Fri, 26 Aug 2016

New package voxel with initial version 1.2.1
Package: voxel
Title: Mass-Univariate Voxelwise Analysis of Medical Imaging Data
Version: 1.2.1
Authors@R: c(person("Angel", "Garcia de la Garza", email = "agarciadlg@gmail.com", role = c("aut", "cre")), person("Simon", "Vandekar", email= "simonv@mail.med.upenn.edu", role="aut"), person("David", "Roalf", email= "roalf@mail.med.upenn.edu", role="aut"), person("Kosha", "Ruparel", email= "kruparel@mail.med.upenn.edu", role="aut"), person("Ruben", "Gur", email= "gur@mail.med.upenn.edu", role="aut"), person("Raquel", "Gur", email= "raquel@mail.med.upenn.edu", role="aut"), person("Theodore", "Satterthwaite", email= "sattertt@mail.med.upenn.edu", role="aut"), person("R. Taki", "Shinohara", email= "rshi@mail.med.upenn.edu", role="aut") )
Description: Functions for the mass-univariate voxelwise analysis of medical imaging data that follows the NIfTI <http://nifti.nimh.nih.gov> format.
Depends: R (>= 3.2.3)
License: GPL-2
URL: https://github.com/angelgar/voxel
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Imports: parallel,stats,mgcv,gamm4,oro.nifti,lmerTest,ggplot2
NeedsCompilation: no
Packaged: 2016-08-26 19:01:17 UTC; AGG
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>
Repository: CRAN
Date/Publication: 2016-08-27 00:43:49

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New package stR with initial version 0.1
Package: stR
Type: Package
Title: STR Decomposition
Version: 0.1
Author: Alexander Dokumentov, Rob J Hyndman
Maintainer: Alexander Dokumentov <alexander.dokumentov@gmail.com>
URL: https://bitbucket.org/alexanderdokumentov/strpackage
License: GPL (>= 2)
Depends: R (>= 3.2.2)
Imports: compiler, Matrix, SparseM, quantreg, MatrixModels, forecast, foreach, stats, methods
Description: Methods for decomposing seasonal data: STR (a Seasonal-Trend decomposition procedure based on Regression) and Robust STR. In some ways, STR is similar to Ridge Regression and Robust STR can be related to LASSO. They allow for multiple seasonal components, multiple linear covariates with constant, flexible and seasonal influence. Seasonal patterns (for both seasonal components and seasonal covariates) can be fractional and flexible over time; moreover they can be either strictly periodic or have a more complex topology. The methods provide confidence intervals for the estimated components. The methods can be used for forecasting.
LazyData: true
RoxygenNote: 5.0.1
Suggests: testthat, demography, knitr, rmarkdown, doParallel, doMC
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-08-26 04:03:05 UTC; adokumen
Repository: CRAN
Date/Publication: 2016-08-27 00:46:43

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Package numDeriv updated to version 2016.8-1 with previous version 2014.2-1 dated 2015-05-04

Title: Accurate Numerical Derivatives
Description: Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.
Author: Paul Gilbert and Ravi Varadhan
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

Diff between numDeriv versions 2014.2-1 dated 2015-05-04 and 2016.8-1 dated 2016-08-26

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Package polycor updated to version 0.7-9 with previous version 0.7-8 dated 2010-04-03

Title: Polychoric and Polyserial Correlations
Description: Computes polychoric and polyserial correlations by quick "two-step" methods or ML, optionally with standard errors; tetrachoric and biserial correlations are special cases.
Author: John Fox [aut, cre]
Maintainer: John Fox <jfox@mcmaster.ca>

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New package metacoder with initial version 0.1.2
Package: metacoder
Title: Tools for Parsing, Manipulating, and Graphing Hierarchical Data
Version: 0.1.2
Authors@R: c( person("Zachary", "Foster", email = "zacharyfoster1989@gmail.com", role = c("aut", "cre")), person("Niklaus", "Grunwald", email = "grunwaln@science.oregonstate.edu", role = c("ths")))
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Description: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
Depends: R (>= 3.0.2)
License: GPL-2 | GPL-3
LazyData: true
Imports: stringr, ggplot2, igraph, scales, grid, taxize, seqinr, reshape2, zoo, traits, RColorBrewer, RCurl, ape, reshape, stats, grDevices, utils, lazyeval, dplyr, magrittr, readr
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Date: 2016-08-01
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-08-26 20:21:09 UTC; USDA-ARS\fosterz
Author: Zachary Foster [aut, cre], Niklaus Grunwald [ths]
Repository: CRAN
Date/Publication: 2016-08-27 00:35:09

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New package MBSGS with initial version 1.0.0
Package: MBSGS
Type: Package
Title: Multivariate Bayesian Sparse Group Selection with Spike and Slab
Version: 1.0.0
Author: Benoit Liquet, Matthew Sutton
Maintainer: Benoit Liquet <benoit.liquet@qut.edu.au>
Imports: MCMCpack, MASS, mgcv, mnormt, truncnorm
Description: An implementation of a Bayesian sparse group model using spike and slab priors in a regression context. It is designed for regression with a multivariate response variable, but also provides an implementation for univariate response.
License: GPL (>= 2.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-08-25 23:05:37 UTC; liquetwe
Repository: CRAN
Date/Publication: 2016-08-27 00:33:23

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Package tibble updated to version 1.2 with previous version 1.1 dated 2016-07-04

Title: Simple Data Frames
Description: Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.
Author: Hadley Wickham [aut], Romain Francois [aut], Kirill Müller [aut, cre], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package XGR updated to version 1.0.3 with previous version 1.0.2 dated 2016-06-26

Title: Exploring Genomic Relations for Precision Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.0.2 dated 2016-06-26 and 1.0.3 dated 2016-08-26

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Package TSsdmx updated to version 2016.8-1 with previous version 2015.12-1 dated 2015-12-16

Title: 'TSdbi' Extension to Connect with 'SDMX'
Description: Methods to retrieve data in the Statistical Data and Metadata Exchange ('SDMX') format from several database. (For example, 'EuroStat', the European Central Bank, the Organisation for Economic Co-operation and Development, the 'Unesco' Institute for Statistics, and the International Labor Organization.) This is a wrapper for package 'RJSDMX'. Comprehensive examples of all the 'TS*' packages is provided in the vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

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Package TSmisc updated to version 2016.8-1 with previous version 2015.1-3 dated 2015-05-02

Title: 'TSdbi' Extensions to Wrap Miscellaneous Data Sources
Description: Methods to retrieve data from several different sources. This include historical quote data from 'Yahoo' and 'Oanda', economic data from 'FRED', and 'xls' and 'csv' data from different sources. Comprehensive examples of all the 'TS*' packages is provided in the vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

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Package TSdata updated to version 2016.8-1 with previous version 2015.4-2 dated 2015-05-22

Title: 'TSdbi' Illustration
Description: Illustrates the various 'TSdbi' packages with a vignette using time series data from several sources. The vignette also illustrates some simple time series manipulation and plotting using packages 'tframe' and 'tfplot'.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

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Package tframePlus updated to version 2016.7-1 with previous version 2015.1-2 dated 2015-04-27

Title: Time Frame Coding Kernel Extensions
Description: Extensions and additional 'tframe' utilities.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

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Package rhandsontable updated to version 0.3.3 with previous version 0.3.2 dated 2016-07-07

Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph], Jeff Allen [ctb], Yihui Xie [ctb], Enzo Martoglio [ctb], Warpechowski Marcin [ctb, cph] (Handsontable.js library), Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library), Aisch Gregor [ctb, cph] (Chroma.js library), F<c3><b6>retagsplatsen [ctb, cph] (Numbro.js library), Draper Adam [ctb, cph] (Numeral.js library), Wood Tim [ctb, cph] (Moment.js library), Chernev Iskren [ctb, cph] (Moment.js library), Moment.js contributors [ctb, cph] (Moment.js library), Bushell David [ctb, cph] (Pikaday.js library), jQuery Foundation [ctb, cph] (jQuery.js library), Splunk Inc [ctb, cph] (Sparkline.js library), Russell Kent [ctb, cph] (Sparkline.js library), Rohan Jon [ctb, cph] (ZeroClipboard library), Greene James [ctb, cph] (ZeroClipboard library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>

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Package rtson updated to version 1.3 with previous version 1.2 dated 2016-06-24

Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>

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Package regspec updated to version 2.3 with previous version 2.1 dated 2016-05-04

Title: Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Description: Computes linear Bayesian spectral estimates from multirate data for second-order stationary time series. Provides credible intervals and methods for plotting various spectral estimates.
Author: Ben Powell [aut, cre], Guy Nason [aut]
Maintainer: Ben Powell <ben.powell@bristol.ac.uk>

Diff between regspec versions 2.1 dated 2016-05-04 and 2.3 dated 2016-08-26

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Package RcppCNPy updated to version 0.2.5 with previous version 0.2.4 dated 2015-01-06

Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write facilities for files created with (or for) the 'NumPy' extension for 'Python'. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with -std=c++11 which is the default starting with release 0.2.3 following the release of R 3.1.0, and available on all platforms following the release of R 3.3.0 with the updated 'Rtools'.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package ragt2ridges updated to version 0.2.1 with previous version 0.2.0 dated 2016-05-24

Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>

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Package plotmo updated to version 3.1.5 with previous version 3.1.4 dated 2015-07-30

Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors while holding the other predictors constant. A poor man's partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package ModelMetrics updated to version 1.1.0 with previous version 1.0.0 dated 2016-08-16

Title: Rapid Calculation of Model Metrics
Description: Collection of metrics for evaluating models written in C++ using 'Rcpp'.
Author: Tyler Hunt [aut, cre]
Maintainer: Tyler Hunt <thunt@snapfinance.com>

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Package mixlm updated to version 1.1.4 with previous version 1.1.3 dated 2016-05-12

Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [ctb], R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Package MicroDatosEs updated to version 0.8.2 with previous version 0.8.01 dated 2016-08-09

Title: Utilities for Official Spanish Microdata
Description: Provides utilities for reading and processing microdata from Spanish official statistics with R.
Author: Carlos J. Gil Bellosta [aut, cre], Carlos Neira [ctb], Diego Paniagua Sánchez [ctb], José Luis Cañadas Reche [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>

Diff between MicroDatosEs versions 0.8.01 dated 2016-08-09 and 0.8.2 dated 2016-08-26

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New package IsoSpecR with initial version 1.0
Encoding: UTF-8
Package: IsoSpecR
Type: Package
Title: An R Interface to the IsoSpec Algorithm
Version: 1.0
Date: 2016-08-15
Author: Mateusz Krzysztof Łącki and Michał Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>
Description: IsoSpec is a fine structure calculator used for obtaining the most probable masses of a chemical compound given the frequencies of the composing isotopes and their masses. It finds the smallest set of isotopologues with a given probability. The probability is assumed to be that of the product of multinomial distributions, each corresponding to one particular element and parametrized by the frequencies of finding these elements in nature. These numbers are supplied by IUPAC - the International Union of Pure and Applied Chemistry.
License: BSD_2_clause + file LICENCE
Depends: R (>= 3.0.0)
Imports: Rcpp (>= 0.12.0)
LazyData: no
LinkingTo: Rcpp
NeedsCompilation: yes
SystemRequirements: C++11
RoxygenNote: 5.0.1
Packaged: 2016-08-26 12:49:05 UTC; mist
Repository: CRAN
Date/Publication: 2016-08-26 20:35:20

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Package grr updated to version 0.9.5 with previous version 0.9.2 dated 2016-02-29

Title: Alternative Implementations of Base R Functions
Description: Alternative implementations of some base R functions, including sort, order, and match. Functions are simplified but can be faster or have other advantages.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>

Diff between grr versions 0.9.2 dated 2016-02-29 and 0.9.5 dated 2016-08-26

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Package gower updated to version 0.1.1 with previous version 0.1.0 dated 2016-08-10

Title: Gower's Distance
Description: Compute Gower's distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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New package DHARMa with initial version 0.1.0
Package: DHARMa
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Version: 0.1.0
Date: 2016-08-25
Authors@R: c(person("Florian", "Hartig", email = "florian.hartig@biologie.uni-regensburg.de", role = c("aut", "cre")))
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals from fitted generalized linear mixed models. Currently supported are 'lme4', 'glm' (except quasi-distributions) and 'lm' model classes. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problem, such as over/underdispersion, zero-inflation, and spatial and temporal autocorrelation.
Depends: R (>= 3.0.0)
Imports: stats, graphics, utils, grDevices, gap, qrnn, lmtest, ape, sfsmisc, MASS, doParallel, foreach, lme4
Suggests: aods3, knitr, testthat
License: GPL (>= 3)
URL: https://github.com/florianhartig/DHARMa
BugReports: https://github.com/florianhartig/DHARMa/issues
LazyData: true
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-08-26 09:38:05 UTC; Florian
Author: Florian Hartig [aut, cre]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Repository: CRAN
Date/Publication: 2016-08-26 19:05:58

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Package burnr updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-10

Title: Advanced Fire History Analysis in R
Description: Basic tools to analyze forest fire history data (e.g. FHX2) in R.
Author: Steven Malevich [aut, cre], Christopher Guiterman [ctb], Ellis Margolis [ctb]
Maintainer: Steven Malevich <malevich@email.arizona.edu>

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Package AbsFilterGSEA updated to version 1.5 with previous version 1.2.1 dated 2016-04-04

Title: Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>

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Package dagitty updated to version 0.2-2 with previous version 0.1-10 dated 2016-03-26

Title: Graphical Analysis of Structural Causal Models
Description: A port of the web-based software 'DAGitty', available at <http://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.
Author: Johannes Textor, Benito van der Zander
Maintainer: Johannes Textor <johannes.textor@gmx.de>

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Package cartography updated to version 1.4.0 with previous version 1.3.0 dated 2016-06-13

Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows various cartographic representations such as proportional symbols, chroropleth, typology, flows or discontinuities. In addition, it also proposes some useful features like cartographic palettes, layout (scale, north arrow, title...), labels, legends or access to cartographic API to ease the graphic presentation of maps.
Author: Timothée Giraud [cre, aut], Nicolas Lambert [aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>

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Package sjstats updated to version 0.4.0 with previous version 0.3.0 dated 2016-07-30

Title: Collection of Convenient Functions for Common Statistical Computations
Description: Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like standard errors or root mean squared errors). Second, these shortcut functions are generic (if appropriate), and can be applied not only to vectors, but also to other objects as well (e.g., the Coefficient of Variation can be computed for vectors, linear models, or linear mixed models; the r2()-function returns the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects). The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models and mixed effects models. However, some of the functions also deal with other statistical measures, like Cronbach's Alpha, Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package catR updated to version 3.10 with previous version 3.9 dated 2016-07-15

Title: Procedures to Generate Patterns under Computerized Adaptive Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>

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Package rpnf updated to version 1.0.5 with previous version 1.0.4 dated 2015-10-12

Title: Point and Figure Package
Description: A set of functions to analyze and print the development of a commodity using the Point and Figure (P&F) approach. A P&F processor can be used to calculate daily statistics for the time series. These statistics can be used for deeper investigations as well as to create plots. Plots can be generated as well known X/O Plots in plain text format, and additionally in a more graphical format.
Author: Sascha Herrmann
Maintainer: Sascha Herrmann <sascha.herrmann.consulting@gmail.com>

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Package rglwidget updated to version 0.2.1 with previous version 0.2 dated 2016-08-25

Title: 'rgl' in 'htmlwidgets' Framework
Description: The contents of this package have been merged into rgl, so it is no longer needed.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between rglwidget versions 0.2 dated 2016-08-25 and 0.2.1 dated 2016-08-26

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Package QuantumClone updated to version 0.16.8.19 with previous version 0.15.11 dated 2015-11-03

Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing.
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>

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Package pbapply updated to version 1.2-2 with previous version 1.2-1 dated 2016-04-19

Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>

Diff between pbapply versions 1.2-1 dated 2016-04-19 and 1.2-2 dated 2016-08-26

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Package DiffusionRgqd updated to version 0.1.3 with previous version 0.1.2 dated 2016-01-20

Title: Inference and Analysis for Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic diffusion processes for both scalar and bivariate diffusion systems. For scalar diffusions, a module is provided for solving first passage time problems for both time-homogeneous and time-inhomogeneous GQDs.
Author: Etienne A.D. Pienaar [aut, cre], Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>

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New package rplexos with initial version 1.1.8
Package: rplexos
Type: Package
Title: Read and Analyze 'PLEXOS' Solutions
Version: 1.1.8
Date: 2016-08-22
Authors@R: c( person("Clayton","Barrows", , "clayton.barrows@nrel.gov", c("cre","ctb")), person("Eduardo", "Ibanez", , "edu.ibanez@gmail.com", c("aut")), person("Jef", "Daniels", , " ", role=c("aut")), person("Marcin", "Kalicinski", , "kalita@poczta.onet.pl", "ctb", "for the included RapidXml source"), person("National Renewable Energy Laboratory", role = "cph") )
Description: Efficiently read and analyze 'PLEXOS' solutions by converting them into 'SQLite' databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios. 'PLEXOS' is a power systems production cost model, created and distributed by Energy Exemplar (see <http://energyexemplar.com/software/plexos-desktop-edition> for more information).
License: MIT + file LICENSE
URL: https://github.com/NREL/rplexos, http://energyexemplar.com/software/plexos-desktop-edition/
BugReports: https://github.com/NREL/rplexos/issues
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.5), dplyr (>= 0.3), RSQLite (>= 1.0), DBI, data.table, tidyr, lubridate, stringi, parallel, doParallel, foreach
Suggests: knitr, testthat, ggplot2
LinkingTo: Rcpp (>= 0.11.5)
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-08-25 15:47:37 UTC; cbarrows
Author: Clayton Barrows [cre, ctb], Eduardo Ibanez [aut], Jef Daniels [aut], Marcin Kalicinski [ctb] (for the included RapidXml source), National Renewable Energy Laboratory [cph]
Maintainer: Clayton Barrows <clayton.barrows@nrel.gov>
Repository: CRAN
Date/Publication: 2016-08-26 07:45:22

More information about rplexos at CRAN
Permanent link

Package rcrossref updated to version 0.5.8 with previous version 0.5.4 dated 2016-07-20

Title: Client for Various 'CrossRef' APIs
Description: Client for various 'CrossRef' APIs, including 'metadata' search with their old and newer search APIs, get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Ted Hart [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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 tests/testthat/test_cr_journals.R |    8 +-
 55 files changed, 922 insertions(+), 525 deletions(-)

More information about rcrossref at CRAN
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Package matchMulti updated to version 1.1.5 with previous version 1.1.4 dated 2016-08-13

Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-level treatments and individual-level outcomes using a network optimization algorithm. Functions for checking balance at the cluster and individual levels are also provided, as are methods for permutation-inference-based outcome analysis.
Author: Luke Keele and Sam Pimentel
Maintainer: Sam Pimentel <spi@wharton.upenn.edu>

Diff between matchMulti versions 1.1.4 dated 2016-08-13 and 1.1.5 dated 2016-08-26

 DESCRIPTION                      |    8 ++++----
 MD5                              |   18 ++++++++++--------
 NAMESPACE                        |    5 ++---
 R/buildCaliper.R                 |only
 R/matchMulti-internal.R          |   19 +++++++++++++++----
 R/matchMulti.R                   |   13 +++++++++----
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 man/matchStudents.Rd             |   13 +++++++++++--
 11 files changed, 57 insertions(+), 28 deletions(-)

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Package ExtremeBounds updated to version 0.1.5.2 with previous version 0.1.5.1 dated 2015-08-10

Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac <hlavac@fas.harvard.edu>
Maintainer: Marek Hlavac <hlavac@fas.harvard.edu>

Diff between ExtremeBounds versions 0.1.5.1 dated 2015-08-10 and 0.1.5.2 dated 2016-08-26

 DESCRIPTION                 |    8 
 MD5                         |   24 -
 NAMESPACE                   |    9 
 R/ExtremeBounds-internal.R  |    4 
 build/vignette.rds          |binary
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 inst/ChangeLog              |    3 
 inst/doc/ExtremeBounds.pdf  |binary
 man/ExtremeBounds.Rd        |    3 
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 man/hist.eba.Rd             |    3 
 man/print.eba.Rd            |    3 
 vignettes/ExtremeBounds.bib | 1038 ++++++++++++++++++++++----------------------
 13 files changed, 571 insertions(+), 558 deletions(-)

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Package energy updated to version 1.7-0 with previous version 1.6.2 dated 2014-10-28

Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.
Author: Maria L. Rizzo and Gabor J. Szekely
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>

Diff between energy versions 1.6.2 dated 2014-10-28 and 1.7-0 dated 2016-08-26

 energy-1.6.2/energy/man/mvnorm.etest.Rd      |only
 energy-1.7-0/energy/DESCRIPTION              |   28 +
 energy-1.7-0/energy/MD5                      |   67 ++--
 energy-1.7-0/energy/NAMESPACE                |   53 ++-
 energy-1.7-0/energy/NEWS                     |   55 ++-
 energy-1.7-0/energy/R/Ecluster.R             |  120 +-------
 energy-1.7-0/energy/R/Eeqdist.R              |   50 +--
 energy-1.7-0/energy/R/Eindep.R               |   95 +++---
 energy-1.7-0/energy/R/Emvnorm.R              |  111 +++----
 energy-1.7-0/energy/R/Epoisson.R             |   22 -
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 energy-1.7-0/energy/R/dcorT.R                |    6 
 energy-1.7-0/energy/R/dcov.R                 |   58 ++--
 energy-1.7-0/energy/R/dcovu.R                |only
 energy-1.7-0/energy/R/disco.R                |  390 +++++++++++++--------------
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 energy-1.7-0/energy/man/dcov.Rd              |   76 ++---
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 energy-1.7-0/energy/man/disco.Rd             |  248 ++++++++---------
 energy-1.7-0/energy/man/edist.Rd             |   70 ++--
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 energy-1.7-0/energy/man/energy-package.Rd    |   14 
 energy-1.7-0/energy/man/energy.hclust.Rd     |   61 ++--
 energy-1.7-0/energy/man/eqdist.etest.Rd      |   90 +++---
 energy-1.7-0/energy/man/indep.test.Rd        |   66 ++--
 energy-1.7-0/energy/man/mvI.test.Rd          |   36 +-
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 energy-1.7-0/energy/src/mvnorm.cpp           |only
 energy-1.7-0/energy/src/partial-dcor.cpp     |only
 energy-1.7-0/energy/src/projection.cpp       |only
 44 files changed, 926 insertions(+), 1031 deletions(-)

More information about energy at CRAN
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