut], Stephane Despreaux [aut], Bernard Ycart [aut]
Maintainer: Adrien Mazoyer <Adrien.Mazoyer@univ-grenoble-alpes.fr>

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Package metacoder updated to version 0.1.3 with previous version 0.1.2 dated 2016-08-26

Title: Tools for Parsing, Manipulating, and Graphing Hierarchical Data
Description: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre], Niklaus Grunwald [ths]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>

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Package minval updated to version 0.7 with previous version 0.6 dated 2017-04-02

Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package evaluates the mass and charge balance, extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to characterize and write models in TSV and SBML formats.
Author: Daniel Osorio [aut, cre], Janneth Gonzalez [aut, ths], Andres Pinzon [aut, ths]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>

Diff between minval versions 0.6 dated 2017-04-02 and 0.7 dated 2017-05-23

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Package kableExtra updated to version 0.2.0 with previous version 0.1.0 dated 2017-03-02

Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: A collection of functions to help build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre], Will Beasley [ctb], Yihui Xie [ctb], Thomas Travison [ctb], GuangChuang Yu [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>

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Package distances updated to version 0.1.2 with previous version 0.1.1 dated 2017-05-21

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@berkeley.edu>

Diff between distances versions 0.1.1 dated 2017-05-21 and 0.1.2 dated 2017-05-23

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Package dataRetrieval updated to version 2.7.2 with previous version 2.7.1 dated 2017-05-19

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut], Jordan Read [ctb], Jordan Walker [ctb], Lindsay Carr [ctb], David Watkins [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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Package crul updated to version 0.3.6 with previous version 0.3.4 dated 2017-03-31

Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Mon, 22 May 2017

Package ZeligEI updated to version 0.1-1 with previous version 0.1-0 dated 2016-05-28

Title: Zelig Ecological Inference Models
Description: Add-on package for Zelig 5. Enables the use of a variety of ecological inference models.
Author: Christopher Gandrud [cre], James Honaker [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>

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Package voxel updated to version 1.3.2 with previous version 1.2.1 dated 2016-08-26

Title: Mass-Univariate Voxelwise Analysis of Medical Imaging Data
Description: Functions for the mass-univariate voxelwise analysis of medical imaging data that follows the NIfTI <http://nifti.nimh.nih.gov> format.
Author: Angel Garcia de la Garza [aut, cre], Simon Vandekar [aut], David Roalf [aut], Kosha Ruparel [aut], Ruben Gur [aut], Raquel Gur [aut], Theodore Satterthwaite [aut], R. Taki Shinohara [aut]
Maintainer: Angel Garcia de la Garza <agarciadlg@gmail.com>

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Package SubVis updated to version 2.0.2 with previous version 2.0.1 dated 2017-01-12

Title: Visual Exploration of Protein Alignments Resulting from Multiple Substitution Matrices
Description: Substitution matrices are important parameters in protein alignment algorithms. These matrices represent the likelihood that an amino acid will be substituted for another during mutation. This tool allows users to apply predefined and custom matrices and then explore the resulting alignments with interactive visualizations. 'SubVis' requires the availability of a web browser.
Author: Scott Barlowe <sabarlowe@email.wcu.edu>
Maintainer: Scott Barlowe <sabarlowe@email.wcu.edu>

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Package sarima updated to version 0.4-5 with previous version 0.4-3 dated 2017-02-06

Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA and related models. The aim of the package is to provide consistent interface for the user. For example, a single function autocorrelations() computes various kinds of theoretical and sample autocorrelations. This is work in progress, see the documentation and vignettes for the current functionality.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package samplingbook updated to version 1.2.2 with previous version 1.2.1 dated 2016-07-10

Title: Survey Sampling Procedures
Description: Sampling procedures from the book 'Stichproben - Methoden und praktische Umsetzung mit R' by Goeran Kauermann and Helmut Kuechenhoff (2010).
Author: Juliane Manitz <r@manitz.org>, contributions by Mark Hempelmann <mark.hempelmann@o2online.de>, Goeran Kauermann <gkauermann@wiwi.uni-bielefeld.de>, Helmut Kuechenhoff <kuechenhoff@stat.uni-muenchen.de>, Shuai Shao <shuai.shao@campus.lmu.de>, Cornelia Oberhauser <conny.oberhauser@gmx.de>, Nina Westerheide <nwesterheide@wiwi.uni-bielefeld.de>, Manuel Wiesenfarth <m.wiesenfarth@uni-goettingen.de>
Maintainer: Juliane Manitz <r@manitz.org>

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Package moveVis updated to version 0.9.1 with previous version 0.9 dated 2017-05-18

Title: Movement Data Visualization
Description: Tools to visualize movement data of any kind, e. g by creating path animations from GPS point data.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>

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Package LatticeKrig updated to version 6.4 with previous version 6.2 dated 2016-12-20

Title: Multiresolution Kriging Based on Markov Random Fields
Description: Methods for the interpolation of large spatial datasets. This package follows a "fixed rank Kriging" approach using a large number of basis functions and provides spatial estimates that are comparable to standard families of covariance functions. Using a large number of basis functions allows for estimates that can come close to interpolating the observations (a spatial model with a small nugget variance.) Moreover, the covariance model for this method can approximate the Matern covariance family but also allows for a multi-resolution model and supports efficient computation of the profile likelihood for estimating covariance parameters. This is accomplished through compactly supported basis functions and a Markov random field model for the basis coefficients. These features lead to sparse matrices for the computations and this package makes of the R spam package for this. An extension of this version over previous ones ( < 5.4 ) is the support for different geometries besides a rectangular domain. The Markov random field approach combined with a basis function representation makes the implementation of different geometries simple where only a few specific functions need to be added with most of the computation and evaluation done by generic routines that have been tuned to be efficient. One benefit of this package's model/approach is the facility to do unconditional and conditional simulation of the field for large numbers of arbitrary points. There is also the flexibility for estimating non-stationary covariances and also the case when the observations are a linear combination (e.g. an integral) of the spatial process. Included are generic methods for prediction, standard errors for prediction, plotting of the estimated surface and conditional and unconditional simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut], Colette Smirniotis [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>

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Package foghorn updated to version 0.4.4 with previous version 0.4.2 dated 2017-02-08

Title: Summarizes CRAN Check Results in the Terminal
Description: The CRAN check results in your R terminal.
Author: Francois Michonneau [aut, cre], Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

Diff between foghorn versions 0.4.2 dated 2017-02-08 and 0.4.4 dated 2017-05-22

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Package FLLat updated to version 1.2-1 with previous version 1.2 dated 2015-09-16

Title: Fused Lasso Latent Feature Model
Description: Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV). Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample. Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.
Author: Gen Nowak [aut, cre], Trevor Hastie [aut], Jonathan R. Pollack [aut], Robert Tibshirani [aut], Nicholas Johnson [aut]
Maintainer: Gen Nowak <gen.nowak@gmail.com>

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Package brglm2 updated to version 0.1.4 with previous version 0.1.3 dated 2017-04-04

Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses, the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre], Kjell Konis [ctb], Euloge Clovis Kenne Pagui [ctb], Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <i.kosmidis@ucl.ac.uk>

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Package GenomicMating updated to version 1.1 with previous version 1.0 dated 2017-03-31

Title: Efficient Breeding by Genomic Mating
Description: Implements the genomic mating approach in the recently published article: Akdemir, D., & Sanchez, J. I. (2016). Efficient Breeding by Genomic Mating. Frontiers in Genetics, 7. <DOI:10.3389/fgene.2016.00210>.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>

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Package backports updated to version 1.1.0 with previous version 1.0.5 dated 2017-01-18

Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>

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Package Rd2md updated to version 0.0.2 with previous version 0.0.1 dated 2017-05-21

Title: Markdown Reference Manuals
Description: The native R functionalities only allow PDF exports of reference manuals. This shall be extended by converting the package documentation files into markdown files and combining them into a markdown version of the package reference manual.
Author: Julian Busch [aut, cre]
Maintainer: Julian Busch <jb@quants.ch>

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Package DA.MRFA updated to version 1.1.2 with previous version 1.1 dated 2017-04-19

Title: Dimensionality Assessment using Minimum Rank Factor Analysis
Description: Performs Parallel Analysis for assessing the dimensionality of a set of variables using Minimum Rank Factor Analysis (see Timmerman & Lorenzo-Seva (2011) <DOI:10.1037/a0023353> and ten Berge & Kiers (1991) <DOI:10.1007/BF02294464> for more information). The package also includes the option to compute Minimum Rank Factor Analysis by itself, as well as the Greater Lower Bound calculation.
Author: David Navarro-Gonzalez, Urbano Lorenzo-Seva
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>

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Package reticulate updated to version 0.8 with previous version 0.7 dated 2017-03-14

Title: R Interface to Python
Description: R interface to Python modules, classes, and functions. When calling into Python R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.
Author: JJ Allaire [aut, cre], Kevin Ushey [ctb], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package diagis updated to version 0.1.2 with previous version 0.1.0 dated 2016-10-29

Title: Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling
Description: Fast functions for effective sample size, weighted multivariate mean and variance computation, and weight diagnostic plot for generic importance sampling type results.
Author: Jouni Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

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Package leaflet.minicharts updated to version 0.3.0 with previous version 0.2.0 dated 2017-05-05

Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with package 'leaflet'. These charts can be used to represent at same time multiple variables on a single map.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

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Package ROI updated to version 0.2-6 with previous version 0.2-5 dated 2017-05-17

Title: R Optimization Infrastructure
Description: The R Optimization Infrastructure ('ROI') is a sophisticated framework for handling optimization problems in R.
Author: Kurt Hornik [aut], David Meyer [aut], Florian Schwendinger [aut], Stefan Theussl [aut, cre], Diethelm Wuertz [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>

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Package dfmta updated to version 1.5 with previous version 1.4 dated 2017-03-27

Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

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Package dfcomb updated to version 2.3 with previous version 2.2 dated 2017-03-27

Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

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Package acebayes updated to version 1.4 with previous version 1.3.4 dated 2017-02-10

Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall, David C. Woods & Maria Adamou
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>

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Package carpenter updated to version 0.2.1 with previous version 0.2.0 dated 2016-07-29

Title: Build Common Tables of Summary Statistics for Reports
Description: Mainly used to build tables that are commonly presented for bio-medical/health research, such as basic characteristic tables or descriptive statistics.
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>

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Package testit updated to version 0.7 with previous version 0.6 dated 2016-11-09

Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.
Author: Yihui Xie
Maintainer: Yihui Xie <xie@yihui.name>

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Package scclust updated to version 0.1.1 with previous version 0.1.0 dated 2017-03-28

Title: Size-Constrained Clustering
Description: Provides wrappers for 'scclust', a C library for computationally efficient size-constrained clustering with near-optimal performance. See <https://github.com/fsavje/scclust> for more information.
Author: Fredrik Savje [aut, cre], Michael Higgins [aut], Jasjeet Sekhon [aut]
Maintainer: Fredrik Savje <fredrik.savje@berkeley.edu>

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Package RcmdrPlugin.UCA updated to version 4.1-1 with previous version 3.1-2 dated 2016-09-20

Title: UCA Rcmdr Plug-in
Description: Some extension to Rcmdr (R Commander), randomness test, variance test for one normal sample and predictions using active model, made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>

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Package plumber updated to version 0.3.2 with previous version 0.3.1 dated 2016-10-04

Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.
Author: Trestle Technology, LLC [aut], Jeff Allen [cre], Frans van Dunné [ctb]
Maintainer: Jeff Allen <cran@trestletech.com>

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Package Rcpp updated to version 0.12.11 with previous version 0.12.10 dated 2017-03-19

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Sun, 21 May 2017

Package rngWELL updated to version 0.10-5 with previous version 0.10-4 dated 2015-07-27

Title: Toolbox for WELL Random Number Generators
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky <savicky@cs.cas.cz>.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

Diff between rngWELL versions 0.10-4 dated 2015-07-27 and 0.10-5 dated 2017-05-21

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Package preseqR updated to version 3.1.0 with previous version 3.0.1 dated 2017-04-19

Title: Predicting the Number of Species in a Random Sample
Description: The relation between the number of species and the number of individuals in a random sample is a classic problem back to Fisher (1943) <doi:10.2307/1411>. We generalize this problem to estimate the number of species represented at least r times in a random sample. In particular when r=1, it becomes the classic problem. We use a mixture of Poisson processes to model sampling procedures and apply a nonparametric empirical Bayes approach to obtain an estimator. For more information on preseqR, see Deng C, Daley T and Smith AD (2015) <doi:10.1007/s40484-015-0049-7> and Deng C and Smith AD (2016) <arXiv:1607.02804v2>.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>

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Package LEGIT updated to version 1.1.1 with previous version 1.1.0 dated 2017-05-11

Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where G is a weighted sum of genetic variants (genetic score) and E is a weighted sum of environments (environmental score) using the alternating optimization algorithm by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly enhanced predictive power over traditional GxE models which include only a single genetic variant and a single environmental exposure. Although this approach was originally made for GxE modelling, it is flexible and does not require the use of genetic and environmental variables. It can also handle more than 2 latent variables (rather than just G and E) and 3-way interactions or more. The LEGIT model produces highly interpretable results and is very parameter-efficient thus it can even be used with small sample sizes (n < 250).
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>

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Package DynTxRegime updated to version 3.01 with previous version 3.0 dated 2017-05-15

Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

Diff between DynTxRegime versions 3.0 dated 2017-05-15 and 3.01 dated 2017-05-21

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Package distances updated to version 0.1.1 with previous version 0.1.0 dated 2017-03-05

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@berkeley.edu>

Diff between distances versions 0.1.0 dated 2017-03-05 and 0.1.1 dated 2017-05-21

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Package GGIR updated to version 1.5-9 with previous version 1.5-7 dated 2017-05-09

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices, .csv-export data from Actigraph devices, and .cwa and .wav-format data from Axivity. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

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Package bib2df updated to version 0.2 with previous version 0.1.1 dated 2016-08-08

Title: Parse a BibTeX File to a Data.frame
Description: Parse a BibTeX file to a data.frame to make it accessible for further analysis and visualization.
Author: Philipp Ottolinger [aut, cre], Thomas Leeper [ctb]
Maintainer: Philipp Ottolinger <philipp@ottolinger.de>

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Package opencpu updated to version 2.0.1 with previous version 2.0 dated 2017-05-14

Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package clisymbols updated to version 1.2.0 with previous version 1.1.0 dated 2017-01-27

Title: Unicode Symbols at the R Prompt
Description: A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the 'figures' 'npm' package (see <https://github.com/sindresorhus/figures>).
Author: Gábor Csárdi [aut, cre], Sindre Sorhus [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between clisymbols versions 1.1.0 dated 2017-01-27 and 1.2.0 dated 2017-05-21

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Package hunspell updated to version 2.5 with previous version 2.4 dated 2017-04-30

Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for languages with rich morphology and complex word compounding or character encoding. The package can check and analyze individual words as well as search for incorrect words within a text, latex, html or xml document. Use the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package ROI.plugin.clp updated to version 0.3 with previous version 0.2 dated 2017-05-11

Title: 'Clp (Coin-or linear programming)' Plugin for the 'R' Optimization Interface
Description: Enhances the R Optimization Infrastructure (ROI) package by registering the COIN-OR Clp open-source solver from the COIN-OR suite <https://projects.coin-or.org/>. It allows for solving linear programming with continuous objective variables keeping sparse constraints definition.
Author: Benoit Thieurmel [aut, cre]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>

Diff between ROI.plugin.clp versions 0.2 dated 2017-05-11 and 0.3 dated 2017-05-21

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Package optimization updated to version 1.0-4 with previous version 1.0-1 dated 2016-12-04

Title: Flexible Optimization
Description: Flexible optimizer with numerous input specifications. It allows a very detailed parameterization and is therefore useful for specific and complex loss functions, like functions with discrete parameter space. Also visualization tools for validation and analysis of the convergence are included.
Author: Kai Husmann and Alexander Lange
Maintainer: Kai Husmann <khusman1@uni-goettingen.de>

Diff between optimization versions 1.0-1 dated 2016-12-04 and 1.0-4 dated 2017-05-21

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Package forestinventory updated to version 0.2.0 with previous version 0.1.0 dated 2016-07-06

Title: Design-Based Global and Small-Area Estimations for Multiphase Forest Inventories
Description: Extensive global and small-area estimation procedures for multiphase forest inventories under the design-based Monte-Carlo approach are provided. The implementation includes estimators for simple and cluster sampling published by Daniel Mandallaz in 2007 (<DOI:10.1201/9781584889779>), 2013 (<DOI:10.1139/cjfr-2012-0381>, <DOI:10.1139/cjfr-2013-0181>, <DOI:10.1139/cjfr-2013-0449>, <DOI:10.3929/ethz-a-009990020>) and 2016 (<DOI:10.3929/ethz-a-010579388>). It provides point estimates, their external- and design-based variances as well as confidence intervals. The procedures have also been optimized for the use of remote sensing data as auxiliary information.
Author: Andreas Hill [aut, cre], Alexander Massey [aut], Daniel Mandallaz [ctb]
Maintainer: Andreas Hill <andreas.hill@usys.ethz.ch>

Diff between forestinventory versions 0.1.0 dated 2016-07-06 and 0.2.0 dated 2017-05-21

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Package edfReader updated to version 1.1.2 with previous version 1.1.1 dated 2016-04-18

Title: Reading EDF(+) and BDF(+) Files
Description: Reads European Data Format files EDF and EDF+, see <http://www.edfplus.info>, BioSemi Data Format files BDF, see <http://www.biosemi.com/faq/file_format.htm>, and BDF+ files, see <http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html>. The files are read in two steps: first the header is read and then the signals (using the header object as a parameter).
Author: Jan Vis [aut, cre]
Maintainer: Jan Vis <jan@visconsultancy.eu>

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Package timereg updated to version 1.9.1 with previous version 1.9.0 dated 2016-10-06

Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, fast cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>

Diff between timereg versions 1.9.0 dated 2016-10-06 and 1.9.1 dated 2017-05-21

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 timereg-1.9.1/timereg/R/clusterindex-reshape.r        |    8 
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More information about timereg at CRAN
Permanent link

Package RANN updated to version 2.5.1 with previous version 2.5 dated 2015-04-20

Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between RANN versions 2.5 dated 2015-04-20 and 2.5.1 dated 2017-05-21

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More information about RANN at CRAN
Permanent link

Package mclust updated to version 5.3 with previous version 5.2.3 dated 2017-03-13

Title: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut], Adrian E. Raftery [aut], Luca Scrucca [aut, cre], Thomas Brendan Murphy [ctb], Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

Diff between mclust versions 5.2.3 dated 2017-03-13 and 5.3 dated 2017-05-21

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More information about mclust at CRAN
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Package IgorR updated to version 0.8.1 with previous version 0.8 dated 2015-05-28

Title: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)
Description: Provides function to read data from the 'Igor Pro' data analysis program by Wavemetrics. The data formats supported are 'Igor' packed experiment format (pxp) and 'Igor' binary wave (ibw). See: http://www.wavemetrics.com/ for details. Also includes functions to load special pxp files produced by the 'Igor Pro' 'Neuromatic' and 'Nclamp' packages for recording and analysing neuronal data. See http://www.neuromatic.thinkrandom.com/ for details.
Author: Greg Jefferis with contributions from Thomas Braun
Maintainer: Greg Jefferis <jefferis@gmail.com>

Diff between IgorR versions 0.8 dated 2015-05-28 and 0.8.1 dated 2017-05-21

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 NAMESPACE                     |    5 ++++-
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More information about IgorR at CRAN
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Package GlobalOptions updated to version 0.0.12 with previous version 0.0.11 dated 2017-03-06

Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between GlobalOptions versions 0.0.11 dated 2017-03-06 and 0.0.12 dated 2017-05-21

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Package dynr updated to version 0.1.10-10 with previous version 0.1.9-20 dated 2017-02-24

Title: Dynamic Modeling in R
Description: Intensive longitudinal data have become increasingly prevalent in various scientific disciplines. Many such data sets are noisy, multivariate, and multi-subject in nature. The change functions may also be continuous, or continuous but interspersed with periods of discontinuities (i.e., showing regime switches). The package \pkg{dynr} (Dynamic Modeling in R) is an R package that implements a set of computationally efficient algorithms for handling a broad class of linear and nonlinear discrete- and continuous-time models with regime-switching properties under the constraint of linear Gaussian measurement functions. The discrete-time models can generally take on the form of a state- space or difference equation model. The continuous-time models are generally expressed as a set of ordinary or stochastic differential equations. All estimation and computations are performed in C, but users are provided with the option to specify the model of interest via a set of simple and easy-to-learn model specification functions in R. Model fitting can be performed using single- subject time series data or multiple-subject longitudinal data.
Author: Lu Ou [aut], Michael D. Hunter [aut, cre], Sy-Miin Chow [aut]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>

Diff between dynr versions 0.1.9-20 dated 2017-02-24 and 0.1.10-10 dated 2017-05-21

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Package imputeTS updated to version 2.3 with previous version 2.2 dated 2017-04-23

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

Diff between imputeTS versions 2.2 dated 2017-04-23 and 2.3 dated 2017-05-21

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 imputeTS-2.3/imputeTS/NEWS                                                             |   11 ++++
 imputeTS-2.3/imputeTS/R/na.kalman.R                                                    |    2 
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 imputeTS-2.3/imputeTS/R/na.seasplit.R                                                  |    6 ++
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Permanent link

Package GWmodel updated to version 2.0-4 with previous version 2.0-3 dated 2017-03-28

Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>

Diff between GWmodel versions 2.0-3 dated 2017-03-28 and 2.0-4 dated 2017-05-21

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Package d3r updated to version 0.6.5 with previous version 0.6.4 dated 2017-04-27

Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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More information about d3r at CRAN
Permanent link

Package aSPU updated to version 1.47 with previous version 1.46 dated 2016-11-08

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single nucleotide polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended 'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.46 dated 2016-11-08 and 1.47 dated 2017-05-21

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More information about aSPU at CRAN
Permanent link

Package plfMA updated to version 1.0.4 with previous version 1.0.3 dated 2016-06-13

Title: A GUI to View, Design and Export Various Graphs of Data
Description: Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>

Diff between plfMA versions 1.0.3 dated 2016-06-13 and 1.0.4 dated 2017-05-21

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Sat, 20 May 2017

Package schumaker updated to version 1.0 with previous version 0.3 dated 2016-02-29

Title: Schumaker Shape-Preserving Spline
Description: This is a shape preserving spline which is guaranteed to be monotonic and concave or convex if the data is monotonic and concave or convex. It does not use any optimisation and is therefore quick and smoothly converges to a fixed point in economic dynamics problems including value function iteration. It also automatically gives the first two derivatives of the spline and options for determining behaviour when evaluated outside the interpolation domain.
Author: Stuart Baumann [aut, cre], Margaryta Klymak[aut]
Maintainer: Stuart Baumann <Stuart@StuartBaumann.com>

Diff between schumaker versions 0.3 dated 2016-02-29 and 1.0 dated 2017-05-20

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Package countyfloods updated to version 0.0.2 with previous version 0.0.1 dated 2017-04-01

Title: Quantify United States County-Level Flood Measurements
Description: Quantifies United States flood impacts at the county level using United States Geological Service (USGS) River Discharge data for the USGS API. This package builds on R packages from the USGS, with the goal of creating county-level time series of flood status that can be more easily joined with county-level impact measurements, including health outcomes. This work was supported in part by grants from the National Institute of Environmental Health Sciences (R00ES022631), the Colorado Water Center, and the National Science Foundation, Integrative Graduate Education and Research Traineeship (IGERT) Grant No. DGE-0966346 "I-WATER: Integrated Water, Atmosphere, Ecosystems Education and Research Program" at Colorado State University.
Author: Rod Lammers [aut, cre], Brooke Anderson [aut]
Maintainer: Rod Lammers <rodlammers@gmail.com>

Diff between countyfloods versions 0.0.1 dated 2017-04-01 and 0.0.2 dated 2017-05-20

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Package AIG updated to version 0.1.5 with previous version 0.1.3 dated 2017-03-15

Title: Automatic Item Generator
Description: A collection of Automatic Item Generators used mainly for psychological research. This package can generate linear syllogistic reasoning, arithmetic and 2D/3D spatial reasoning items. It is recommended for research purpose only.
Author: Bao Sheng Loe (Aiden) [aut,cre,cph]
Maintainer: Bao Sheng Loe (Aiden) <bsl28@cam.ac.uk>

Diff between AIG versions 0.1.3 dated 2017-03-15 and 0.1.5 dated 2017-05-20

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Package nabor updated to version 0.4.7 with previous version 0.4.6 dated 2015-05-28

Title: Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions
Description: An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). 'libnabo' has speed and space advantages over the 'ANN' library wrapped by package 'RANN'. 'nabor' includes a knn function that is designed as a drop-in replacement for 'RANN' function nn2. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.
Author: Stephane Mangenat (for 'libnabo'), Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between nabor versions 0.4.6 dated 2015-05-28 and 0.4.7 dated 2017-05-20

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Package dendroextras updated to version 0.2.2 with previous version 0.2.1 dated 2014-08-04

Title: Extra Functions to Cut, Label and Colour Dendrogram Clusters
Description: Provides extra functions to manipulate dendrograms that build on the base functions provided by the 'stats' package. The main functionality it is designed to add is the ability to colour all the edges in an object of class 'dendrogram' according to cluster membership i.e. each subtree is coloured, not just the terminal leaves. In addition it provides some utility functions to cut 'dendrogram' and 'hclust' objects and to set/get labels.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between dendroextras versions 0.2.1 dated 2014-08-04 and 0.2.2 dated 2017-05-20

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Package bigQueryR updated to version 0.3.1 with previous version 0.3.0 dated 2017-05-03

Title: Interface with Google BigQuery with Shiny Compatibility
Description: Interface with 'Google BigQuery', see <https://cloud.google.com/bigquery/> for more information. This package uses 'googleAuthR' so is compatible with similar packages, including 'Google Cloud Storage' (<https://cloud.google.com/storage/>) for result extracts.
Author: Mark Edmondson [aut, cre], Hadley Wickham [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>

Diff between bigQueryR versions 0.3.0 dated 2017-05-03 and 0.3.1 dated 2017-05-20

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Package PowerTOST updated to version 1.4-5 with previous version 1.4-4 dated 2017-03-16

Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability and/or uncertain theta0. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability and/or uncertain theta0. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits (EMA recommended) based on simulations. Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively adjust alpha in order to maintain the overall consumer risk in ABEL studies and adapt the sample size for the loss in power. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate power and sample size for the BE decision via the FDA procedure for highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances) ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / sample size estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut], Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

Diff between PowerTOST versions 1.4-4 dated 2017-03-16 and 1.4-5 dated 2017-05-20

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Package mousetrap updated to version 3.1.0 with previous version 3.0.0 dated 2017-02-10

Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized experiments, is a method that is becoming increasingly popular in the cognitive sciences. The mousetrap package offers functions for importing, preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
Author: Pascal J. Kieslich [aut, cre], Dirk U. Wulff [aut], Felix Henninger [aut], Jonas M. B. Haslbeck [aut], Sarah Brockhaus [ctb]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>

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Package clusterSEs updated to version 2.4 with previous version 2.3.3 dated 2017-03-05

Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller (2010) <DOI:10.1198/jbes.2009.08046>, pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller (2008) <DOI:10.1162/rest.90.3.414>. Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>

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Package bookdown updated to version 0.4 with previous version 0.3 dated 2016-11-28

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre], JJ Allaire [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

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Fri, 19 May 2017

Package stratbr updated to version 1.1 with previous version 1.0 dated 2017-05-11

Title: Optimal Stratification in Stratified Sampling
Description: An Optimization Algorithm Applied to Stratification Problem.This function aims at constructing optimal strata with an optimization algorithm based on a global optimisation technique called Biased Random Key Genetic Algorithms.
Author: Jose Brito, Pedro Silva and Tomas Veiga
Maintainer: Jose Brito <jambrito@gmail.com>

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Package stepR updated to version 2.0-1 with previous version 1.0-7 dated 2017-04-20

Title: Multiscale Change-Point Inference
Description: Allows fitting of step-functions to univariate serial data where neither the number of jumps nor their positions is known by implementing the multiscale regression estimators SMUCE and HSMUCE. In addition, confidence intervals for the change-point locations and bands for the unknown signal can be obtained.
Author: Pein Florian [aut], Thomas Hotz [aut], Hannes Sieling [aut], Timo Aspelmeier [cre]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>

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Package simputation updated to version 0.2.2 with previous version 0.2.1 dated 2017-01-27

Title: Simple Imputation
Description: Easy to use interfaces to a number of imputation methods that fit in the not-a-pipe operator of the 'magrittr' package.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between simputation versions 0.2.1 dated 2017-01-27 and 0.2.2 dated 2017-05-19

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Package QuantTools updated to version 0.5.5 with previous version 0.5.4 dated 2017-02-26

Title: Enhanced Quantitative Trading Modelling
Description: Download and organize historical market data from multiple sources like Yahoo (<https://finance.yahoo.com>), Google (<https://www.google.com/finance>), Finam (<https://www.finam.ru/profile/moex-akcii/sberbank/export/>), MOEX (<https://www.moex.com/en/derivatives/contracts.aspx>) and IQFeed (<https://www.iqfeed.net/symbolguide/index.cfm?symbolguide=lookup>). Code your trading algorithms in modern C++11 with powerful event driven tick processing API including trading costs and exchange communication latency and transform detailed data seamlessly into R. In just few lines of code you will be able to visualize every step of your trading model from tick data to multi dimensional heat maps.
Author: Stanislav Kovalevsky
Maintainer: Stanislav Kovalevsky <so.kovalevsky@gmail.com>

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Package MIIVsem updated to version 0.5.2 with previous version 0.4.8 dated 2016-10-27

Title: Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
Description: Functions for estimating structural equation models using instrumental variables.
Author: Zachary Fisher [aut, cre], Keneth Bollen [aut], Kathleen Gates [aut], Mikko Rönkkö [aut]
Maintainer: Zachary Fisher <fish.zachary@gmail.com>

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Package kdevine updated to version 0.4.1 with previous version 0.4.0 dated 2017-04-27

Title: Multivariate Kernel Density Estimation with Vine Copulas
Description: Implements the vine copula based kernel density estimator of Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does not suffer from the curse of dimensionality and is therefore well suited for high-dimensional applications.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

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Package joineR updated to version 1.2.0 with previous version 1.1.0 dated 2017-02-02

Title: Joint Modelling of Repeated Measurements and Time-to-Event Data
Description: Analysis of repeated measurements and time-to-event data via random effects joint models. Fits the joint models proposed by Henderson and colleagues <doi:10.1093/biostatistics/1.4.465> (single event time) and by Williamson and colleagues (2008) <doi:10.1002/sim.3451> (competing risks events time) to a single continuous repeated measure. The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-varying covariates. The longitudinal outcome is modelled using a linear mixed effects model. The association is captured by a latent Gaussian process. The model is estimated using am Expectation Maximization algorithm. Some plotting functions and the variogram are also included. This project is funded by the Medical Research Council (Grant numbers G0400615 and MR/M013227/1).
Author: Pete Philipson [aut], Ines Sousa [aut], Peter J. Diggle [aut], Paula Williamson [aut], Ruwanthi Kolamunnage-Dona [aut], Robin Henderson [aut], Graeme L. Hickey [aut, cre], Maria Sudell [ctb]
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>

Diff between joineR versions 1.1.0 dated 2017-02-02 and 1.2.0 dated 2017-05-19

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 joineR-1.2.0/joineR/DESCRIPTION                                                                              |   30 
 joineR-1.2.0/joineR/MD5                                                                                      |  190 +--
 joineR-1.2.0/joineR/NEWS.md                                                                                  |   35 
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 joineR-1.2.0/joineR/R/joint.R                                                                                |  535 ++++++----
 joineR-1.2.0/joineR/R/jointSE.R                                                                              |  147 +-
 joineR-1.2.0/joineR/R/jointdata.R                                                                            |   11 
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 joineR-1.2.0/joineR/R/liver.R                                                                                |   21 
 joineR-1.2.0/joineR/R/longst.R                                                                               |   16 
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 joineR-1.2.0/joineR/R/plot.vargm.R                                                                           |   10 
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 joineR-1.2.0/joineR/R/summarybal.R                                                                           |    7 
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 joineR-1.2.0/joineR/R/to.balanced.R                                                                          |    5 
 joineR-1.2.0/joineR/R/to.unbalanced.R                                                                        |    5 
 joineR-1.2.0/joineR/R/variogram.R                                                                            |    7 
 joineR-1.2.0/joineR/README.md                                                                                |   25 
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 joineR-1.2.0/joineR/man/joineR.Rd                                                                            |   35 
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 joineR-1.2.0/joineR/man/jointSE.Rd                                                                           |   30 
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 joineR-1.2.0/joineR/man/liver.Rd                                                                             |   21 
 joineR-1.2.0/joineR/man/mental.Rd                                                                            |   17 
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 joineR-1.2.0/joineR/man/plot.vargm.Rd                                                                        |    7 
 joineR-1.2.0/joineR/man/points.jointdata.Rd                                                                  |    9 
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Package ipdw updated to version 0.2-6 with previous version 0.2-5 dated 2016-07-26

Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate geo-referenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek <stachel2@msu.edu>
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package bmrm updated to version 3.3 with previous version 3.0 dated 2015-01-15

Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk under L1 or L2 regularization. Implements the algorithm proposed by Teo et al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR 2012). The package comes with lot of loss functions for machine learning which make it powerful for big data analysis. The applications includes: structured prediction, linear SVM, multi-class SVM, f-beta optimization, ROC optimization, ordinal regression, quantile regression, epsilon insensitive regression, least mean square, logistic regression, least absolute deviation regression (see package examples), etc... all with L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados <julien.prados@unige.ch>

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Package kutils updated to version 1.0 with previous version 0.93 dated 2017-01-26

Title: Project Management Tools
Description: Tools for data importation, recoding, and inspection that are used at the University of Kansas Center for Research Methods and Data Analysis. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding. We are eager to have community feedback about the variable key and the vignette about it.
Author: Paul Johnson [aut, cre], Benjamin Kite [aut], Kenna Whitley [ctb], Po-Yi Chen [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>

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Package DTRreg updated to version 1.2 with previous version 1.1 dated 2016-11-03

Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and Q-Learning
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation.
Author: Michael Wallace, Erica E M Moodie, David A Stephens and Gabrielle Simoneau
Maintainer: Michael Wallace <michael.wallace@uwaterloo.ca>

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Package dataRetrieval updated to version 2.7.1 with previous version 2.7.0 dated 2017-05-15

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut], Jordan Read [ctb], Jordan Walker [ctb], Lindsay Carr [ctb], David Watkins [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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