Thu, 20 Oct 2016

Package MultNonParam updated to version 1.2.5 with previous version 1.2.3 dated 2016-08-28

Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>

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New package MullerPlot with initial version 0.1.2
Package: MullerPlot
Type: Package
Title: Generates Muller Plot from Population/Abundance/Frequency Dynamics Data
Version: 0.1.2
Date: 2016-10-17
Authors@R: c( person("Farnoush", "Farahpour", email = "farnoush.farahpour@uni-due.de", role = c("aut", "cre")), person("Mohammadkarim", "Saeedghalati", email = "m.saeedghalati@uni-due.de", role = c("aut")), person("Daniel", "Hoffmann", email = "daniel.hoffmann@uni-due.de", role = c("aut")))
Maintainer: Farnoush Farahpour <farnoush.farahpour@uni-due.de>
Description: Generates Muller plot from parental/genealogy/phylogeny information and population/abundance/frequency dynamics data. Muller plots are plots which combine information about succession of different OTUs (genotypes, phenotypes, species, ...) and information about dynamics of their abundances (populations or frequencies) over time. They are powerful and fascinating tools to visualize evolutionary dynamics. They may be employed also in study of diversity and its dynamics, i.e. how diversity emerges and how changes over time. They are called Muller plots in honor of Hermann Joseph Muller which used them to explain his idea of Muller's ratchet (Muller, 1932, American Naturalist). A big difference between Muller plots and normal box plots of abundances is that a Muller plot depicts not only the relative abundances but also succession of OTUs based on their genealogy/phylogeny/parental relation. In a Muller plot, horizontal axis is time/generations and vertical axis represents relative abundances of OTUs at the corresponding times/generations. Different OTUs are usually shown with polygons with different colors and each OTU originates somewhere in the middle of its parent area in order to illustrate their succession in evolutionary process. To generate a Muller plot one needs the genealogy/phylogeny/parental relation of OTUs and their abundances over time. MullerPlot package has the tools to generate Muller plots which clearly depict the origin of successors of OTUs.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: grDevices,RColorBrewer,graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-10-20 09:26:10 UTC; farnoush
Author: Farnoush Farahpour [aut, cre], Mohammadkarim Saeedghalati [aut], Daniel Hoffmann [aut]
Repository: CRAN
Date/Publication: 2016-10-20 23:16:11

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New package MHTdiscrete with initial version 0.1.0
Package: MHTdiscrete
Type: Package
Title: Multiple Hypotheses Testing for Discrete Data
Version: 0.1.0
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>
Description: A Comprehensive tool for almost all existing multiple testing methods for discrete data. The package also provides some novel multiple testing procedures controlling FWER/FDR for discrete data. In order to make decisions conveniently, given discrete p-values and their domains, the [method].p.adjust function returns adjusted p-values, which can be used to compare with the nominal significant level alpha.
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-20 14:20:10 UTC; kaijingzhang
Repository: CRAN
Date/Publication: 2016-10-20 23:16:05

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New package corlink with initial version 1.0.0
Package: corlink
Title: Record Linkage, Incorporating Imputation for Missing Agreement Patterns, and Modeling Correlation Patterns Between Fields
Version: 1.0.0
Authors@R: person("John", "Ferguson", email = "john.ferguson@nuigalway.ie", role = c("aut", "cre"))
Description: A matrix of agreement patterns and counts for record pairs is the input for the procedure. An EM algorithm is used to impute plausible values for missing record pairs. A second EM algorithm, incorporating possible correlations between per-field agreement, is used to estimate posterior probabilities that each pair is a true match - i.e. constitutes the same individual.
Depends: R (>= 3.2.4)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-20 08:57:58 UTC; 0118158S
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@nuigalway.ie>
Repository: CRAN
Date/Publication: 2016-10-20 23:17:42

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Package tuneR updated to version 1.3.1 with previous version 1.3.0 dated 2016-09-15

Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ... Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de> with contributions from Sebastian Krey, Olaf Mersmann, Sarah Schnackenberg, Guillaume Guenard, Andrea Preusser, Anita Thieler, Johanna Mielke and Claus Weihs, as well as code fragments and ideas from the former package 'sound' by Matthias Heymann and functions from 'rastamat' by Daniel P. W. Ellis. The included parts of the libmad MPEG audio decoder library are authored by Underbit Technologies.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

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Package TRADER updated to version 1.2-2 with previous version 1.2-1 dated 2016-02-10

Title: Tree Ring Analysis of Disturbance Events in R
Description: Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data.
Author: Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>

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Package trackeR updated to version 0.0.4 with previous version 0.0.3 dated 2016-06-23

Title: Infrastructure for Running and Cycling Data from GPS-Enabled Tracking Devices
Description: The aim of this package is to provide infrastructure for handling running and cycling data from GPS-enabled tracking devices. After extraction and appropriate manipulation of the training or competition attributes, the data are placed into session-based and unit-aware data objects of class trackeRdata (S3 class). The information in the resulting data objects can then be visualised, summarised, and analysed through corresponding flexible and extensible methods.
Author: Hannah Frick [aut, cre], Ioannis Kosmidis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>

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Package Thermimage updated to version 2.2.3 with previous version 2.2.1 dated 2016-08-04

Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing jpg to windows OS).
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>

Diff between Thermimage versions 2.2.1 dated 2016-08-04 and 2.2.3 dated 2016-10-20

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Package pavo updated to version 0.5-6 with previous version 0.5-5 dated 2016-03-08

Title: Perceptual Analysis, Visualization and Organization of Spectral Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color from spectral data.
Author: Rafael Maia [aut, cre], Chad Eliason [aut], Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>

Diff between pavo versions 0.5-5 dated 2016-03-08 and 0.5-6 dated 2016-10-20

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Package NMOF updated to version 0.40-0 with previous version 0.36-2 dated 2015-10-20

Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book "Numerical Methods and Optimization in Finance" by M. 'Gilli', D. 'Maringer' and E. Schumann (2011), ISBN 978-0123756626. The package provides implementations of several optimisation heuristics, such as Differential Evolution, Genetic Algorithms and Threshold Accepting. There are also functions for the valuation of financial instruments, such as bonds and options, and functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>

Diff between NMOF versions 0.36-2 dated 2015-10-20 and 0.40-0 dated 2016-10-20

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Package NAM updated to version 1.5.0 with previous version 1.4.8 dated 2016-09-21

Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>

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Package icpsrdata updated to version 0.2.0 with previous version 0.1.1 dated 2016-07-24

Title: Reproducible Data Retrieval from the ICPSR Archive
Description: Reproducible, programmatic retrieval of datasets from the Inter-university Consortium for Political and Social Research archive.
Author: Frederick Solt [aut, cre], Kellen Gracey [aut], Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>

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Package Barnard updated to version 1.8 with previous version 1.7 dated 2016-10-19

Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>

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Package anytime updated to version 0.0.4 with previous version 0.0.3 dated 2016-10-14

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package acepack updated to version 1.4.0 with previous version 1.3-3.3 dated 2013-05-03

Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided. The first, Alternative Conditional Expectations (ACE), is an algorithm to find the fixed point of maximal correlation, i.e. it finds a set of transformed response variables that maximizes R^2 using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations for Multiple Regression and Correlation". Journal of the American Statistical Association. 80:580-598. <doi:10.1080/01621459.1985.10478157>]. Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity and Variance Stabilization". Journal of the American Statistical Association. 83:394-405. <doi:10.1080/01621459.1988.10478610>].
Author: Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley, Shawn Garbett, Jonathan Baron
Maintainer: Shawn Garbett <shawn.garbett@vanderbilt.edu>

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Package SafeBayes updated to version 1.1 with previous version 1.0 dated 2016-05-23

Title: Generalized and Safe-Bayesian Ridge and Lasso Regression
Description: Functions for Generalized and Safe-Bayesian Ridge and Lasso Regression models with both fixed and varying variance.
Author: Rianne de Heide [aut, cre], Gustavo de los Campos [ctb], Paulino Perez Rodriguez [ctb], Bob Wheeler [ctb]
Maintainer: Rianne de Heide <r.de.heide@cwi.nl>

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Package yuima updated to version 1.2.3 with previous version 1.1.6 dated 2016-09-10

Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>

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Package wavethresh updated to version 4.6.8 with previous version 4.6.6 dated 2013-10-21

Title: Wavelets Statistics and Transforms
Description: Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <G.P.Nason@bristol.ac.uk>

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Package gaston updated to version 1.4.7 with previous version 1.4.6 dated 2016-07-11

Title: Genetic Data Manipulation (Quality Control, GRM and LD Computations, PCA), Linear and Logistic Mixed Models (AIREML Algorithm), Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>

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Package Rsurrogate updated to version 2.0 with previous version 1.0 dated 2015-10-23

Title: Robust Estimation of the Proportion of Treatment Effect Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>

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Package rgeos updated to version 0.3-21 with previous version 0.3-20 dated 2016-09-07

Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut], Colin Rundel [aut], Edzer Pebesma [ctb], Rainer Stuetz [ctb], Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package mgm updated to version 1.1-7 with previous version 1.1-6 dated 2016-06-16

Title: Estimating Time-Varying Mixed Graphical Models
Description: Estimation of time-varying Mixed Graphical models and mixed VAR models using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>

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Package lessR updated to version 3.5.1 with previous version 3.5.0 dated 2016-08-29

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package grpSLOPE updated to version 0.2.0 with previous version 0.1.0 dated 2016-04-24

Title: Group Sorted L1 Penalized Estimation
Description: Group SLOPE is a penalized linear regression method that is used for adaptive selection of groups of significant predictors in a high-dimensional linear model. The Group SLOPE method can control the (group) false discovery rate at a user-specified level (i.e., control the expected proportion of irrelevant among all selected groups of predictors).
Author: Alexej Gossmann [aut, cre], Damian Brzyski [aut], Weijie Su [aut], Malgorzata Bogdan [aut], Ewout van den Berg [ctb] (A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3), Emmanuel Candes [ctb] (A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3)
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>

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Package ggrepel updated to version 0.6.3 with previous version 0.5 dated 2016-02-08

Title: Repulsive Text and Label Geoms for 'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.
Author: Kamil Slowikowski [aut, cre]
Maintainer: Kamil Slowikowski <kslowikowski@fas.harvard.edu>

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Package aplore3 updated to version 0.9 with previous version 0.7 dated 2014-12-21

Title: Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic Regression" (3rd Ed., 2013)
Description: An unofficial companion to "Applied Logistic Regression" by D.W. Hosmer, S. Lemeshow and R.X. Sturdivant (3rd ed., 2013) containing the dataset used in the book.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>

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 man/burn_eval_2.Rd            |    3 +-
 man/chdage.Rd                 |    5 ++--
 man/glow11m.Rd                |    3 +-
 man/glow500.Rd                |    3 +-
 man/glow_bonemed.Rd           |    3 +-
 man/glow_mis_comp.Rd          |    3 +-
 man/glow_mis_wmissing.Rd      |    3 +-
 man/glow_rand.Rd              |    3 +-
 man/icu.Rd                    |    5 ++--
 man/lowbwt.Rd                 |    5 ++--
 man/myopia.Rd                 |    3 +-
 man/nhanes.Rd                 |    3 +-
 man/polypharm.Rd              |    3 +-
 man/scale_example.Rd          |    3 +-
 27 files changed, 103 insertions(+), 84 deletions(-)

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New package ABC.RAP with initial version 0.9.0
Package: ABC.RAP
Title: Array Based CpG Region Analysis Pipeline
Version: 0.9.0
Author: Abdulmonem Alsaleh [cre, aut], Robert Weeks [aut], Ian Morison [aut], RStudio [ctb]
Maintainer: Abdulmonem Alsaleh <a.alsaleh@hotmail.co.nz>
Contact: Ian Morison <ian.morison@otago.ac.nz>
Description: It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.
License: GPL-3
Depends: R (>= 3.1.0)
Imports: graphics, stats, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
SystemRequirements: GNU make
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2016-10-20 01:50:08 UTC; abdul
Repository: CRAN
Date/Publication: 2016-10-20 10:52:16

More information about ABC.RAP at CRAN
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