Wed, 27 Jul 2016

Package vipor updated to version 0.4.3 with previous version 0.4.2 dated 2016-07-03

Title: Plot Categorical Data Using Quasirandom Noise and Density Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

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Package hunspell updated to version 1.4.3 with previous version 1.4.2 dated 2016-07-13

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

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Package Surrogate updated to version 0.1-74 with previous version 0.1-73 dated 2016-05-16

Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package kinn updated to version 0.2 with previous version 0.1 dated 2016-05-22

Title: An Implementation of 'kinn' Algorithm, a Graph Based Regression Model
Description: A graph based regression model from flat unstructured dataset. Each line in the input data set is treated as a node from which an edge to another line (node) can be formed. In the training process, a model is created which contains sparse graph adjacency matrix. This model is then used for prediction by taking a predictor and the model as inputs and outputs a prediction which is an average of the most similar node and its neighbours in the model graph.
Author: Yossi Keshet
Maintainer: Yossi Keshet <jossiekat@icloud.com>

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Package bnspatial updated to version 1.0 with previous version 0.9 dated 2016-06-02

Title: Spatial Implementation of Bayesian Networks and Mapping
Description: Package for the spatial implementation of Bayesian Networks and mapping in geographical space. It makes maps of expected value (or most likely state) given known and unknown conditions, maps of uncertainty measured as coefficient of variation or Shannon index (entropy), maps of probability associated to any states of any node of the network. Some additional features are provided as well: parallel processing options, data discretization routines and function wrappers designed for users with minimal knowledge of the R language. Outputs can be exported to any common GIS format. Development was funded by the European Union FP7 (2007-2013), under project ROBIN (agreement 283093).
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dmasan@ceh.ac.uk>

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Package RecordLinkage updated to version 0.4-10 with previous version 0.4-9 dated 2016-05-03

Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain.
Author: Andreas Borg <borga@uni-mainz.de>, Murat Sariyar <murat.sariyar@charite.de>
Maintainer: Andreas Borg <borga@uni-mainz.de>

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Package ordinalNet updated to version 1.5 with previous version 1.4 dated 2015-12-10

Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty. Supported models include cumulative logit, probit, cauchit, and complementary log-log. The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Michael Wurm [aut, cre], Bret Hanlon [ths]
Maintainer: Michael Wurm <wurm@wisc.edu>

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Package oec updated to version 1.0.2 with previous version 1.0 dated 2016-07-26

Title: The Observatory of Economic Complexity
Description: Use The Observatory of Economic Complexity's API from R console to obtain international trade data to create spreadsheets (csv format) and D3Plus visualizations.
Author: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
Maintainer: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>

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Package dggridR updated to version 0.1.8 with previous version 0.1.7 dated 2016-07-23

Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>

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Package ddalpha updated to version 1.2.0.1 with previous version 1.2.0 dated 2016-07-25

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 ph2bye updated to version 0.1.2 with previous version 0.1.1 dated 2016-07-25

Title: Phase II Clinical Trial Design Using Bayesian Methods
Description: Calculate the Bayesian posterior/predictive probability and determine the sample size and stopping boundaries for single-arm Phase II design.
Author: Yalin Zhu, Rui Qin
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>

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Package list updated to version 8.1 with previous version 8.0 dated 2015-05-19

Title: Statistical Methods for the Item Count Technique and List Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011), Blair and Imai (2012), Blair, Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock, Crawford, and Green (2015). This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, and a method for combining list experiments with direct questions. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Kosuke Imai [aut, cre], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

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Package birk updated to version 2.1.2 with previous version 2.1.1 dated 2016-07-14

Title: MA Birk's Functions
Description: Collection of tools to make R more convenient. Includes tools to summarize data using statistics not available with base R and manipulate objects for analyses.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

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Tue, 26 Jul 2016

Package zoib updated to version 1.4.1 with previous version 1.4.0 dated 2016-07-11

Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong
Maintainer: Fang Liu <fang.liu.131@nd.edu>

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Package SNPMClust updated to version 1.3 with previous version 1.2 dated 2016-03-28

Title: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays
Description: Bivariate Gaussian genotype clustering and calling for Illumina microarrays, building on the package 'mclust'. Pronounced snip-em-clust.
Author: Stephen W. Erickson and Joshua C. Callaway
Maintainer: Joshua C. Callaway <joshcllw@gmail.com>

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Package nCal updated to version 2016.7-26 with previous version 2015.3-3 dated 2015-03-04

Title: Nonlinear Calibration
Description: Performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>, Xuesong Yu <xyu@scharp.org>
Maintainer: Youyi Fong <yfong@fhcrc.org>

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Package MVar.pt updated to version 1.9.3 with previous version 1.9.2 dated 2016-07-17

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package ipdw updated to version 0.2-5 with previous version 0.2-4 dated 2016-03-03

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

Diff between ipdw versions 0.2-4 dated 2016-03-03 and 0.2-5 dated 2016-07-26

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Package fasteraster updated to version 1.0.4 with previous version 1.0 dated 2016-07-21

Title: Raster Image Processing and Vector Recognition
Description: If there is a need to recognise edges on a raster image or a bitmap or any kind of a matrix, one can find packages that does only 90 degrees vectorization. Typically the nature of artefact images is linear and can be vectorized in much more efficient way than draw a series of 90 degrees lines. The fasteraster package does recognition of lines using only one pass.
Author: Andy Bosyi
Maintainer: Andy Bosyi <andy@bosyi.com>

Diff between fasteraster versions 1.0 dated 2016-07-21 and 1.0.4 dated 2016-07-26

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Package cellranger updated to version 1.1.0 with previous version 1.0.0 dated 2015-06-20

Title: Translate Spreadsheet Cell Ranges to Rows and Columns
Description: Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
Author: Jennifer Bryan [cre, aut], Hadley Wickham [ctb]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>

Diff between cellranger versions 1.0.0 dated 2015-06-20 and 1.1.0 dated 2016-07-26

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Package PortfolioEffectEstim updated to version 1.3 with previous version 1.2 dated 2016-02-04

Title: High Frequency Price Estimators by PortfolioEffect
Description: R interface to PortfolioEffect cloud service for estimating high frequency price variance, quarticity, microstructure noise variance, and other metrics in both aggregate and rolling window flavors. Constructed estimators could use client-side market data or access HF intraday price history for all major US Equities. See https://www.portfolioeffect.com/ for more information on the PortfolioEffect high frequency portfolio analytics platform.
Author: Andrey Kostin [aut, cre], Aleksey Zemnitskiy [aut], Oleg Nechaev [aut]
Maintainer: Andrey Kostin <andrey.kostin@portfolioeffect.com>

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Package palr updated to version 0.0.6 with previous version 0.0-4 dated 2015-06-11

Title: Colour Palettes for Data
Description: Colour palettes for data, based on some well known public data sets.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package lsl updated to version 0.5.5 with previous version 0.5.1 dated 2015-12-01

Title: Latent Structure Learning
Description: Conduct structural equation modeling via penalized likelihood.
Author: Po-Hsien Huang [aut, cre]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>

Diff between lsl versions 0.5.1 dated 2015-12-01 and 0.5.5 dated 2016-07-26

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Package JAGUAR updated to version 3.0.1 with previous version 3.0.0 dated 2015-09-24

Title: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya <c.acharya@duke.edu>

Diff between JAGUAR versions 3.0.0 dated 2015-09-24 and 3.0.1 dated 2016-07-26

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Package ghit updated to version 0.2.10 with previous version 0.2.5 dated 2016-03-15

Title: Lightweight GitHub Package Installer
Description: A lightweight, vectorized drop-in replacement for 'devtools::install_github()' that uses native git and R methods to clone and install a package from GitHub.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between ghit versions 0.2.5 dated 2016-03-15 and 0.2.10 dated 2016-07-26

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Package georob updated to version 0.2-4 with previous version 0.2-3 dated 2016-03-02

Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust and Gaussian (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift kriging predictions, along with utility functions for variogram modelling in ad-hoc geostatistical analyses, model building, model evaluation by cross-validation and for unbiased back-transformation of kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut], Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>

Diff between georob versions 0.2-3 dated 2016-03-02 and 0.2-4 dated 2016-07-26

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Package EGRET updated to version 2.6.0 with previous version 2.4.3 dated 2016-03-04

Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

Diff between EGRET versions 2.4.3 dated 2016-03-04 and 2.6.0 dated 2016-07-26

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Package DoseFinding updated to version 0.9-15 with previous version 0.9-14 dated 2016-02-02

Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis of dose-finding experiments (with focus on pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models (using Bayesian and non-Bayesian estimation), calculating optimal designs and an implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp <bbnkmp@gmail.com>

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Package dataRetrieval updated to version 2.5.10 with previous version 2.5.5 dated 2016-04-20

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

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Package Rdpack updated to version 0.4-20 with previous version 0.4-18 dated 2015-07-15

Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of Rd objects, including function reprompt() for updating existing Rd documentation for functions, methods and classes and function rebib() for import of references from 'bibtex' files. There is also a macro for importing 'bibtex' references which an be used in Rd files and 'roxygen' comments without importing this package.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between Rdpack versions 0.4-18 dated 2015-07-15 and 0.4-20 dated 2016-07-26

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Package mirtCAT updated to version 1.0 with previous version 0.9 dated 2016-06-24

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Package also contains tools useful for performing Monte Carlo simulations for studying the behaviour of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between mirtCAT versions 0.9 dated 2016-06-24 and 1.0 dated 2016-07-26

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

Title: Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups in a Phylogeny
Description: Requires rooted resolved phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.
Author: Orlando Schwery
Maintainer: Orlando Schwery <oschwery@vols.utk.edu>

Diff between MonoPhy versions 1.1 dated 2016-03-11 and 1.2 dated 2016-07-26

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Package curl updated to version 1.1 with previous version 1.0 dated 2016-07-23

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 1.0 dated 2016-07-23 and 1.1 dated 2016-07-26

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Package ChannelAttribution updated to version 1.8 with previous version 1.7 dated 2016-07-19

Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>

Diff between ChannelAttribution versions 1.7 dated 2016-07-19 and 1.8 dated 2016-07-26

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Package psychotools updated to version 0.4-1 with previous version 0.4-0 dated 2015-01-19

Title: Infrastructure for Psychometric Modeling
Description: Infrastructure for psychometric modeling such as data classes (for item response data and paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, partial credit, rating scale, multinomial processing tree models), extractor functions for different types of parameters (item, person, threshold, discrimination), unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture models in package "psychomix" and psychometric tree models in package "psychotree".
Author: Achim Zeileis [aut, cre], Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Abou El-Komboz [aut], Julia Kopf [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between psychotools versions 0.4-0 dated 2015-01-19 and 0.4-1 dated 2016-07-26

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Package corr2D updated to version 0.1.10 with previous version 0.1.9 dated 2016-06-06

Title: Implementation of 2D Correlation Analysis
Description: Implementation of two-dimensional (2D) correlation analysis based on the Fourier-transformation approach described by Isao Noda (I. Noda (1993) <DOI:10.1366/0003702934067694>). Additionally there are two plot functions for the resulting correlation matrix: The first one creates colored 2D plots, while the second one generates 3D plots.
Author: Robert Geitner [cre, aut], Robby Fritzsch [aut], Thomas Bocklitz [aut], Juergen Popp [ctb, cph]
Maintainer: Robert Geitner <robert.geitner@uni-jena.de>

Diff between corr2D versions 0.1.9 dated 2016-06-06 and 0.1.10 dated 2016-07-26

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Package Bchron updated to version 4.2.4 with previous version 4.2.2 dated 2016-06-21

Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM). The package includes a vignette which can be accessed via the vignette.
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>

Diff between Bchron versions 4.2.2 dated 2016-06-21 and 4.2.4 dated 2016-07-26

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Package AmostraBrasil updated to version 1.2 with previous version 1.1 dated 2016-06-15

Title: Generates Samples or Complete List of Brazilian IBGE (Instituto Brasileiro De Geografia e Estatistica) Census Households, Geocoding it by Google Maps
Description: Generates samples or complete list of Brazilian IBGE (Instituto Brasileiro de Geografia e Estatistica, see <http://www.ibge.gov.br/> for more information) census households, geocoding it by Google Maps. The package connects IBGE site and downloads maps and census data.
Author: Celso Stephan;Ricardo Cordeiro
Maintainer: Celso Stephan <celso.stephan@gmail.com>

Diff between AmostraBrasil versions 1.1 dated 2016-06-15 and 1.2 dated 2016-07-26

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Package SizeEstimation updated to version 1.1.1 with previous version 1.1.0 dated 2016-07-13

Title: Estimating the Sizes of Populations at Risk of HIV Infection from Multiple Data Sources Using a Bayesian Hierarchical Model
Description: This function develops an algorithm for presenting a Bayesian hierarchical model for estimating the sizes of local and national drug injected populations in Bangladesh. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion.
Author: Le Bao, Adrian E. Raftery, Kyongwon Kim
Maintainer: Kyongwon Kim<kbk5206@psu.edu>

Diff between SizeEstimation versions 1.1.0 dated 2016-07-13 and 1.1.1 dated 2016-07-26

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Package SIDES updated to version 1.3 with previous version 1.2 dated 2016-07-12

Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between SIDES versions 1.2 dated 2016-07-12 and 1.3 dated 2016-07-26

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Package random.polychor.pa updated to version 1.1.4-2 with previous version 1.1.4-1 dated 2014-08-12

Title: A Parallel Analysis with Polychoric Correlation Matrices
Description: The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis.
Author: Fabio Presaghi [aut, cre], Marta Desimoni [ctb]
Maintainer: Fabio Presaghi <fabio.presaghi@uniroma1.it>

Diff between random.polychor.pa versions 1.1.4-1 dated 2014-08-12 and 1.1.4-2 dated 2016-07-26

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Package preprosim updated to version 0.2.0 with previous version 0.1.0 dated 2016-05-28

Title: Lightweight Data Quality Simulation for Classification
Description: Data quality simulation can be used to check the robustness of data analysis findings and learn about the impact of data quality contaminations on classification. This package helps to add contaminations (noise, missing values, outliers, low variance, irrelevant features, class swap (inconsistency), class imbalance and decrease in data volume) to data and then evaluate the simulated data sets for classification accuracy. As a lightweight solution simulation runs can be set up with no or minimal up-front effort.
Author: Markus Vattulainen [aut, cre]
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>

Diff between preprosim versions 0.1.0 dated 2016-05-28 and 0.2.0 dated 2016-07-26

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Package lightsout updated to version 0.3 with previous version 0.2.1 dated 2016-01-06

Title: Implementation of the 'Lights Out' Puzzle Game
Description: Lights Out is a puzzle game consisting of a grid of lights that are either on or off. Pressing any light will toggle it and its adjacent lights. The goal of the game is to switch all the lights off. This package provides an interface to play the game on different board sizes, both through the command line or with a visual application. Puzzles can also be solved using the automatic solver included. View a demo online at http://daattali.com/shiny/lightsout/.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between lightsout versions 0.2.1 dated 2016-01-06 and 0.3 dated 2016-07-26

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Package LARF updated to version 1.4 with previous version 1.3 dated 2015-02-09

Title: Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An <weihuaan@indiana.edu>

Diff between LARF versions 1.3 dated 2015-02-09 and 1.4 dated 2016-07-26

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Mon, 25 Jul 2016

Package vcfR updated to version 1.2.0 with previous version 1.1.0 dated 2016-05-26

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

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Package DDRTree updated to version 0.1.4 with previous version 0.1.3 dated 2016-02-02

Title: Learning Principal Graphs with DDRTree
Description: Project data into a reduced dimensional space and construct a principal graph from the reduced dimension.
Author: Xiaojie Qiu, Cole Trapnell, Qi Mao, Li Wang
Maintainer: Xiaojie Qiu <xqiu@uw.edu>

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Package boral updated to version 1.0.1 with previous version 1.0 dated 2016-06-17

Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>

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Package VCA updated to version 1.3.2 with previous version 1.3.1 dated 2016-04-04

Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>

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Package texmexseq updated to version 0.3 with previous version 0.2 dated 2016-05-26

Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>

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Package runjags updated to version 2.0.4-2 with previous version 2.0.3-2 dated 2016-03-31

Title: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.
Author: Matthew Denwood [aut, cre], Martyn Plummer [cph] (Copyright holder of the code in /src/distributions/jags, src/distributions/DPar1.*, configure.ac, and original copyright holder of some modified code where indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>

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Package longpower updated to version 1.0-16 with previous version 1.0-15 dated 2016-05-17

Title: Sample Size Calculations for Longitudinal Data
Description: The longpower package contains functions for computing power and sample size for linear models of longitudinal data based on the formula due to Liu and Liang (1997) and Diggle et al (2002). Either formula is expressed in terms of marginal model or Generalized Estimating Equations (GEE) parameters. This package contains functions which translate pilot mixed effect model parameters (e.g. random intercept and/or slope) into marginal model parameters so that the formulas of Diggle et al or Liu and Liang formula can be applied to produce sample size calculations for two sample longitudinal designs assuming known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue <mdonohue@usc.edu>

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Package ifaTools updated to version 0.11 with previous version 0.10 dated 2016-05-16

Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

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Package frailtypack updated to version 2.9.4 with previous version 2.9.3.1 dated 2016-07-08

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>

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Package HK80 updated to version 0.0.2 with previous version 0.0.1 dated 2014-05-02

Title: Conversion Tools for HK80 Geographical Coordinate System
Description: This is a collection of functions for converting coordinates between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems used in Hong Kong SAR, based on the algorithms described in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Mapping Office Lands Department, Hong Kong Government (1995).
Author: Jinlong Zhang [aut, cre]
Maintainer: Jinlong Zhang <jinlongzhang01@gmail.com>

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Package equateIRT updated to version 2.0-1 with previous version 2.0 dated 2016-03-30

Title: Direct, Chain and Average Equating Coefficients with Standard Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

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Package ddalpha updated to version 1.2.0 with previous version 1.1.3.1 dated 2015-07-24

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 CORElearn updated to version 1.48.0 with previous version 1.47.1 dated 2015-09-04

Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R interface. It contains several machine learning model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leaves, random forests, kNN, naive Bayes, and locally weighted regression. All predictions obtained with these models can be explained and visualized with ExplainPrediction package. The package is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, and DKM. These methods can be used for example to discretize numeric attributes. Its additional feature is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class, enabling analysis according to the Kano model of customer satisfaction. Several algorithms support parallel multithreaded execution via OpenMP. The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>

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Package condformat updated to version 0.4.0 with previous version 0.2.0 dated 2016-03-07

Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R. It renders a data frame with cells formatted according to criteria defined by rules, using a syntax similar to 'ggplot2'. The table is printed either opening a web browser or within the 'RStudio' viewer if available. The conditional formatting rules allow to highlight cells matching a condition or add a gradient background to a given column. This package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>

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Package CALF updated to version 0.1.3 with previous version 0.1.2 dated 2016-03-25

Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>

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Package Chaos01 updated to version 1.0.1 with previous version 1.0.0 dated 2016-07-18

Title: 0-1 Test for Chaos
Description: Computes and plot the results of the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is available in parallel for the independent values of parameter c.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>

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Package BacArena updated to version 1.5.1 with previous version 1.5.0 dated 2016-07-14

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

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Package mvst updated to version 1.0.1 with previous version 1.0 dated 2016-07-20

Title: Bayesian Inference for the Multivariate Skew-t Model
Description: Estimates the multivariate skew-t and nested models, as described in the articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal model: a population Monte Carlo approach. Comput. Statist. Data Anal. <doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. Objective Bayesian analysis for the multivariate skew-t model (to appear).
Author: Antonio Parisi [aut, cre], Brunero Liseo [aut], Dirk Eddelbuettel [ctb], Romain Francois [ctb]
Maintainer: Antonio Parisi <antonio.parisi@uniroma2.it>

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Package jomo updated to version 2.2-0 with previous version 2.1-2 dated 2016-04-04

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>

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Package r.jive updated to version 1.7 with previous version 1.5 dated 2016-06-14

Title: Perform JIVE Decompositions for Multi-Source Data
Description: Performs the JIVE decompositions on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data. It provides two methods of rank selection when the rank is unknown, a permutation test and a BIC selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.
Author: Michael J. O'Connell and Eric F. Lock
Maintainer: Michael J. O'Connell <oconn725@umn.edu>

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Package gesca updated to version 1.0.3 with previous version 1.0.2 dated 2016-05-04

Title: Generalized Structured Component Analysis (GSCA)
Description: Fit a variety of component-based structural equation models.
Author: Heungsun Hwang, Sunmee Kim, Sungyoung Lee, Taesung Park
Maintainer: Sunmee Kim <sunmee.kim@mail.mcgill.ca>

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Package elastic updated to version 0.7.0 with previous version 0.6.0 dated 2016-01-07

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' (<https://www.elastic.co/products/elasticsearch>), 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>

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Sun, 24 Jul 2016

Package tigger updated to version 0.2.7 with previous version 0.2.5 dated 2016-06-13

Title: R Tools for Inferring New Immunoglobulin Alleles from Rep-Seq Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig) repertoire-sequencing (Rep-Seq) data, including detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences.
Author: Daniel Gadala-Maria [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer: Daniel Gadala-Maria <daniel.gadala-maria@yale.edu>

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Package copula updated to version 0.999-15 with previous version 0.999-14 dated 2015-10-26

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme value and some more copula families. Methods for density, distribution, random number generation, bivariate dependence measures, perspective and contour plots. Fitting copula models including variance estimates. Independence and serial (univariate and multivariate) independence tests, and other copula related tests. Empirical copula and multivariate CDF. Goodness-of-fit tests for copulas based on multipliers, the parametric bootstrap with several transformation options. Merged former package 'nacopula' for nested Archimedean copulas: Efficient sampling algorithms, various estimators, goodness-of-fit tests and related tools and special functions.
Author: Marius Hofert <marius.hofert@uwaterloo.ca>, Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>, Martin Maechler <maechler@stat.math.ethz.ch>, and Jun Yan <jun.yan@uconn.edu>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package pollstR updated to version 1.4.0 with previous version 1.3.0 dated 2016-04-21

Title: Client for the HuffPost Pollster API
Description: Client for the HuffPost Pollster API, which provides access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre], Thomas J. Leeper [aut], Drew Linzer [aut]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

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Package Kpart updated to version 1.2.0 with previous version 1.1 dated 2012-12-19

Title: Cubic Spline Fitting with Knot Selection
Description: Cubic spline fitting along with knot selection, includes support for additional variables.
Author: Eric Golinko
Maintainer: Eric Golinko <egolinko@gmail.com>

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Package mcparallelDo updated to version 1.1.0 with previous version 1.0.0 dated 2015-12-09

Title: A Simplified Interface for Running Commands on Parallel Processes
Description: Provides a function that wraps mcparallel() and mccollect() from 'parallel' with temporary variables and a task handler. Wrapped in this way the results of an mcparallel() call can be returned to the R session when the fork is complete without explicitly issuing a specific mccollect() to retrieve the value. Outside of top-level tasks, multiple mcparallel() jobs can be retrieved with a single call to mcparallelDoCheck().
Author: Russell S. Pierce
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>

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Package RcppArmadillo updated to version 0.7.200.2.0 with previous version 0.7.100.3.1 dated 2016-06-03

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.7.100.3.1 dated 2016-06-03 and 0.7.200.2.0 dated 2016-07-24

 ChangeLog                                             |   32 
 DESCRIPTION                                           |   12 
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 build/vignette.rds                                    |binary
 configure                                             |   30 
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 inst/doc/RcppArmadillo-unitTests.pdf                  |binary
 inst/include/RcppArmadilloExtensions/fixprob.h        |   15 
 inst/include/RcppArmadilloExtensions/sample.h         |   91 
 inst/include/armadillo_bits/BaseCube_bones.hpp        |    8 
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 inst/include/armadillo_bits/Base_bones.hpp            |    5 
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 inst/include/armadillo_bits/Mat_bones.hpp             |    4 
 inst/include/armadillo_bits/Mat_meat.hpp              |   30 
 inst/include/armadillo_bits/Proxy.hpp                 | 1673 +++++++++---------
 inst/include/armadillo_bits/SpBase_bones.hpp          |    5 
 inst/include/armadillo_bits/SpBase_meat.hpp           |   54 
 inst/include/armadillo_bits/SpMat_meat.hpp            |    6 
 inst/include/armadillo_bits/arma_rng_cxx98.hpp        |    8 
 inst/include/armadillo_bits/arma_version.hpp          |    6 
 inst/include/armadillo_bits/auxlib_meat.hpp           |   16 
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 inst/include/armadillo_bits/diskio_meat.hpp           |   16 
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 inst/include/armadillo_bits/fn_svds.hpp               |    8 
 inst/include/armadillo_bits/glue_conv_meat.hpp        |   10 
 inst/include/armadillo_bits/gmm_diag_meat.hpp         |    6 
 inst/include/armadillo_bits/newarp_SortEigenvalue.hpp |    1 
 inst/include/armadillo_bits/op_all_bones.hpp          |   12 
 inst/include/armadillo_bits/op_all_meat.hpp           |   53 
 inst/include/armadillo_bits/op_any_bones.hpp          |   12 
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 inst/include/armadillo_bits/op_expmat_bones.hpp       |    5 
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 inst/include/armadillo_bits/op_logmat_meat.hpp        |   16 
 inst/include/armadillo_bits/op_max_bones.hpp          |   12 
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 inst/include/armadillo_bits/op_mean_bones.hpp         |    3 
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 61 files changed, 2798 insertions(+), 1242 deletions(-)

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Package sEparaTe updated to version 0.1.2 with previous version 0.1.1 dated 2016-06-15

Title: Maximum Likelihood Estimation and Likelihood Ratio Test Functions for Separable Variance-Covariance Structures
Description: It combines maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance-covariance matrices, two procedures, and unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures.
Author: Ameur Manceur [aut], Timothy Schwinghamer [aut, cre], Pierre Dutilleul [aut, cph]
Maintainer: Timothy Schwinghamer <schwinghamer@hotmail.com>

Diff between sEparaTe versions 0.1.1 dated 2016-06-15 and 0.1.2 dated 2016-07-24

 DESCRIPTION   |   14 +++++++-------
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 4 files changed, 16 insertions(+), 16 deletions(-)

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Package sbrl updated to version 1.1 with previous version 1.0 dated 2016-06-15

Title: Scalable Bayesian Rule Lists Model
Description: An implementation of Scalable Bayesian Rule Lists Algorithm.
Author: Hongyu Yang [aut, cre], Morris Chen [ctb], Cynthia Rudin [aut, ctb], Margo Seltzer [aut, ctb]
Maintainer: Hongyu Yang <hongyuy@mit.edu>

Diff between sbrl versions 1.0 dated 2016-06-15 and 1.1 dated 2016-07-24

 DESCRIPTION         |    9 -
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Package pbmcapply updated to version 1.1.0 with previous version 1.0.0 dated 2016-07-06

Title: Tracking the Progress of Mc*pply with Progress Bar
Description: A light-weight package helps you track and visualize the progress of parallel version of vectorized R functions (mc*apply). The package works on *nix (Linux, Unix such as macOS) system only due to the lack of fork() functionality, which is essential for mcapply, on Windows.
Author: Kevin Kuang
Maintainer: Kevin kuang <kvn.kuang@mail.utoronto.ca>

Diff between pbmcapply versions 1.0.0 dated 2016-07-06 and 1.1.0 dated 2016-07-24

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Package icpsrdata updated to version 0.1.1 with previous version 0.1.0 dated 2016-05-20

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

Diff between icpsrdata versions 0.1.0 dated 2016-05-20 and 0.1.1 dated 2016-07-24

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Package htmlTable updated to version 1.6 with previous version 1.5 dated 2016-01-18

Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package also contains a few text formatting functions that help outputting text compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>

Diff between htmlTable versions 1.5 dated 2016-01-18 and 1.6 dated 2016-07-24

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More information about htmlTable at CRAN
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Package recmap updated to version 0.5.4 with previous version 0.5.3 dated 2016-07-13

Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2 construction heuristic (see 'citation("recmap")' for details). This algorithm draws maps according to a given statistical value (e.g. election results, population or epidemiological data). The basic idea of the RecMap algorithm is that each map region (e.g. different countries) is represented by a rectangle. The area of each rectangle represents the statistical value given as input (maintain zero cartographic error). Documentation about 'RecMap' is provided by a vignette included in this package and a 'RecMap gallery' site at <http://cartodraw.science/recmap/gallery>.
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>

Diff between recmap versions 0.5.3 dated 2016-07-13 and 0.5.4 dated 2016-07-24

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Package repr updated to version 0.9 with previous version 0.7 dated 2016-05-13

Title: Serializable Representations
Description: String and binary representations of objects for several formats / mime types.
Author: Philipp Angerer [aut, cre], Thomas Kluyver [aut], Jan Schulz [aut], abielr [ctb], Denilson Figueiredo de Sa [ctb], Jim Hester [ctb], karldw [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>

Diff between repr versions 0.7 dated 2016-05-13 and 0.9 dated 2016-07-24

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Package stmCorrViz updated to version 1.3 with previous version 1.2 dated 2015-07-12

Title: A Tool for Structural Topic Model Visualizations
Description: Generates an interactive visualization of topic correlations/ hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and Tingley. The package performs a hierarchical clustering of topics which are then exported to a JSON object and visualized using D3.
Author: Antonio Coppola, Margaret Roberts, Brandon Stewart, Dustin Tingley
Maintainer: Antonio Coppola <acoppola@alumni.harvard.edu>

Diff between stmCorrViz versions 1.2 dated 2015-07-12 and 1.3 dated 2016-07-24

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Sat, 23 Jul 2016

Package ssa updated to version 1.2.1 with previous version 1.2.0 dated 2016-06-29

Title: Simultaneous Signal Analysis
Description: Procedures for analyzing simultaneous signals, e.g., features that are simultaneously significant in two different studies. Includes methods for detecting simultaneous signals, for identifying them under false discovery rate control, and for leveraging them to improve prediction.
Author: Dave Zhao [aut, cre]
Maintainer: Dave Zhao <sdzhao@illinois.edu>

Diff between ssa versions 1.2.0 dated 2016-06-29 and 1.2.1 dated 2016-07-23

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Package RSVGTipsDevice updated to version 1.0-7 with previous version 1.0-4 dated 2011-11-27

Title: An R SVG Graphics Device with Dynamic Tips and Hyperlinks
Description: A graphics device for R that uses the w3.org xml standard for Scalable Vector Graphics. This version supports tooltips with 1 to 3 lines, hyperlinks, and line styles.
Author: Tony Plate <tplate@acm.org>, based on RSvgDevice by T Jake Luciani <jakeluciani@yahoo.com>
Maintainer: Tony Plate <tplate@acm.org>

Diff between RSVGTipsDevice versions 1.0-4 dated 2011-11-27 and 1.0-7 dated 2016-07-23

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Package oro.nifti updated to version 0.5.5.2 with previous version 0.5.2 dated 2015-05-07

Title: Rigorous - NIfTI + ANALYZE + AFNI : Input / Output
Description: Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [aut], Karsten Tabelow [ctb], Jon Clayden [ctb], John Muschelli [ctb]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>

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Package curl updated to version 1.0 with previous version 0.9.7 dated 2016-04-10

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 0.9.7 dated 2016-04-10 and 1.0 dated 2016-07-23

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More information about curl at CRAN
Permanent link

Package taxize updated to version 0.7.9 with previous version 0.7.8 dated 2016-06-17

Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, and getting taxonomic 'hierarchies'.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Zachary Foster [aut], Carl Boettiger [aut], Karthik Ram [aut], Ignasi Bartomeus [aut], John Baumgartner [aut], James O'Donnell [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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More information about taxize at CRAN
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Package SphericalCubature updated to version 1.2 with previous version 1.1 dated 2016-05-17

Title: Numerical Integration over Spheres and Balls in n-Dimensions; Multivariate Polar Coordinates
Description: Provides several methods to integrate functions over the unit sphere and ball in n-dimensional Euclidean space. Routines for converting to/from multivariate polar/spherical coordinates are also provided.
Author: John P. Nolan, American University
Maintainer: John P. Nolan <jpnolan@american.edu>

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Package rosetteApi updated to version 1.2.0 with previous version 1.0 dated 2016-05-22

Title: Rosette API
Description: Rosette is an API for multilingual text analysis and information extraction. More information can be found at <https://developer.rosette.com>.
Author: Sam Hausmann
Maintainer: Sam Hausmann <shausmann@basistech.com>

Diff between rosetteApi versions 1.0 dated 2016-05-22 and 1.2.0 dated 2016-07-23

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Package nopp updated to version 1.0.8 with previous version 1.0.6 dated 2015-08-21

Title: Nash Optimal Party Positions
Description: Estimation of party/candidate ideological positions that correspond to a Nash equilibrium along a one-dimensional space.
Author: Luigi Curini, Stefano M. Iacus
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>

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Package lmenssp updated to version 1.2 with previous version 1.1 dated 2015-07-17

Title: Linear Mixed Effects Models with Non-Stationary Stochastic Processes
Description: Contains functions to estimate model parameters and filter, smooth and forecast random effects coefficients for mixed models with stationary and non-stationary stochastic processes under multivariate normal and t response distributions, diagnostic checks, bootstrap standard error calculation, etc.
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar <ozgur.asar@acibadem.edu.tr>

Diff between lmenssp versions 1.1 dated 2015-07-17 and 1.2 dated 2016-07-23

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Package commonmark updated to version 0.9 with previous version 0.8 dated 2016-03-30

Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown syntax. This package uses the libcmark reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre], John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between commonmark versions 0.8 dated 2016-03-30 and 0.9 dated 2016-07-23

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Package fastSOM updated to version 1.0.0 with previous version 0.9 dated 2012-10-04

Title: Fast Calculation of Spillover Measures
Description: Functions for computing spillover measures, especially spillover tables and spillover indices, as well as their average, minimal, and maximal values.
Author: Stefan Kloessner [aut, cre], Sven Wagner [aut]
Maintainer: Stefan Kloessner <S.Kloessner@mx.uni-saarland.de>

Diff between fastSOM versions 0.9 dated 2012-10-04 and 1.0.0 dated 2016-07-23

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Package ISOpureR updated to version 1.0.20 with previous version 1.0.18 dated 2015-07-24

Title: Deconvolution of Tumour Profiles
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros <Paul.Boutros@oicr.on.ca>

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Package fulltext updated to version 0.1.8 with previous version 0.1.6 dated 2016-01-22

Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats used in and outside of R.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between fulltext versions 0.1.6 dated 2016-01-22 and 0.1.8 dated 2016-07-23

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Package dggridR updated to version 0.1.7 with previous version 0.1.5 dated 2016-07-20

Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>

Diff between dggridR versions 0.1.5 dated 2016-07-20 and 0.1.7 dated 2016-07-23

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Fri, 22 Jul 2016

Package cobalt updated to version 1.1.0 with previous version 1.0.0 dated 2016-07-15

Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', and 'CBPS' for assessing balance on the output of their preprocessing functions. Users can also specify their data not generated through the above packages.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah@unc.edu>

Diff between cobalt versions 1.0.0 dated 2016-07-15 and 1.1.0 dated 2016-07-22

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Package track updated to version 1.1.9 with previous version 1.1.8 dated 2015-04-01

Title: Store Objects on Disk Automatically
Description: Automatically stores objects in files on disk so that files are rewritten when objects are changed, and so that objects are accessible but do not occupy memory until they are accessed. Keeps track of times when objects are created and modified, and caches some basic characteristics of objects to allow for fast summaries of objects. Also provides a command history mechanism that saves the last command to a history file after each command completes.
Author: Tony Plate <tplate@acm.org>
Maintainer: Tony Plate <tplate@acm.org>

Diff between track versions 1.1.8 dated 2015-04-01 and 1.1.9 dated 2016-07-22

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Package TimeWarp updated to version 1.0.15 with previous version 1.0.12 dated 2015-04-01

Title: Date Calculations and Manipulation
Description: Date sequence, relative date calculations, and date manipulation with business days and holidays. Works with Date and POSIXt classes.
Author: Tony Plate, Jeffrey Horner, Lars Hansen
Maintainer: Tony Plate <tplate@acm.org>

Diff between TimeWarp versions 1.0.12 dated 2015-04-01 and 1.0.15 dated 2016-07-22

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Package pullword updated to version 0.2 with previous version 0.1 dated 2015-02-20

Title: R Interface to Pullword Service
Description: R Interface to Pullword Service for natural language processing in Chinese. It enables users to extract valuable words from text by deep learning models. For more details please visit the official site (in Chinese) http://pullword.com/.
Author: Tong He <hetong007@gmail.com>
Maintainer: Tong He <hetong007@gmail.com>

Diff between pullword versions 0.1 dated 2015-02-20 and 0.2 dated 2016-07-22

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Package Holidays updated to version 1.0-7 with previous version 1.0-6 dated 2015-03-13

Title: Holiday and Half-Day Data, for Use with the 'TimeWarp' Package
Description: Contains trading holiday and half-day data that is automatically registered when loaded.
Author: Jeffery Horner, Lars Hansen, Tony Plate
Maintainer: Tony Plate <tplate@acm.org>

Diff between Holidays versions 1.0-6 dated 2015-03-13 and 1.0-7 dated 2016-07-22

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 NEWS        |    3 +++
 3 files changed, 9 insertions(+), 6 deletions(-)

More information about Holidays at CRAN
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Package scriptests updated to version 1.0-16 with previous version 1.0-15 dated 2015-03-14

Title: Transcript-Based Unit Tests that are Easy to Create and Maintain
Description: Support for using .Rt (transcript) tests in the tests directory of a package. Provides more convenience and features than the standard .R/.Rout.save tests. Tests can be run under R CMD check and also interactively. Provides source.pkg() for quickly loading code, DLLs, and data from a package for use in an edit/compile/test development cycle.
Author: Tony Plate
Maintainer: Tony Plate <tplate@acm.org>

Diff between scriptests versions 1.0-15 dated 2015-03-14 and 1.0-16 dated 2016-07-22

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