Mon, 06 Jul 2015

Package StAMPP updated to version 1.4 with previous version 1.3 dated 2014-09-01

Title: Statistical Analysis of Mixed Ploidy Populations
Description: Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton <luke.pembleton@ecodev.vic.gov.au>

Diff between StAMPP versions 1.3 dated 2014-09-01 and 1.4 dated 2015-07-06

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Package HiddenMarkov updated to version 1.8-4 with previous version 1.8-3 dated 2015-04-12

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.harte@gns.cri.nz>

Diff between HiddenMarkov versions 1.8-3 dated 2015-04-12 and 1.8-4 dated 2015-07-06

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Sun, 05 Jul 2015

Package schoRsch updated to version 1.2 with previous version 1.1 dated 2014-08-23

Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>

Diff between schoRsch versions 1.1 dated 2014-08-23 and 1.2 dated 2015-07-05

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Package SamplerCompare updated to version 1.2.7 with previous version 1.2.6 dated 2015-02-22

Title: A Framework for Comparing the Performance of MCMC Samplers
Description: A framework for running sets of MCMC samplers on sets of distributions with a variety of tuning parameters, along with plotting functions to visualize the results of those simulations. See sc-intro.pdf for an introduction.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by G. W. Stewart.
Maintainer: Madeleine Thompson <madeleineth@gmail.com>

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Package rredis updated to version 1.7.0 with previous version 1.6.9 dated 2014-09-15

Title: "Redis" Key/Value Database Client
Description: R client interface to the "Redis" key-value database.
Author: B. W. Lewis
Maintainer: B. W. Lewis <blewis@illposed.net>

Diff between rredis versions 1.6.9 dated 2014-09-15 and 1.7.0 dated 2015-07-05

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Package Rlibeemd updated to version 1.3.4 with previous version 1.3.3 dated 2015-06-24

Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface), Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

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Package rcdd updated to version 1.1-9 with previous version 1.1-8 dated 2014-03-30

Title: Computational Geometry
Description: R interface to (some of) cddlib (http://www.ifor.math.ethz.ch/~fukuda/cdd_home/cdd.html). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Glen D. Meeden <glen@stat.umn.edu>, incorporates code from cddlib (ver 0.94f) written by Komei Fukuda <fukuda@ifor.math.ethz.ch>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package potts updated to version 0.5-4 with previous version 0.5-3 dated 2015-06-06

Title: Markov Chain Monte Carlo for Potts Models
Description: Does Markov chain Monte Carlo (MCMC) simulation of Potts models and composite likelihood inference for Potts models.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif Johnson <leif@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

Diff between potts versions 0.5-3 dated 2015-06-06 and 0.5-4 dated 2015-07-05

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Package LeafArea updated to version 0.1.1 with previous version 0.1.0 dated 2015-04-20

Title: Rapid Digital Image Analysis of Leaf Area
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
Author: Masatoshi Katabuchi <mattocci27@gmail.com>
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>

Diff between LeafArea versions 0.1.0 dated 2015-04-20 and 0.1.1 dated 2015-07-05

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Package GSE updated to version 3.2 with previous version 3.1 dated 2014-09-25

Title: Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>

Diff between GSE versions 3.1 dated 2014-09-25 and 3.2 dated 2015-07-05

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Package baseline updated to version 1.2-1 with previous version 1.2-0 dated 2015-03-11

Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between baseline versions 1.2-0 dated 2015-03-11 and 1.2-1 dated 2015-07-05

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Package gromovlab updated to version 0.7-6 with previous version 0.6-16 dated 2015-05-25

Title: Gromov-Hausdorff Type Distances for Labeled Metric Spaces
Description: Computing Gromov-Hausdorff type l^p distances for labeled metric spaces. These distances were introduced in V.Liebscher, Gromov meets Phylogenetics - new Animals for the Zoo of Metrics on Tree Space. preprint arXiv:1504.05795, for phylogenetic trees but may apply to much more situations.
Author: Volkmar Liebscher
Maintainer: Volkmar Liebscher <volkmar.liebscher@uni-greifswald.de>

Diff between gromovlab versions 0.6-16 dated 2015-05-25 and 0.7-6 dated 2015-07-05

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Package genderizeR updated to version 1.2.0 with previous version 1.1.0 dated 2015-04-22

Title: Gender Prediction Based on First Names
Description: Utilizes the 'genderize.io' API to predict gender from first names extracted from a text vector. The accuracy of prediction could be controlled by two parameters: counts of a first name in the database and probability of prediction.
Author: Kamil Wais [aut, cre]
Maintainer: Kamil Wais <kamil.wais@gmail.com>

Diff between genderizeR versions 1.1.0 dated 2015-04-22 and 1.2.0 dated 2015-07-05

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Package lctools updated to version 0.2-3 with previous version 0.2-2 dated 2015-04-15

Title: Local Correlation, Spatial Inequalities and Other Tools
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <skalo@hua.gr>

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Package rLTP updated to version 0.1.2 with previous version 0.1 dated 2015-01-28

Title: R Interface to LTP-Cloud Service
Description: R interface to LTP-Cloud service for Natural Language Processing in Chinese. For more details please visit http://www.ltp-cloud.com/. Visit https://github.com/hetong007/rLTP for up-to-date version.
Author: Tong He <hetong007@gmail.com>
Maintainer: Tong He <hetong007@gmail.com>

Diff between rLTP versions 0.1 dated 2015-01-28 and 0.1.2 dated 2015-07-05

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Package qdap updated to version 2.2.2 with previous version 2.2.1 dated 2015-05-11

Title: Bridging the Gap Between Qualitative Data and Quantitative Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb], Dason Kurkiewicz [ctb], Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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Package latex2exp updated to version 0.3.1 with previous version 0.3.0 dated 2015-07-02

Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>

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Package bit64 updated to version 0.9-5 with previous version 0.9-4 dated 2014-04-09

Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support interactive data exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel

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Package biosignalEMG updated to version 1.0.3 with previous version 1.0.2 dated 2015-04-09

Title: Standard Processing Tools for Electromyogram Signals
Description: Data processing tools for electromyogram (EMG) signals to compute the rectified, integrated and averaged EMG. Tools to plot the ensemble average of the EMG.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>

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Package AHR updated to version 1.2 with previous version 1.1 dated 2015-07-03

Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as defined by Kalbfleisch and Prentice. The underlying survival functions of the event of interest in each group can be estimated using either the (weighted) Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition probabilities in Markov multi-state models. Right-censored and left-truncated data is supported. Moreover, the difference in restricted mean survival can be estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>

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Sat, 04 Jul 2015

Package spocc updated to version 0.3.0 with previous version 0.2.4 dated 2015-01-22

Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources, including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics' Engine 'eBird', and 'AntWeb'. Includes functionality for retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package RedditExtractoR updated to version 1.1.1 with previous version 1.0.0 dated 2015-06-16

Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. The retrieved data has flat structure, i.e. the relationship between comments is not preserved.This may be addressed in the next update of this package. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 3 functions, one for extracting relevant URLS, one for extracting features out of given URLs and one that does both together.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

Diff between RedditExtractoR versions 1.0.0 dated 2015-06-16 and 1.1.1 dated 2015-07-04

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Package curl updated to version 0.9.1 with previous version 0.9 dated 2015-06-19

Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https://, ftps://), 'gzip' compression, authentication, and other 'libcurl' goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut], Hadley Wickham [ctb], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between curl versions 0.9 dated 2015-06-19 and 0.9.1 dated 2015-07-04

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Package trust updated to version 0.1-7 with previous version 0.1-6 dated 2014-03-29

Title: Trust Region Optimization
Description: Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package smoothtail updated to version 2.0.4 with previous version 2.0.3 dated 2014-02-06

Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma in [-1,0], offers several estimates to compute estimates of gamma. The estimates are based on the principle of replacing the order statistics by quantiles of a distribution function based on a log--concave density function. This procedure is justified by the fact that the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Ru{f}{i}bach <kaspar.rufibach@gmail.com> and Samuel Mueller <samuel.mueller@sydney.edu.au>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package reporttools updated to version 1.1.2 with previous version 1.1.1 dated 2013-11-06

Title: Generate LaTeX Tables of Descriptive Statistics
Description: These functions are especially helpful when writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between reporttools versions 1.1.1 dated 2013-11-06 and 1.1.2 dated 2015-07-04

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Package RcppRedis updated to version 0.1.4 with previous version 0.1.3 dated 2014-12-10

Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package patchSynctex updated to version 0.1-3 with previous version 0.1-2 dated 2015-05-01

Title: Communication Between Editor and Viewer for Literate Programs
Description: This utility eases the debugging of literate documents ('noweb' files) by patching the synchronization information (the '.synctex(.gz)' file) produced by 'pdflatex' with concordance information produced by 'Sweave' or 'knitr' and 'Sweave' or 'knitr' ; this allows for bilateral communication between a text editor (visualizing the 'noweb' source) and a viewer (visualizing the resultant 'PDF'), thus bypassing the intermediate 'TeX' file.
Author: Jan Gleixner [aut], Daniel Hicks [ctb], Emmanuel Charpentier [aut, cre]
Maintainer: Emmanuel Charpentier <emm.charpentier@free.fr>

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Package OrdFacReg updated to version 1.0.6 with previous version 1.0.5 dated 2014-09-06

Title: Least Squares, Logistic, and Cox-Regression with Ordered Predictors
Description: In biomedical studies, researchers are often interested in assessing the association between one or more ordinal explanatory variables and an outcome variable, at the same time adjusting for covariates of any type. The outcome variable may be continuous, binary, or represent censored survival times. In the absence of a precise knowledge of the response function, using monotonicity constraints on the ordinal variables improves efficiency in estimating parameters, especially when sample sizes are small. This package implements an active set algorithm that efficiently computes such estimators.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between OrdFacReg versions 1.0.5 dated 2014-09-06 and 1.0.6 dated 2015-07-04

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Package nat.utils updated to version 0.5.1 with previous version 0.5 dated 2015-07-02

Title: File System Utility Functions for 'NeuroAnatomy Toolbox'
Description: Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

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Package googleVis updated to version 0.5.9 with previous version 0.5.8 dated 2015-01-21

Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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Package GLDreg updated to version 1.0.3 with previous version 1.0.2 dated 2015-03-05

Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>

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Package GLDEX updated to version 2.0.0.3 with previous version 2.0.0.2 dated 2014-12-22

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDEX versions 2.0.0.2 dated 2014-12-22 and 2.0.0.3 dated 2015-07-04

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Package forams updated to version 2.0-5 with previous version 2.0-4 dated 2014-02-18

Title: Foraminifera and Community Ecology Analyses
Description: SHE, FORAM Index and ABC Method analyses and custom plot functions for community data.
Author: Rodrigo Aluizio
Maintainer: Rodrigo Aluizio <r.aluizio@gmail.com>

Diff between forams versions 2.0-4 dated 2014-02-18 and 2.0-5 dated 2015-07-04

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Package gdata updated to version 2.17.0 with previous version 2.16.1 dated 2015-05-01

Title: Various R Programming Tools for Data Manipulation
Description: Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni Magnusson, Jim Rogers, and others
Maintainer: Gregory R. Warnes <greg@warnes.net>

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Package VTrack updated to version 1.11 with previous version 1.10 dated 2015-07-02

Title: A Collection of Tools for the Analysis of Remote Acoustic Telemetry Data
Description: Designed to facilitate the assimilation, analysis and synthesis of animal location and movement data collected by the VEMCO suite of acoustic transmitters and receivers. As well as database and geographic information capabilities the principal feature of VTrack is the qualification and identification of ecologically relevant events from the acoustic detection and sensor data. This procedure condenses the acoustic detection database by orders of magnitude, greatly enhancing the synthesis of acoustic detection data.
Author: Ross G. Dwyer, Mathew E. Watts, Hamish A. Campbell & Craig E. Franklin
Maintainer: Ross Dwyer <ross.dwyer@uq.edu.au>

Diff between VTrack versions 1.10 dated 2015-07-02 and 1.11 dated 2015-07-04

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Package kinfit updated to version 1.1.14 with previous version 1.1.13 dated 2014-11-25

Title: Routines for Fitting Kinetic Models to Chemical Degradation Data
Description: The FOCUS Kinetics Report first published in 2006 describes mathematical models and recommends statistical methods for the evaluation of chemical degradation data. This package implements fitting the kinetic models suitable for observations of the decline of a single chemical compound (no metabolite formation/decline or multi-compartment kinetics). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. 'kinfit' is maintained, but not actively developed at the moment. Please check the 'mkin' package for an actively developed package for kinetic evaluations of degradation data.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

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Package ecespa updated to version 1.1-8 with previous version 1.1-7 dated 2013-03-13

Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on spatstat), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones".
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@upm.es>

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Fri, 03 Jul 2015

Package R6 updated to version 2.1.0 with previous version 2.0.1 dated 2014-10-29

Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>

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Package pooh updated to version 0.3-1 with previous version 0.3 dated 2015-01-05

Title: Partial Orders and Relations
Description: Finds equivalence classes corresponding to a symmetric relation or undirected graph. Finds total order consistent with partial order or directed graph (so-called topological sort).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package Interatrix updated to version 1.1.1 with previous version 1.0 dated 2015-03-19

Title: Compute Chi-Square Measures with Corrections
Description: Chi-square tests are computed with corrections.
Author: Aurélie Siberchicot, Eléonore Hellard, Dominique Pontier, David Fouchet and Franck Sauvage
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Package ddalpha updated to version 1.1.2.3 with previous version 1.1.2.2 dated 2015-07-01

Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut], Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>

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Package openxlsx updated to version 3.0.0 with previous version 2.4.0 dated 2015-03-07

Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre], Luca Braglia [ctb]
Maintainer: Alexander Walker <Alexander.Walker1989@gmail.com>

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Package NLP updated to version 0.1-8 with previous version 0.1-7 dated 2015-05-06

Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between NLP versions 0.1-7 dated 2015-05-06 and 0.1-8 dated 2015-07-03

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Package nadiv updated to version 2.14.0 with previous version 2.13.3 dated 2015-06-03

Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>

Diff between nadiv versions 2.13.3 dated 2015-06-03 and 2.14.0 dated 2015-07-03

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Package hive updated to version 0.2-0 with previous version 0.1-16 dated 2014-02-21

Title: Hadoop InteractiVE
Description: Hadoop InteractiVE facilitates distributed computing via the MapReduce paradigm through R and Hadoop. An easy to use interface to Hadoop, the Hadoop Distributed File System (HDFS), and Hadoop Streaming is provided.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>

Diff between hive versions 0.1-16 dated 2014-02-21 and 0.2-0 dated 2015-07-03

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Package mldr updated to version 0.2.25 with previous version 0.1.70 dated 2015-02-13

Title: Exploratory Data Analysis and Manipulation of Multi-Label Data Sets
Description: Exploratory data analysis and manipulation functions for multi-label data sets along with an interactive Shiny application to ease their use.
Author: David Charte [cre], Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>

Diff between mldr versions 0.1.70 dated 2015-02-13 and 0.2.25 dated 2015-07-03

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Package metaplus updated to version 0.7-4 with previous version 0.7-2 dated 2015-06-03

Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals from the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath <ken.beath@mq.edu.au>
Maintainer: Ken Beath <ken.beath@mq.edu.au>

Diff between metaplus versions 0.7-2 dated 2015-06-03 and 0.7-4 dated 2015-07-03

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Package gnumeric updated to version 0.7-4 with previous version 0.7-2 dated 2012-10-30

Title: Read Data from Files Readable by Gnumeric
Description: Read data files readable by gnumeric into R. Can read whole sheet or a range, from several file formats, including the native format of gnumeric. Reading is done by using ssconvert (a file converter utility included in the gnumeric distribution http://projects.gnome.org/gnumeric/) to convert the requested part to CSV. From gnumeric files (but not other formats) can list sheet names and sheet sizes or read all sheets.
Author: Karoly Antal <antalk2@gmail.com>.
Maintainer: Karoly Antal <antalk2@gmail.com>

Diff between gnumeric versions 0.7-2 dated 2012-10-30 and 0.7-4 dated 2015-07-03

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Package tagcloud updated to version 0.6 with previous version 0.5 dated 2014-11-06

Title: Tag Clouds
Description: Generating Tag and Word Clouds.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between tagcloud versions 0.5 dated 2014-11-06 and 0.6 dated 2015-07-03

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Package selectMeta updated to version 1.0.8 with previous version 1.0.7 dated 2014-09-06

Title: Estimation of Weight Functions in Meta Analysis
Description: Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. In this package we provide implementations of several parametric and nonparametric weight functions. The novelty in Rufibach (2011) is the proposal of a non-increasing variant of the nonparametric weight function of Dear & Begg (1992). The new approach potentially offers more insight in the selection process than other methods, but is more flexible than parametric approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992) under a monotonicity constraint we use a differential evolution algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al (2009). In addition, we offer a method to compute a confidence interval for the overall effect size theta, adjusted for selection bias as well as a function that computes the simulation-based p-value to assess the null hypothesis of no selection as described in Rufibach (2011, Section 6).
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between selectMeta versions 1.0.7 dated 2014-09-06 and 1.0.8 dated 2015-07-03

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 NAMESPACE                         |    2 ++
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Package paramlink updated to version 0.9-7 with previous version 0.9-6 dated 2014-04-01

Title: Parametric Linkage Analysis in R
Description: Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>

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Package MuMIn updated to version 1.15.1 with previous version 1.14.0 dated 2015-06-04

Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria (AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>

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Package logcondiscr updated to version 1.0.6 with previous version 1.0.5 dated 2014-02-05

Title: Estimate a Log-Concave Probability Mass Function from Discrete i.i.d. Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), allows to compute the maximum likelihood estimator (MLE) of probability mass function (pmf) under the assumption that it is log-concave, see Weyermann (2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main functions of the package are 'logConDiscrMLE' that allows computation of the log-concave MLE, 'logConDiscrCI' that computes pointwise confidence bands for the MLE, and 'kInflatedLogConDiscr' that computes a mixture of a log-concave PMF and a point mass at k.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Fadoua Balabdaoui <fadoua@ceremade.dauphine.fr> and Hanna Jankowski <hkj@mathstat.yorku.ca> and Kathrin Weyermann <kathrin.weyermann@bkw-fmb.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between logcondiscr versions 1.0.5 dated 2014-02-05 and 1.0.6 dated 2015-07-03

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Package IBDsim updated to version 0.9-5 with previous version 0.9-4 dated 2014-05-30

Title: Simulation of Chromosomal Regions Shared by Family Members
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>

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Package GPareto updated to version 1.0.1 with previous version 1.0.0 dated 2014-12-17

Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. kriging models, are applied to global multiobjective optimization of black-box functions. Multiobjective Expected Improvement and Stepwise Uncertainty Reduction sequential infill criteria are available. A quantification of uncertainty on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mickael.binois@mines-stetienne.fr>

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Package goftest updated to version 1.0-3 with previous version 1.0-2 dated 2014-06-24

Title: Classical Goodness-of-Fit Tests for Univariate Distributions
Description: Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms.
Author: Julian Faraway [aut], George Marsaglia [aut], John Marsaglia [aut], Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>

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Package gamlss updated to version 4.3-5 with previous version 4.3-4 dated 2015-02-03

Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph], Bob Rigby [aut], Vlasios Voudouris [ctb], Calliope Akantziliotou [ctb], Marco Enea [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

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Package EpiContactTrace updated to version 0.9.1 with previous version 0.9.0 dated 2015-07-02

Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing and visualisation of network of contacts.
Author: Maria Noremark [aut], Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

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Package tm updated to version 0.6-2 with previous version 0.6-1 dated 2015-05-07

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre], Kurt Hornik [aut], Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>

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Package rgbif updated to version 0.8.6 with previous version 0.8.4 dated 2015-06-08

Title: Interface to the Global 'Biodiversity' Information Facility 'API'
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, and getting counts of occurrence records.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Vijay Barve [aut], Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rgbif versions 0.8.4 dated 2015-06-08 and 0.8.6 dated 2015-07-03

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Package modehunt updated to version 1.0.7 with previous version 1.0.6 dated 2011-11-29

Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations X(1), ..., X(n) from a density f, provides five methods to perform a multiscale analysis about f as well as the necessary critical values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive correction term Gamma in either method offers another two approaches which are more powerful on small scales and less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically equivalent to the first and was introduced in Rufibach and Walther (2010).
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Guenther Walther <gwalther@stanford.edu>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package spd updated to version 2.0-1 with previous version 2.0-0 dated 2014-07-02

Title: Semi Parametric Distribution
Description: The Semi Parametric Piecewise Distribution blends the Generalized Pareto Distribution for the tails with a kernel based interior.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

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Package rseedcalc updated to version 1.3 with previous version 1.2 dated 2013-10-10

Title: Estimating the Proportion of Genetically Modified Seeds in Seedlots via Multinomial Group Testing
Description: Estimate the percentage of seeds in a seedlot that contain stacks of genetically modified traits. Estimates are calculated using a multinomial group testing model with maximum likelihood estimation of the parameters.
Author: Kevin Wright [aut, cre], Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>

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Package gistr updated to version 0.3.0 with previous version 0.2.0 dated 2015-05-01

Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g., http://en.wikipedia.org/wiki/GitHub#Gist, https://help.github.com/articles/about-gists/). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut], Karthik Ram [aut], Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package gld updated to version 2.3 with previous version 2.2.1 dated 2014-02-19

Title: Estimation and Use of the Generalised (Tukey) Lambda Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form. This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution. It provides the density function, distribution function, and Quantile-Quantile plots. It implements a variety of estimation methods for the distribution, including diagnostic plots. Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation. These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>
Maintainer: Robert King <Robert.King@newcastle.edu.au>

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Package corrgram updated to version 1.8 with previous version 1.7 dated 2015-02-13

Title: Plot a Correlogram
Description: Calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>

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Package abd updated to version 0.2-8 with previous version 0.2-7 dated 2015-02-02

Title: The Analysis of Biological Data
Description: The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Author: Kevin M. Middleton <middletonk@missouri.edu>, Randall Pruim <rpruim@calvin.edu>
Maintainer: Kevin M. Middleton <middletonk@missouri.edu>

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Thu, 02 Jul 2015

Package TestScorer updated to version 1.7.1 with previous version 1.7 dated 2015-04-20

Title: GUI for Entering Test Items and Obtaining Raw and Transformed Scores
Description: GUI for entering test items and obtaining raw and transformed scores. The results are shown on the console and can be saved to a tabular text file for further statistical analysis. The user can define his own tests and scoring procedures through a GUI.
Author: Manel Salamero
Maintainer: Manel Salamero <manelsalamero@gmail.com>

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Package rnrfa updated to version 0.2.0 with previous version 0.1.5 dated 2014-11-07

Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow Archive. The package contains R wrappers to the UK NRFA data temporary-API. There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>

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Package rmgarch updated to version 1.2-9 with previous version 1.2-8 dated 2014-06-30

Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

Diff between rmgarch versions 1.2-8 dated 2014-06-30 and 1.2-9 dated 2015-07-02

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Package PtProcess updated to version 3.3-10 with previous version 3.3-9 dated 2015-04-12

Title: Time Dependent Point Process Modelling
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte <d.harte@gns.cri.nz>

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Package powerGWASinteraction updated to version 1.1.3 with previous version 1.1.1 dated 2014-12-21

Title: Power Calculations for GxE and GxG Interactions for GWAS
Description: Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.
Author: Charles Kooperberg <clk@fredhutch.org> and Li Hsu <lih@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>

Diff between powerGWASinteraction versions 1.1.1 dated 2014-12-21 and 1.1.3 dated 2015-07-02

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Package polspline updated to version 1.1.11 with previous version 1.1.9 dated 2013-11-20

Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>

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Package maSAE updated to version 0.1-3 with previous version 0.1-2 dated 2014-04-28

Title: Mandallaz' Model-Assisted Small Area Estimators
Description: An S4 implementation of the unbiased extension of the model-assisted synthetic-regression estimator proposed by Mandallaz (2013), Mandallaz et al. (2013) and Mandallaz (2014). It yields smaller variances than the standard bias correction, the generalised regression estimator.
Author: Andreas Dominik Cullmann [aut, cre], Daniel Mandallaz [ctb], Alexander Francis Massey [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_masae@arcor.de>

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Package logspline updated to version 2.1.8 with previous version 2.1.5 dated 2013-04-24

Title: Logspline Density Estimation Routines
Description: Routines for the logspline density estimation. oldlogspline uses the same algorithm as the logspline 1.0.x package - the Kooperberg and Stone (1992) algorithm (with an improved interface). The recommended routine logspline uses an algorithm from Stone et al (1997).
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>

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More information about logspline at CRAN
Permanent link

Package LogicReg updated to version 1.5.8 with previous version 1.5.6 dated 2015-01-23

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>

Diff between LogicReg versions 1.5.6 dated 2015-01-23 and 1.5.8 dated 2015-07-02

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 MD5                          |   44 +++++++++++++++++++++----------------------
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More information about LogicReg at CRAN
Permanent link

Package logcondens updated to version 2.1.4 with previous version 2.1.3 dated 2015-06-10

Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Lutz Duembgen <duembgen@stat.unibe.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between logcondens versions 2.1.3 dated 2015-06-10 and 2.1.4 dated 2015-07-02

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Permanent link

Package WriteXLS updated to version 3.6.1 with previous version 3.6.0 dated 2015-06-24

Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>

Diff between WriteXLS versions 3.6.0 dated 2015-06-24 and 3.6.1 dated 2015-07-02

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 inst/Perl/Spreadsheet/WriteExcel/OLEwriter.pm        |    4 
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 inst/Perl/Spreadsheet/WriteExcel/Worksheet.pm        |    4 
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 69 files changed, 6483 insertions(+), 3252 deletions(-)

More information about WriteXLS at CRAN
Permanent link

Package ump updated to version 0.5-6 with previous version 0.5-4 dated 2014-04-02

Title: Uniformly Most Powerful Tests
Description: Does uniformly most powerful (UMP) and uniformly most powerful unbiased (UMPU) tests. At present only distribution implemented is binomial distribution. Also does fuzzy tests and confidence intervals (following Geyer and Meeden, Statistical Science, 2005) for the binomial distribution (one-tailed procedures based on UMP test and two-tailed procedures based on UMPU test).
Author: Charles J. Geyer <charlie@stat.umn.edu> and Glen D. Meeden <glen@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

Diff between ump versions 0.5-4 dated 2014-04-02 and 0.5-6 dated 2015-07-02

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More information about ump at CRAN
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Package tileHMM updated to version 1.0-7 with previous version 1.0-6 dated 2013-12-12

Title: Hidden Markov Models for ChIP-on-Chip Analysis
Description: Methods and classes to build HMMs that are suitable for the analysis of ChIP-chip data. The provided parameter estimation methods include the Baum-Welch algorithm and Viterbi training as well as a combination of both.
Author: Peter Humburg [aut, cre]
Maintainer: Peter Humburg <peter.humburg@gmail.com>

Diff between tileHMM versions 1.0-6 dated 2013-12-12 and 1.0-7 dated 2015-07-02

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More information about tileHMM at CRAN
Permanent link

Package parma updated to version 1.5-2 with previous version 1.5-1 dated 2014-02-23

Title: Portfolio Allocation and Risk Management Applications
Description: Methods for Portfolio Optimization and Risk Management.
Author: Alexios Ghalanos and Bernhard Pfaff
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

Diff between parma versions 1.5-1 dated 2014-02-23 and 1.5-2 dated 2015-07-02

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More information about parma at CRAN
Permanent link

Package nat.utils updated to version 0.5 with previous version 0.4.2 dated 2014-06-16

Title: File System Utility Functions for 'NeuroAnatomy Toolbox'
Description: Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between nat.utils versions 0.4.2 dated 2014-06-16 and 0.5 dated 2015-07-02

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More information about nat.utils at CRAN
Permanent link

Package mountainplot updated to version 1.1 with previous version 1.0 dated 2015-01-26

Title: Mountain Plots, Folded Empirical Cumulative Distribution Plots
Description: Lattice functions for drawing folded empirical cumulative distribution plots, or mountain plots. A mountain plot is similar to an empirical CDF plot, except that the curve increases from 0 to 0.5, then decreases from 0.5 to 1 using an inverted scale at the right side. See: Monti (1995), Folded empirical distribution function curves-mountain plots. The American Statistician, 49, 342-345.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>

Diff between mountainplot versions 1.0 dated 2015-01-26 and 1.1 dated 2015-07-02

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More information about mountainplot at CRAN
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Package lucid updated to version 1.3 with previous version 1.2 dated 2015-04-14

Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>

Diff between lucid versions 1.2 dated 2015-04-14 and 1.3 dated 2015-07-02

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More information about lucid at CRAN
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Package HandTill2001 updated to version 0.2-10 with previous version 0.2-9 dated 2013-11-23

Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and Robert J. Till (2001). A Simple Generalisation of the Area Under the ROC Curve for Multiple Class Classification Problems. Machine Learning, 45 (2), p. 171--186. DOI:10.1023/A:1010920819831.
Author: Andreas Dominik Cullmann [aut, cre], Edgar Kublin [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_handtill2001@arcor.de>

Diff between HandTill2001 versions 0.2-9 dated 2013-11-23 and 0.2-10 dated 2015-07-02

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Permanent link

Package exactci updated to version 1.3-1 with previous version 1.3-0 dated 2014-09-25

Title: Exact P-Values and Matching Confidence Intervals for Simple Discrete Parametric Cases
Description: Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>

Diff between exactci versions 1.3-0 dated 2014-09-25 and 1.3-1 dated 2015-07-02

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More information about exactci at CRAN
Permanent link

Package elastic updated to version 0.5.0 with previous version 0.4.0 dated 2015-05-01

Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API' (http://elasticsearch.org), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with 'APIs' for 'indices', documents, nodes, clusters, an interface to the cat 'API', and more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between elastic versions 0.4.0 dated 2015-05-01 and 0.5.0 dated 2015-07-02

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Package DSL updated to version 0.1-6 with previous version 0.1-5 dated 2014-02-21

Title: Distributed Storage and List
Description: An abstract DList class helps storing large list-type objects in a distributed manner. Corresponding high-level functions and methods for handling distributed storage (DStorage) and lists allows for processing such DLists on distributed systems efficiently. In doing so it uses a well defined storage backend implemented based on the DStorage class.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre], Christian Buchta [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>

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Package bpcp updated to version 1.2.6 with previous version 1.2.5 dated 2015-06-04

Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>

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Package gsscopu updated to version 0.9-3 with previous version 0.9-2 dated 2014-12-06

Title: Copula Density and 2-D Hazard Estimation using Smoothing Splines
Description: A collection of routines for the estimation of copula density and 2-D hazard function using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

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Package gss updated to version 2.1-5 with previous version 2.1-4 dated 2014-12-06

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

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Package EpiContactTrace updated to version 0.9.0 with previous version 0.8.8 dated 2013-11-05

Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing and visualisation of network of contacts.
Author: Maria Noremark [aut], Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

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Package AGSDest updated to version 2.3 with previous version 2.2 dated 2015-01-29

Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence intervals based on the stage-wise ordering in group sequential designs and adaptive group sequential designs. For adaptive group sequential designs the confidence intervals are based on the conditional rejection probability principle. Currently the procedures do not support the use of futility boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>

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Package scuba updated to version 1.8-0 with previous version 1.7-0 dated 2013-12-15

Title: Diving Calculations and Decompression Models
Description: Code for describing and manipulating scuba diving profiles (depth-time curves) and decompression models, for calculating the predictions of decompression models, for calculating maximum no-decompression time and decompression tables, and for performing mixed gas calculations.
Author: Adrian Baddeley [aut, cre], Vittorio Broglio [ctb, dtc], Pedro Antonio Neves [ctb, dtc], Andrew Bassom [ctb], Peter Buzzacott [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>

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Package RenextGUI updated to version 1.3-0 with previous version 1.0-2 dated 2013-10-08

Title: GUI for Renext
Description: Graphical User Interface for Renext.
Author: Yves Deville <deville.yves@alpestat.com> and IRSN <renext@irsn.fr>
Maintainer: Lise Bardet <lise.bardet@irsn.fr>

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Package rEMM updated to version 1.0-10 with previous version 1.0-9 dated 2015-05-15

Title: Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Description: Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph], Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package recommenderlab updated to version 0.1-6 with previous version 0.1-5 dated 2014-08-18

Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package neuroim updated to version 0.0.4 with previous version 0.0.3 dated 2014-04-04

Title: Read, Write, and Process Brain Imaging Data
Description: A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.
Author: Bradley R. Buchsbaum
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>

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More information about neuroim at CRAN
Permanent link

Package meta updated to version 4.3-0 with previous version 4.2-0 dated 2015-05-08

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between meta versions 4.2-0 dated 2015-05-08 and 4.3-0 dated 2015-07-02

 DESCRIPTION       |    8 
 MD5               |   44 +--
 NAMESPACE         |   30 +-
 NEWS              |   40 +++
 R/asin2p.R        |    4 
 R/chklogical.R    |    5 
 R/forest.meta.R   |  632 +++++++++++++++++++++++++++++++++++++++---------------
 R/format.p.R      |    2 
 R/meta-internal.R |    8 
 R/metabin.R       |   16 -
 R/metacont.R      |    2 
 R/metainc.R       |    2 
 R/metaprop.R      |    6 
 R/metareg.R       |   32 ++
 R/settings.meta.R |   23 +
 R/subgroup.R      |   54 ++--
 man/forest.Rd     |  108 ++++++++-
 man/metacr.Rd     |    2 
 man/metainf.Rd    |    1 
 man/metareg.Rd    |   49 +++-
 man/print.meta.Rd |    2 
 man/print.rm5.Rd  |    2 
 man/read.rm5.Rd   |    2 
 23 files changed, 795 insertions(+), 279 deletions(-)

More information about meta at CRAN
Permanent link


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