Tue, 30 Aug 2016

Package molaR updated to version 4.2 with previous version 4.1 dated 2016-07-28

Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>

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Package elementR updated to version 1.1 with previous version 1.0 dated 2016-08-30

Title: A Shiny Application for Reducing Elemental LA-ICPMS Data from Solid Structures
Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LA-ICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The elementR package provides a reactive and user friendly interface for conducting all steps needed for an optimal data reduction while leaving maximum control for user.
Author: Charlotte Sirot, Francois Guilhaumon, Franck Ferraton, Audrey Darnaude, Jacques Panfili, Amber Child
Maintainer: Charlotte Sirot <charlott.sirot@gmail.com>

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Package dynsurv updated to version 0.3-2 with previous version 0.3-0 dated 2016-07-14

Title: Dynamic Models for Survival Data
Description: Functions to fit time-varying coefficient models for interval censored and right censored survival data. Three major approaches are implemented: 1) Bayesian Cox model with time-independent, time-varying or dynamic coefficients for right censored and interval censored data; 2) Spline based time-varying coefficient Cox model for right censored data; 3) Transformation model with time-varying coefficients for right censored data using estimating equations.
Author: Wenjie Wang [cre, aut], Ming-Hui Chen [aut], Xiaojing Wang [aut], Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

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Package BIGDAWG updated to version 1.5.5 with previous version 1.5.4 dated 2016-08-28

Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>

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Package LogicReg updated to version 1.5.9 with previous version 1.5.8 dated 2015-07-02

Title: Logic Regression
Description: Routines for fitting Logic Regression models.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>

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Package selectr updated to version 0.3-0 with previous version 0.2-3 dated 2014-12-24

Title: Translate CSS Selectors to XPath Expressions
Description: Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://pythonhosted.org/cssselect/>).
Author: Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]
Maintainer: Simon Potter <simon@sjp.co.nz>

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New package PASenseWear with initial version 1.0
Package: PASenseWear
Type: Package
Title: Summarize Daily Physical Activity from 'SenseWear' Accelerometer Data
Version: 1.0
Date: 2016-08-29
Author: Yukun Zhang [aut,cre], Milad Yavari [aut], Bob Haennel[aut], Haocheng Li [aut,ctb]
Maintainer: Yukun Zhang <yukzhang@ucalgary.ca>
Depends: R (>= 3.2.5), ggplot2
Description: Provide summary table of daily physical activity and per-person/grouped heat map for accelerometer data from SenseWear Armband. See <https://templehealthcare.wordpress.com/the-sensewear-armband/> for more information about SenseWear Armband.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-30 16:25:18 UTC; yk
Repository: CRAN
Date/Publication: 2016-08-30 19:22:39

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Package mpath updated to version 0.2-4 with previous version 0.2-3 dated 2016-08-29

Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>

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Package mvnfast updated to version 0.1.5 with previous version 0.1.4 dated 2016-01-08

Title: Fast Multivariate Normal Methods
Description: Provides computationally efficient tools related to the multivariate normal distribution. The main functionalities are: simulating multivariate normal random vectors, evaluating multivariate normal densities and Mahalanobis distances. These tools are very efficient thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

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Package landscapeR updated to version 1.1 with previous version 1.0.0 dated 2016-05-22

Title: Categorical Landscape Simulation Facilities
Description: Package is aimed at simulating categorical maps on actual geographical realms, starting from either empty landscapes, or landscapes provided by the user (e.g. land use maps). landscapeR allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscape in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dmasan@ceh.ac.uk>

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Package CorrectOverloadedPeaks updated to version 1.2.14 with previous version 1.2.13 dated 2016-07-22

Title: Correct Overloaded Peaks from GC-APCI-MS Data
Description: Analyzes and modifies metabolomics raw data (generated using GC-APCI-MS, Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass Spectrometry) to correct overloaded signals, i.e. ion intensities exceeding detector saturation leading to a cut-off peak. Data in xcmsRaw format are accepted as input and mzXML files can be processed alternatively. Overloaded signals are detected automatically and modified using an Gaussian or Isotopic-Ratio approach, QC plots are generated and corrected data are stored within the original xcmsRaw or mzXML respectively to allow further processing.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@charite.de>

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New package cartogram with initial version 0.0.1
Package: cartogram
Title: Create Cartograms with R
Version: 0.0.1
Authors@R: person("Sebastian", "Jeworutzki", email = "sebastian.jeworutzki@ruhr-uni-bochum.de", role = c("aut", "cre"))
Description: Construct a continuous area cartogram by a rubber sheet distortion algorithm.
URL: https://github.com/sjewo/cartogram
BugReports: https://github.com/sjewo/cartogram/issues
Imports: maptools, rgeos, sp
Suggests: rgdal
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-30 13:52:44 UTC; sj
Author: Sebastian Jeworutzki [aut, cre]
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>
Repository: CRAN
Date/Publication: 2016-08-30 18:47:55

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Package BayesBD updated to version 1.0 with previous version 0.1 dated 2015-11-17

Title: Bayesian Inference for Image Boundaries
Description: Provides tools for carrying out a Bayesian analysis of image boundaries. Functions are provided for both binary (Bernoulli) and continuous (Gaussian) images. Examples, along with an interactive shiny function illustrate how to perform simulations, analyze custom data, and plot estimates and credible intervals.
Author: Nicholas Syring, Meng Li
Maintainer: Nicholas Syring <nasyrin@gmail.com>

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Package archivist.github updated to version 0.2.2 with previous version 0.2.1 dated 2016-06-27

Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre], Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>

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Package spam updated to version 1.4-0 with previous version 1.3-0 dated 2015-10-29

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with SparseM/Matrix are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

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New package elementR with initial version 1.0
Package: elementR
Type: Package
Title: A Shiny Application for Reducing Elemental LA-ICPMS Data from Solid Structures
Version: 1.0
Date: 2016-08-26
Author: Charlotte Sirot, Francois Guilhaumon, Franck Ferraton, Audrey Darnaude, Jacques Panfili, Amber Child
Maintainer: Charlotte Sirot <charlott.sirot@gmail.com>
Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LA-ICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The elementR package provides a reactive and user friendly interface for conducting all steps needed for an optimal data reduction while leaving maximum control for user.
Repository: CRAN
Depends: R (>= 3.2.3)
Imports: gdata, shiny,devtools, shinyjs, gnumeric, R6, shinydashboard, abind, stringr, lmtest, tcltk,tcltk2, reader, readODS, readxl
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-08-30 09:16:53 UTC; cha
Date/Publication: 2016-08-30 15:22:25

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Package tweenr updated to version 0.1.4 with previous version 0.1.3 dated 2016-03-29

Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that plugs right into functions such as gg_animate() from the 'gganimate' package. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package naturalsort updated to version 0.1.3 with previous version 0.1.2 dated 2014-01-31

Title: Natural Ordering
Description: Provides functions related to human natural ordering. It handles adjacent digits in a character sequence as a number so that natural sort function arranges a character vector by their numbers, not digit characters. It is typically seen when operating systems lists file names. For example, a sequence a-1.png, a-2.png, a-10.png looks naturally ordered because 1 < 2 < 10 and natural sort algorithm arranges so whereas general sort algorithms arrange it into a-1.png, a-10.png, a-2.png owing to their third and fourth characters.
Author: Kosei Abe
Maintainer: Kosei Abe <mail@recyclebin.jp>

Diff between naturalsort versions 0.1.2 dated 2014-01-31 and 0.1.3 dated 2016-08-30

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Package infuser updated to version 0.2.4 with previous version 0.2.3 dated 2016-04-06

Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>

Diff between infuser versions 0.2.3 dated 2016-04-06 and 0.2.4 dated 2016-08-30

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New package episheet with initial version 0.1.0
Package: episheet
Type: Package
Title: Rothman's Episheet
Version: 0.1.0
Authors@R: c( person("James", "Black", , "james@epijim.uk", c("aut", "cre")), person("Ken Rothman", role = "cph") )
Maintainer: James Black <james@epijim.uk>
Description: A collection of R functions supporting the text book Modern Epidemiology, Second Edition, by Kenneth J.Rothman and Sander Greenland. ISBN 13: 978-0781755641 See <http://www.krothman.org/> for more information.
License: GPL (>= 2)
URL: https://github.com/epijim/episheet
BugReports: https://github.com/epijim/episheet/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
Imports: dplyr, tidyr, ggplot2, magrittr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-08-30 06:11:34 UTC; blackj9
Author: James Black [aut, cre], Ken Rothman [cph]
Repository: CRAN
Date/Publication: 2016-08-30 12:50:30

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Package RSSOP updated to version 1.1 with previous version 1.0 dated 2016-08-29

Title: Simulation of Supply Reservoir Systems using Standard Operation Policy
Description: Reservoir Systems Standard Operation Policy. A system for simulation of supply reservoirs. It proposes functionalities for plotting and evaluation of supply reservoirs systems.
Author: Rezgar Arabzadeh, Parisa Aberi, Kaveh Panaghi, Shahab Araghinejad, Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

Diff between RSSOP versions 1.0 dated 2016-08-29 and 1.1 dated 2016-08-30

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Package represtools updated to version 0.1.2 with previous version 0.1.1 dated 2016-06-21

Title: Reproducible Research Tools
Description: Reproducible research tools automates the creation of an analysis directory structure and work flow. There are R markdown skeletons which encapsulate typical analytic work flow steps. Functions will create appropriate modules which may pass data from one step to another.
Author: Brian Fannin [aut, cre]
Maintainer: Brian Fannin <FanninQED@Yahoo.com>

Diff between represtools versions 0.1.1 dated 2016-06-21 and 0.1.2 dated 2016-08-30

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Package MetaIntegrator updated to version 1.0.1 with previous version 1.0.0 dated 2016-08-05

Title: MetaIntegrator- Meta-Analysis of Gene Expression Data
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). Methodology described in: <http://biorxiv.org/content/early/2016/08/25/071514>.
Author: Winston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Maintainer: Winston A. Haynes <hayneswa@stanford.edu>

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Package HiddenMarkov updated to version 1.8-7 with previous version 1.8-4 dated 2015-07-06

Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte <d.s.harte@gmail.com>

Diff between HiddenMarkov versions 1.8-4 dated 2015-07-06 and 1.8-7 dated 2016-08-30

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Package Ckmeans.1d.dp updated to version 3.4.6-1 with previous version 3.4.6 dated 2016-06-02

Title: Optimal and Fast Univariate k-Means Clustering
Description: A fast dynamic programming algorithm for optimal univariate k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to heuristic k-means algorithms, this method guarantees optimality and reproducibility. Its advantage in efficiency and accuracy over heuristic k-means clustering is increasingly pronounced as the number of clusters k increases.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

Diff between Ckmeans.1d.dp versions 3.4.6 dated 2016-06-02 and 3.4.6-1 dated 2016-08-30

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