Tue, 23 Apr 2019

Package sdcHierarchies updated to version 0.18 with previous version 0.17 dated 2019-03-07

Title: Create and (Interactively) Modify Nested Hierarchies
Description: Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats. These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>

Diff between sdcHierarchies versions 0.17 dated 2019-03-07 and 0.18 dated 2019-04-23

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Package Polychrome updated to version 1.2.1 with previous version 1.2.0 dated 2019-03-17

Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>

Diff between Polychrome versions 1.2.0 dated 2019-03-17 and 1.2.1 dated 2019-04-23

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Package ClassComparison updated to version 3.1.7 with previous version 3.1.6 dated 2018-05-17

Title: Classes and Methods for "Class Comparison" Problems on Microarrays
Description: Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package MachineShop updated to version 1.3.0 with previous version 1.2.0 dated 2019-02-15

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package ggforce updated to version 0.2.2 with previous version 0.2.1 dated 2019-03-12

Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between ggforce versions 0.2.1 dated 2019-03-12 and 0.2.2 dated 2019-04-23

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Package stars updated to version 0.3-1 with previous version 0.3-0 dated 2019-02-24

Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Michael Sumner [ctb] (<https://orcid.org/0000-0002-2471-7511>), Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package fields updated to version 9.7 with previous version 9.6.1 dated 2019-04-22

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research. See the Fields URL for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>

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Package ecmwfr updated to version 1.2.1 with previous version 1.2.0 dated 2019-04-19

Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Climate Data Store (CDS; <https://cds.climate.copernicus.eu>). Allows for easy downloads of weather forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] (<https://orcid.org/0000-0002-5070-8109>), Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>), Elio Campitelli [ctb] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>

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Package AzureAuth updated to version 1.0.2 with previous version 1.0.1 dated 2019-03-22

Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure.
Author: Hong Ooi [aut, cre], httr development team [ctb] (Original OAuth listener code), Scott Holden [ctb] (Advice on AAD authentication), Chris Stone [ctb] (Advice on AAD authentication), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package Eagle updated to version 1.4.0 with previous version 1.3.0 dated 2019-01-31

Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre], Joshua Bowden [ctb], Ryan Stephenson [ctb], Hyun Kang [ctb], Noah Zaitlen [ctb], Claire Wade [ctb], Andrew Kirby [ctb], David Heckerman [ctb], Mark Daly [ctb], Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>

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Package ptmixed updated to version 0.0.2 with previous version 0.0.1 dated 2019-02-12

Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits Poisson-Tweedie generalized linear mixed model. Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre], Pietro Spitali [aut], Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>

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Package Unicode updated to version 12.0.0-1 with previous version 11.0.0-1 dated 2018-06-30

Title: Unicode Data and Utilities
Description: Data from Unicode 12.0.0 and related utilities.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package shar updated to version 0.3.1 with previous version 0.3 dated 2019-03-25

Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location of the species is needed and about the environmental conditions. To test for significance habitat associations, one of the two components is randomized. Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>

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Package PythonInR updated to version 0.1-7 with previous version 0.1-6 dated 2018-09-17

Title: Use 'Python' from Within 'R'
Description: Interact with 'Python' <https://www.python.org/> from within 'R'.
Author: Florian Schwendinger [aut, cre], Kimyen Truong [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>

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Package ISOcodes updated to version 2019.04.22 with previous version 2019.02.13 dated 2019-02-13

Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.
Author: Christian Buchta [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package EML updated to version 2.0.0 with previous version 1.0.3 dated 2017-05-02

Title: Read and Write Ecological Metadata Language Files
Description: Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Matthew B. Jones [aut] (<https://orcid.org/0000-0003-0077-4738>), Mitchell Maier [ctb] (<https://orcid.org/0000-0001-6955-0535>), Bryce Mecum [ctb] (<https://orcid.org/0000-0002-0381-3766>), Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>), Jeanette Clark [ctb] (<https://orcid.org/0000-0003-4703-1974>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package ed50 updated to version 0.1.1 with previous version 0.1.0 dated 2018-11-28

Title: Estimate ED50 and Its Confidence Interval
Description: Functions of five estimation method for ED50 (50 percent effective dose) are provided, and they are respectively Dixon-Mood method (1948) <doi:10.2307/2280071>, Choi's original turning point method (1990) <doi:10.2307/2531453> and it's modified version given by us, as well as logistic regression and isotonic regression. Besides, the package also supports comparison between two estimation results.
Author: Yongbo Gan, Zhijian Yang, Wei Mei
Maintainer: Yongbo Gan <yongbogan@whu.edu.cn>

Diff between ed50 versions 0.1.0 dated 2018-11-28 and 0.1.1 dated 2019-04-23

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 MD5                 |   12 ++++----
 NAMESPACE           |   13 +++++++--
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More information about ed50 at CRAN
Permanent link

Package clustrd updated to version 1.3 with previous version 1.2.2 dated 2018-05-06

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between clustrd versions 1.2.2 dated 2018-05-06 and 1.3 dated 2019-04-23

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More information about clustrd at CRAN
Permanent link

Package lctools updated to version 0.2-7 with previous version 0.2-6 dated 2017-08-04

Title: Local Correlation, Spatial Inequalities, Geographically Weighted Regression and Other Tools
Description: Provides researchers and educators with easy-to-learn user friendly tools for calculating key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data. These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I), several Geographically Weighted Regression techniques and other Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <stamatis@lctools.science>

Diff between lctools versions 0.2-6 dated 2017-08-04 and 0.2-7 dated 2019-04-23

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Package RealVAMS updated to version 0.4-3 with previous version 0.4-1 dated 2018-04-20

Title: Multivariate VAM Fitting
Description: Fits a multivariate value-added model (VAM), see Broatch, Green, and Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. The inner loop of the pseudo-likelihood routine (estimation of a linear mixed model) occurs in the framework of the EM algorithm presented by Karl, Yang, and Lohr (2013) <DOI:10.1016/j.csda.2012.10.004>. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew T. Karl, Jennifer Broatch, and Jennifer Green
Maintainer: Andrew Karl <akarl@asu.edu>

Diff between RealVAMS versions 0.4-1 dated 2018-04-20 and 0.4-3 dated 2019-04-23

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Package mscstts updated to version 0.5.1 with previous version 0.4.0 dated 2018-11-19

Title: R Client for the Microsoft Cognitive Services 'Text-to-Speech' REST API
Description: R Client for the Microsoft Cognitive Services 'Text-to-Speech' REST API, including voice synthesis. A valid account must be registered at the Microsoft Cognitive Services website <https://www.microsoft.com/cognitive-services/> in order to obtain a (free) API key. Without an API key, this package will not work properly.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between mscstts versions 0.4.0 dated 2018-11-19 and 0.5.1 dated 2019-04-23

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Package cgam updated to version 1.13 with previous version 1.12 dated 2018-11-08

Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Mary C. Meyer (2013)<doi:10.1080/10485252.2013.797577> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>

Diff between cgam versions 1.12 dated 2018-11-08 and 1.13 dated 2019-04-23

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Mon, 22 Apr 2019

Package testthat updated to version 2.1.0 with previous version 2.0.1 dated 2018-10-13

Title: Unit Testing for R
Description: Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd], R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between testthat versions 2.0.1 dated 2018-10-13 and 2.1.0 dated 2019-04-22

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Package rcdd updated to version 1.2-2 with previous version 1.2 dated 2017-06-12

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 oak updated to version 0.2.3 with previous version 0.2.1 dated 2018-11-06

Title: Trees Creation and Manipulation
Description: Functions and classes to create and manipulate trees and nodes.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

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Package tidyquant updated to version 0.5.6 with previous version 0.5.5 dated 2018-05-09

Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

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Package SamplingStrata updated to version 1.4-1 with previous version 1.4 dated 2019-01-02

Title: Optimal Stratification of Sampling Frames for Multipurpose Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen, Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>

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Package randomForestSRC updated to version 2.9.0 with previous version 2.8.0 dated 2019-01-02

Title: Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. Handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. New fast interface using subsampling and confidence regions for variable importance.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

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Package dqrng updated to version 0.2.0 with previous version 0.1.1 dated 2019-03-11

Title: Fast Pseudo Random Number Generators
Description: Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011 <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.
Author: Ralf Stubner [aut, cre], daqana GmbH [cph], David Blackman [ctb], Melissa O'Neill [ctb], Sebastiano Vigna [ctb], Aaron Lun [ctb]
Maintainer: Ralf Stubner <ralf.stubner@daqana.com>

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Package taxonomizr updated to version 0.5.3 with previous version 0.5.1 dated 2018-08-31

Title: Functions to Work with NCBI Accessions and Taxonomy
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
Author: Scott Sherrill-Mix [aut, cre]
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

Diff between taxonomizr versions 0.5.1 dated 2018-08-31 and 0.5.3 dated 2019-04-22

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Package subtee updated to version 0.3-5 with previous version 0.3-4 dated 2019-01-07

Title: Subgroup Treatment Effect Estimation in Clinical Trials
Description: Naive and adjusted treatment effect estimation for subgroups. Model averaging (Bornkamp et.al, 2016 <doi:10.1002/pst.1796>) and bagging (Rosenkranz, 2016 <doi:10.1002/bimj.201500147>) are proposed to address the problem of selection bias in treatment effect estimates for subgroups. The package can be used for all commonly encountered type of outcomes in clinical trials (continuous, binary, survival, count). Additional functions are provided to build the subgroup variables to be used and to plot the results using forest plots.
Author: Nicolas Ballarini [aut, cre], Bjoern Bornkamp [aut], Marius Thomas [aut, cre], Baldur Magnusson [ctb]
Maintainer: Nicolas Ballarini <nicolas.ballarini@meduniwien.ac.at>

Diff between subtee versions 0.3-4 dated 2019-01-07 and 0.3-5 dated 2019-04-22

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Package shiny updated to version 1.3.2 with previous version 1.3.1 dated 2019-04-12

Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre], Joe Cheng [aut], JJ Allaire [aut], Yihui Xie [aut], Jonathan McPherson [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Dave Gandy [ctb, cph] (Font-Awesome font), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between shiny versions 1.3.1 dated 2019-04-12 and 1.3.2 dated 2019-04-22

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Package sdnet updated to version 2.4.0 with previous version 2.3.8 dated 2016-05-09

Title: Soft-Discretization-Based Bayesian Network Inference
Description: Fitting discrete Bayesian networks using soft-discretized data. Soft-discretization is based on mixture of normal distributions. Also implemented is a supervised Bayesian network learning employing Kullback-Leibler divergence. For more information see Balov (2013) <DOI:10.1186/1755-8794-6-S3-S1>.
Author: Nikolay Balov
Maintainer: Nikolay Balov <nhbalov@gmail.com>

Diff between sdnet versions 2.3.8 dated 2016-05-09 and 2.4.0 dated 2019-04-22

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Package quotedargs updated to version 0.1.3 with previous version 0.1.2 dated 2018-03-26

Title: A Way of Writing Functions that Quote their Arguments
Description: A facility for writing functions that quote their arguments, may sometimes evaluate them in the environment where they were quoted, and may pass them as quoted to other functions.
Author: Radford Neal
Maintainer: Radford Neal <radfordneal@gmail.com>

Diff between quotedargs versions 0.1.2 dated 2018-03-26 and 0.1.3 dated 2019-04-22

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Package plothelper updated to version 0.1.1 with previous version 0.1.0 dated 2019-04-07

Title: New Plots Based on 'ggplot2' and Functions to Create Regular Shapes
Description: An extension to 'ggplot2' with miscellaneous functions. It contains two groups of functions: Functions in the first group draw 'ggplot2' - based plots: gg_shading_bar() draws barplot with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio changes. Functions in the second group generate coordinates for regular shapes and make linear transformations.
Author: Jiang Wu [aut, cre] (from Capital Normal University)
Maintainer: Jiang Wu <textidea@sina.com>

Diff between plothelper versions 0.1.0 dated 2019-04-07 and 0.1.1 dated 2019-04-22

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Package FedData updated to version 2.5.7 with previous version 2.5.6 dated 2019-01-11

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from seven datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC); the International Tree Ring Data Bank; and the National Land Cover Database (NLCD).
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

Diff between FedData versions 2.5.6 dated 2019-01-11 and 2.5.7 dated 2019-04-22

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Package crch updated to version 1.0-2 with previous version 1.0-1 dated 2018-01-23

Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with conditional heteroscedasticity are provided. First, continuous distributions can be used for the (right and/or left censored or truncated) response with separate linear predictors for the mean and variance. Second, cumulative link models for ordinal data (obtained by interval-censoring continuous data) can be employed for heteroscedastic extended logistic regression (HXLR). In the latter type of models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre] (<https://orcid.org/0000-0002-1027-3673>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Reto Stauffer [aut] (<https://orcid.org/0000-0002-3798-5507>)
Maintainer: Jakob Messner <jwmm@elektro.dtu.dk>

Diff between crch versions 1.0-1 dated 2018-01-23 and 1.0-2 dated 2019-04-22

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Package GGMselect updated to version 0.1-12.2 with previous version 0.1-12.1 dated 2018-02-01

Title: Gaussian Graphs Models Selection
Description: Graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: ORPHANED

Diff between GGMselect versions 0.1-12.1 dated 2018-02-01 and 0.1-12.2 dated 2019-04-22

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Package fpc updated to version 2.1-11.2 with previous version 2.1-11.1 dated 2018-07-20

Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Author: Christian Hennig <c.hennig@ucl.ac.uk>
Maintainer: ORPHANED

Diff between fpc versions 2.1-11.1 dated 2018-07-20 and 2.1-11.2 dated 2019-04-22

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Package TSSS updated to version 1.2.4 with previous version 1.2.3 dated 2019-04-15

Title: Time Series Analysis with State Space Model
Description: Functions for statistical analysis, modeling and simulation of time series with state space model, based on the methodology in Kitagawa (1993, ISBN: 4-00-007703-1 and 2005, ISBN: 4-00-005455-4).
Author: The Institute of Statistical Mathematics, based on the program by Genshiro Kitagawa
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>

Diff between TSSS versions 1.2.3 dated 2019-04-15 and 1.2.4 dated 2019-04-22

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Package FSelectorRcpp updated to version 0.3.1 with previous version 0.3.0 dated 2018-11-12

Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf> with a sparse matrix support. It is also equipped with a parallel backend.
Author: Zygmunt Zawadzki [aut, cre], Marcin Kosinski [aut], Krzysztof Slomczynski [ctb], Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between FSelectorRcpp versions 0.3.0 dated 2018-11-12 and 0.3.1 dated 2019-04-22

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Package DepthProc updated to version 2.1.1 with previous version 2.0.4 dated 2018-09-02

Title: Statistical Depth Functions for Multivariate Analysis
Description: Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Author: Zygmunt Zawadzki [aut, cre], Daniel Kosiorowski [aut], Krzysztof Slomczynski [ctb], Mateusz Bocian [ctb], Anna Wegrzynkiewicz [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between DepthProc versions 2.0.4 dated 2018-09-02 and 2.1.1 dated 2019-04-22

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Package multimark updated to version 2.1.0 with previous version 2.0.1 dated 2017-06-30

Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks
Description: Traditional and spatial capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using non-spatial or spatial capture-recapture data consisting of a single conventional mark or multiple non-invasive marks.
Author: Brett T. McClintock [aut, cre], Acho Arnold [ctb, cph] (C original matrix library, https://github.com/najela/matrix.h), Barry Brown [ctb] (Fortran original ranlib library), James Lovato [ctb] (Fortran original ranlib library), John Burkardt [ctb] (C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib), Cleve Moler [ctb] (C original linpack library, http://www.kkant.net/geist/ranlib/), Arjun Gopalaswamy [ctb] (modified snippets of R package SPACECAP code)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>

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Package Rramas updated to version 0.1-6 with previous version 0.1-5 dated 2017-11-24

Title: Matrix Population Models
Description: Analyzes and predicts from matrix population models (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>

Diff between Rramas versions 0.1-5 dated 2017-11-24 and 0.1-6 dated 2019-04-22

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Package DDD updated to version 4.0 with previous version 3.9 dated 2019-03-19

Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

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Package Zelig updated to version 5.1.6.1 with previous version 5.1.6 dated 2018-02-27

Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common statistical models found across packages into a unified interface, and provides a common architecture for estimation and interpretation, as well as bridging functions to absorb increasingly more models into the package. Zelig allows each individual package, for each statistical model, to be accessed by a common uniformly structured call and set of arguments. Moreover, Zelig automates all the surrounding building blocks of a statistical work-flow--procedures and algorithms that may be essential to one user's application but which the original package developer did not use in their own research and might not themselves support. These include bootstrapping, jackknifing, and re-weighting of data. In particular, Zelig automatically generates predicted and simulated quantities of interest (such as relative risk ratios, average treatment effects, first differences and predicted and expected values) to interpret and visualize complex models.
Author: Christine Choirat [aut], Christopher Gandrud [aut, cre], James Honaker [aut], Kosuke Imai [aut], Gary King [aut], Olivia Lau [aut], IQSS Harvard University [cph]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>

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Package virtualspecies updated to version 1.4-4.1 with previous version 1.4-4 dated 2018-09-10

Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package integrates the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism.
Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>

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Package Smisc updated to version 0.3.9.1 with previous version 0.3.9 dated 2017-11-21

Title: Sego Miscellaneous
Description: A collection of functions for statistical computing and data manipulation in R. Includes routines for data ingestion, operating on dataframes and matrices, conversion to and from lists, converting factors, filename manipulation, programming utilities, parallelization, plotting, statistical and mathematical operations, and time series.
Author: Landon Sego [aut, cre]
Maintainer: Landon Sego <LHS@byu.net>

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Package robustloggamma updated to version 1.0-2.1 with previous version 1.0-2 dated 2016-05-16

Title: Robust Estimation of the Generalized log Gamma Model
Description: Robust estimation of the generalized log gamma model is provided using Quantile Tau estimator, Weighted Likelihood estimator and Truncated Maximum Likelihood estimator. Functions for regression and censored data are also available.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it>, Alfio Marazzi <Alfio.Marazzi@chuv.ch>, Victor Yohai <vyohai@uolsinectis.com.ar> and Alex Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>

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Package rms updated to version 5.1-3.1 with previous version 5.1-3 dated 2019-01-27

Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. 'rms' is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. 'rms' works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

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Package pamr updated to version 1.56.1 with previous version 1.56 dated 2019-02-01

Title: Pam: Prediction Analysis for Microarrays
Description: Some functions for sample classification in microarrays.
Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Maintainer: Rob Tibshirani <tibs@stanford.edu>

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Package LCA updated to version 0.1.1 with previous version 0.1 dated 2013-09-30

Title: Localised Co-Dependency Analysis
Description: Performs model fitting and significance estimation for Localised Co-Dependency between pairs of features of a numeric dataset.
Author: Ed Curry [aut, cre]
Maintainer: Ed Curry <e.curry@imperial.ac.uk>

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Package jmv updated to version 0.9.6.1 with previous version 0.9.6 dated 2018-12-11

Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives, t-tests, ANOVAs, regression, correlation matrices, proportion tests, contingency tables, and factor analysis. This package is also useable from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>

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Package infer updated to version 0.4.0.1 with previous version 0.4.0 dated 2018-11-15

Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.
Author: Andrew Bray [aut, cre], Chester Ismay [aut], Ben Baumer [aut], Mine Cetinkaya-Rundel [aut], Evgeni Chasnovski [ctb], Ted Laderas [ctb], Nick Solomon [ctb], Johanna Hardin [ctb], Albert Y. Kim [ctb], Neal Fultz [ctb], Doug Friedman [ctb], Richie Cotton [ctb], Brian Fannin [ctb]
Maintainer: Andrew Bray <abray@reed.edu>

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Package igraph updated to version 1.2.4.1 with previous version 1.2.4 dated 2019-02-13

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package genetics updated to version 1.3.8.1.2 with previous version 1.3.8.1.1 dated 2019-02-01

Title: Population Genetics
Description: Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
Author: Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.
Maintainer: Gregory Warnes <greg@warnes.net>

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Package fields updated to version 9.6.1 with previous version 9.6 dated 2018-01-29

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>

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Package DiagrammeR updated to version 1.0.1 with previous version 1.0.0 dated 2018-03-01

Title: Graph/Network Visualization
Description: Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>

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Package copula updated to version 0.999-19.1 with previous version 0.999-19 dated 2018-12-21

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] (<https://orcid.org/0000-0001-8009-4665>), Ivan Kojadinovic [aut] (<https://orcid.org/0000-0002-2903-1543>), Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>), Johanna G. Nešlehová [ctb] (evTestK(), <https://orcid.org/0000-0001-9634-4796>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package archetypes updated to version 2.2-0.1 with previous version 2.2-0 dated 2014-04-10

Title: Archetypal Analysis
Description: The main function archetypes implements a framework for archetypal analysis supporting arbitrary problem solving mechanisms for the different conceptual parts of the algorithm.
Author: Manuel J. A. Eugster [aut, cre], Friedrich Leisch [aut], Sohan Seth [ctb]
Maintainer: Manuel J. A. Eugster <manuel@mjae.net>

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Package mpmi updated to version 0.43 with previous version 0.42 dated 2016-11-20

Title: Mixed-Pair Mutual Information Estimators
Description: Uses a kernel smoothing approach to calculate Mutual Information for comparisons between all types of variables including continuous vs continuous, continuous vs discrete and discrete vs discrete. Uses a nonparametric bias correction giving Bias Corrected Mutual Information (BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited to large genomic datasets.
Author: Chris Pardy
Maintainer: Chris Pardy <cooliomcdude@gmail.com>

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Package demography updated to version 1.22 with previous version 1.21 dated 2019-01-18

Title: Forecasting Mortality, Fertility, Migration and Population Data
Description: Functions for demographic analysis including lifetable calculations; Lee-Carter modelling; functional data analysis of mortality rates, fertility rates, net migration numbers; and stochastic population forecasting.
Author: Rob J Hyndman with contributions from Heather Booth, Leonie Tickle and John Maindonald.
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>

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Package ezpickr updated to version 1.0.5 with previous version 1.0.4 dated 2019-03-23

Title: Easy Data Import Using GUI File Picker and Seamless Communication Between an Excel and R
Description: Choosing any rectangular data file using interactive GUI dialog box, and seamlessly manipulating tidy data between an 'Excel' window and R session.
Author: JooYoung Seo [aut, cre] (<https://orcid.org/0000-0002-4064-6012>), Soyoung Choi [aut] (<https://orcid.org/0000-0002-0998-3352>), hyun seung Lee [ctb], Jonghoen Kim [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>

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Package smapr updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-24

Title: Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
Description: Facilitates programmatic access to NASA Soil Moisture Active Passive (SMAP) data with R. It includes functions to search for, acquire, and extract SMAP data.
Author: Maxwell Joseph [aut, cre], Matthew Oakley [aut], Zachary Schira [aut]
Maintainer: Maxwell Joseph <maxwell.b.joseph@colorado.edu>

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Package RSocrata updated to version 1.7.6-3 with previous version 1.7.5-3 dated 2019-01-25

Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with 'Socrata' open data portals <http://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>

Diff between RSocrata versions 1.7.5-3 dated 2019-01-25 and 1.7.6-3 dated 2019-04-22

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Package rfPermute updated to version 2.1.7 with previous version 2.1.6 dated 2018-07-07

Title: Estimate Permutation p-Values for Random Forest Importance Metrics
Description: Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed. Provides summary and visualization functions for 'randomForest' results.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between rfPermute versions 2.1.6 dated 2018-07-07 and 2.1.7 dated 2019-04-22

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Package haploR updated to version 2.0.9 with previous version 2.0.7 dated 2019-01-18

Title: Query 'HaploReg', 'RegulomeDB', 'LDlink'
Description: A set of utilities for querying 'HaploReg' <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>, 'RegulomeDB' <http://www.regulomedb.org>, and LDlink <https://analysistools.nci.nih.gov/LDlink> web-based tools. The package connects to 'HaploReg', 'RegulomeDB' and 'LDlink', searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Author: Ilya Y. Zhbannikov [aut, cre], Konstantin G. Arbeev [aut], Anatoliy I. Yashin [aut]
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

Diff between haploR versions 2.0.7 dated 2019-01-18 and 2.0.9 dated 2019-04-22

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Package fastDummies updated to version 1.3.0 with previous version 1.2.0 dated 2018-06-21

Title: Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre], Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

Diff between fastDummies versions 1.2.0 dated 2018-06-21 and 1.3.0 dated 2019-04-22

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Package coop updated to version 0.6-2 with previous version 0.6-1 dated 2017-11-14

Title: Co-Operation: Fast Covariance, Correlation, and Cosine Similarity Operations
Description: Fast implementations of the co-operations: covariance, correlation, and cosine similarity. The implementations are fast and memory-efficient and their use is resolved automatically based on the input data, handled by R's S3 methods. Full descriptions of the algorithms and benchmarks are available in the package vignettes.
Author: Drew Schmidt [aut, cre], Christian Heckendorf [ctb] (Caught some memory errors.)
Maintainer: Drew Schmidt <wrathematics@gmail.com>

Diff between coop versions 0.6-1 dated 2017-11-14 and 0.6-2 dated 2019-04-22

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Package codemetar updated to version 0.1.8 with previous version 0.1.7 dated 2019-03-12

Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>), Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>), Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>), rOpenSci [fnd] (https://ropensci.org/), Katrin Leinweber [ctb] (<https://orcid.org/0000-0001-5135-5758>), Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>), Arfon Smith [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>), Michael Rustler [ctb] (<https://orcid.org/0000-0003-0647-7726>), Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Sun, 21 Apr 2019

Package gravity updated to version 0.9.7 with previous version 0.9.0 dated 2018-11-22

Title: Estimation Methods for Gravity Models
Description: A wrapper of different standard estimation methods for gravity models. This package provides estimation methods for log-log models and multiplicative models.
Author: Anna-Lena Woelwer [aut, cph], Jan Pablo Burgard [aut, cph], Joshua Kunst [aut, cph], Mauricio Vargas [aut, cre, cph] (<https://orcid.org/0000-0003-1017-7574>), Romain Francois [ctb] (adapted parts of the code to use dplyr 0.8.0), Lionel Henry [ctb] (simplified parts of the code)
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>

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Package tradestatistics updated to version 0.2 with previous version 0.1 dated 2019-04-06

Title: Open Trade Statistics API Wrapper and Utility Program
Description: Access 'Open Trade Statistics' API from R to download international trade data.
Author: Mauricio Vargas [aut, cre, cph] (<https://orcid.org/0000-0003-1017-7574>), Joshua Kunst [ctb] (contributed to different parts of the pre-release code), Emily Riederer [rev] (reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/274), Mark Padgham [rev] (reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/274), Amanda Dobbyn [rev] (reviewed an archived package that evolved into the current package for rOpenSci, see https://github.com/ropensci/onboarding/issues/217), Jorge Cimentada [rev] (reviewed an archived package that evolved into the current package for rOpenSci, see https://github.com/ropensci/onboarding/issues/217), UN Comtrade [dtc], Center for International Development at Harvard University [dtc], The Observatory of Economic Complexity [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>

Diff between tradestatistics versions 0.1 dated 2019-04-06 and 0.2 dated 2019-04-21

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Package proxyC updated to version 0.1.3 with previous version 0.1.2 dated 2019-04-19

Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph] (<https://orcid.org/0000-0001-6519-5265>), Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>

Diff between proxyC versions 0.1.2 dated 2019-04-19 and 0.1.3 dated 2019-04-21

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Package ioanalysis updated to version 0.1.3 with previous version 0.1.1 dated 2019-03-10

Title: Input Output Analysis
Description: Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>, Ghosh, A. (1958) <doi:10.2307/2550694>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
Author: John Wade [aut, cre], Ignacio Sarmiento-Barbieri [aut]
Maintainer: John Wade <jjpwade2@illinois.edu>

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Package dendroTools updated to version 1.0.4 with previous version 1.0.3 dated 2019-03-28

Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the Tree-ring research community. There are four core functions. The first one is daily_response(), which finds the optimal sequence of days that are related to one or more tree-ring proxy records. Similar function is daily_response_seasorr(), which implements partial correlations in the analysis of daily response functions. For the enthusiast of monthly data, there is monthly_response() function. The last core function is compare_methods(), which effectively compares several linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>

Diff between dendroTools versions 1.0.3 dated 2019-03-28 and 1.0.4 dated 2019-04-21

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Package trialr updated to version 0.1.0 with previous version 0.0.7 dated 2019-03-03

Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in 'RStan' and R. Some designs are implemented in R for the first time (e.g. 'EffTox' by Thall and Cook, 2004, <https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>). Given the emphasis on flexibility in Bayesian analysis, the implementations in a common language and style may serve as a cookbook to encourage the use of Bayesian methods in trials. Compiled 'RStan' models are provided in addition to helper classes and functions to perform simulations and inference on observed trial outcomes. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a published Bayesian design you want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre] (<https://orcid.org/0000-0002-3921-0166>), Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>

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Package ReinforcementLearning updated to version 1.0.3 with previous version 1.0.2 dated 2018-04-08

Title: Model-Free Reinforcement Learning
Description: Performs model-free reinforcement learning in R. This implementation enables the learning of an optimal policy based on sample sequences consisting of states, actions and rewards. In addition, it supplies multiple predefined reinforcement learning algorithms, such as experience replay. Methodological details can be found in Sutton and Barto (1998) <ISBN:0262039249>.
Author: Nicolas Proellochs [aut, cre], Stefan Feuerriegel [aut]
Maintainer: Nicolas Proellochs <nicolas.proellochs@is.uni-freiburg.de>

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Package splitstackshape updated to version 1.4.8 with previous version 1.4.6 dated 2018-07-23

Title: Stack and Reshape Datasets After Splitting Concatenated Values
Description: Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.
Author: Ananda Mahto
Maintainer: Ananda Mahto <mrdwab@gmail.com>

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Package emmeans updated to version 1.3.4 with previous version 1.3.3 dated 2019-03-02

Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and compact letter displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph], Henrik Singmann [ctb], Jonathon Love [ctb], Paul Buerkner [ctb], Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

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Package randtoolbox updated to version 1.30.0 with previous version 1.17.1 dated 2018-02-14

Title: Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some generator tests - the gap test, the serial test, the poker test. See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided without the rngWELL dependency on demand. Take a look at the Distribution task view of types and tests of random number generators. Version in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

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Package Luminescence updated to version 0.9.0.110 with previous version 0.8.6 dated 2018-10-05

Title: Comprehensive Luminescence Dating Data Analysis [upcoming]
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] (<https://orcid.org/0000-0002-0734-2199>), Christoph Burow [aut, trl, dtc] (<https://orcid.org/0000-0002-5023-4046>), Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>), Margret C. Fuchs [aut], Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>), Manfred Fischer [aut, trl], Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>), Norbert Mercier [ctb] (<https://orcid.org/0000-0002-6375-9108>), Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>), Claire Christophe [ctb], Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>), Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>), Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>), Anne Philippe [ctb], Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>), Svenja Riedesel [ctb] (<https://orcid.org/0000-0003-2936-8776>), Martin Autzen [ctb], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>

Diff between Luminescence versions 0.8.6 dated 2018-10-05 and 0.9.0.110 dated 2019-04-21

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More information about Luminescence at CRAN
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Package greybox updated to version 0.5.0 with previous version 0.4.1 dated 2019-01-27

Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regression model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

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Package ftsa updated to version 5.5 with previous version 5.4 dated 2019-01-30

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] (<https://orcid.org/0000-0002-2140-5352>), Han Lin Shang [aut, cre, cph] (<https://orcid.org/0000-0003-1769-6430>)
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>

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Package CrossVA updated to version 0.9.7 with previous version 0.9.6 dated 2019-04-18

Title: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.
Author: Eungang Choi [aut], Sam Clark [aut], Zehang Li [aut], Jason Thomas [aut, cre]
Maintainer: Jason Thomas <jarathomas@gmail.com>

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Package CHNOSZ updated to version 1.3.2 with previous version 1.3.1 dated 2019-03-03

Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.
Author: Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>), R Core Team [ctb] (code derived from R's pmax())
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>

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Package ocp updated to version 0.1.1 with previous version 0.1.0 dated 2018-12-27

Title: Bayesian Online Changepoint Detection
Description: Implements the Bayesian online changepoint detection method by Adams and MacKay (2007) <arXiv:0710.3742> for univariate or multivariate data. Gaussian and Poisson probability models are implemented. Provides post-processing functions with alternative ways to extract changepoints.
Author: Andrea Pagotto
Maintainer: Andrea Pagotto <ajpagotto@gmail.com>

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Package munsellinterpol updated to version 2.3-1 with previous version 2.2-1 dated 2019-01-30

Title: Interpolate Munsell Renotation Data from Hue/Chroma to CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl], Paul Centore [aut, cph], Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>

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Package g3viz updated to version 1.1.0 with previous version 1.0.4 dated 2019-04-06

Title: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram
Description: R interface for 'g3-lollipop' JavaScript library. Visualize genetic mutation data using an interactive lollipop diagram in RStudio or your browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <g3viz.group@gmail.com>

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Package xtable updated to version 1.8-4 with previous version 1.8-3 dated 2018-08-29

Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]
Maintainer: David Scott <d.scott@auckland.ac.nz>

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Package mboxr updated to version 0.1.5 with previous version 0.1.4 dated 2019-02-24

Title: Reading, Extracting, and Converting an Mbox File into a Tibble
Description: Importing and converting an mbox file into a tibble object.
Author: JooYoung Seo [aut, cre] (<https://orcid.org/0000-0002-4064-6012>), Soyoung Choi [aut] (<https://orcid.org/0000-0002-0998-3352>)
Maintainer: JooYoung Seo <jooyoung@psu.edu>

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Package janitor updated to version 1.2.0 with previous version 1.1.1 dated 2018-07-31

Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and isolate duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness. Advanced R users can already do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.
Author: Sam Firke [aut, cre], Bill Denney [ctb], Chris Haid [ctb], Ryan Knight [ctb], Malte Grosser [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>

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Package boxoffice updated to version 1.2.2 with previous version 1.2.1 dated 2019-01-16

Title: Downloads Box Office Information for Given Dates
Description: Download daily box office information (how much each movie earned in theaters) using data from either Box Office Mojo (<http://www.boxofficemojo.com/>) or The Numbers (<http://www.the-numbers.com/>).
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

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Sat, 20 Apr 2019

Package dbarts updated to version 0.9-11 with previous version 0.9-7 dated 2018-12-18

Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre], Hugh Chipman [aut], Robert McCulloch [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>

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Package Power2Stage updated to version 0.5.2 with previous version 0.5-1 dated 2018-04-03

Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies
Description: Contains functions to obtain the operational characteristics of bioequivalence studies with 2-stage designs (TSD) via simulations.
Author: Detlew Labes [aut, cre], Benjamin Lang [aut, ctb], Helmut Schütz [aut, ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

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Package NNMIS updated to version 1.0.1 with previous version 1.0.0 dated 2017-10-18

Title: Nearest Neighbor Based Multiple Imputation for Survival Data with Missing Covariates
Description: Imputation for both missing covariates and censored observations (optional) for survival data with missing covariates by the nearest neighbor based multiple imputation algorithm as described in Hsu et al. (2006) <doi:10.1002/sim.2452>, and Hsu and Yu (2018) <doi: 10.1177/0962280218772592>. Note that the current version can only impute for a situation with one missing covariate.
Author: Di Ran, Chiu-Hsieh Hsu, Mandi Yu
Maintainer: Chiu-Hsieh Hsu <pablo1639@gmail.com>

Diff between NNMIS versions 1.0.0 dated 2017-10-18 and 1.0.1 dated 2019-04-20

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Package music updated to version 0.1.1 with previous version 0.1.0 dated 2019-02-20

Title: Learn and Experiment with Music Theory
Description: An aid for learning and using music theory. You can build chords, scales, and chord progressions using 12-note equal temperament tuning (12-ET) or user-defined tuning. Includes functions to visualize notes on a piano using ASCII plots in the console and to plot waveforms using base graphics. It allows simple playback of notes and chords using the 'audio' package.
Author: Efstathios D. Gennatas [aut, cre]
Maintainer: Efstathios D. Gennatas <gennatas@gmail.com>

Diff between music versions 0.1.0 dated 2019-02-20 and 0.1.1 dated 2019-04-20

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Package hdf5r updated to version 1.2.0 with previous version 1.1.1 dated 2019-03-26

Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre], Mario Annau [aut], Novartis Institute for BioMedical Research (NIBR) [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>

Diff between hdf5r versions 1.1.1 dated 2019-03-26 and 1.2.0 dated 2019-04-20

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Package corrr updated to version 0.3.2 with previous version 0.3.1 dated 2019-03-06

Title: Correlations in R
Description: A tool for exploring correlations. It makes it possible to easily perform routine tasks when exploring correlation matrices such as ignoring the diagonal, focusing on the correlations of certain variables against others, or rearranging and visualising the matrix in terms of the strength of the correlations.
Author: Simon Jackson [aut, cre], Jorge Cimentada [ctb], Edgar Ruiz [aut]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>

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Package cdata updated to version 1.0.9 with previous version 1.0.8 dated 2019-03-30

Title: Fluid Data Transformations
Description: Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . This package introduces the idea of control table specification of data transforms (later also adapted from 'cdata' by 'tidyr'). Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package reproj updated to version 0.3.0 with previous version 0.2.0 dated 2018-12-30

Title: Coordinate System Transformations for Map Data
Description: Transform coordinates via 'PROJ' using the library directly, by wrapping the 'proj4' package. The 'reproj' function handles the need for radian units for either source or target and allows removing an explicit source definition in methods that extend the generic. The 'PROJ' library is available at <https://proj4.org/>.
Author: Michael D. Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>)
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

Diff between reproj versions 0.2.0 dated 2018-12-30 and 0.3.0 dated 2019-04-20

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Fri, 19 Apr 2019

Package proxyC updated to version 0.1.2 with previous version 0.1.0 dated 2018-12-31

Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph] (<https://orcid.org/0000-0001-6519-5265>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>

Diff between proxyC versions 0.1.0 dated 2018-12-31 and 0.1.2 dated 2019-04-19

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Package ncmeta updated to version 0.0.4 with previous version 0.0.3 dated 2018-10-26

Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or servers. This package leverages and extends the lower level functions of the 'RNetCDF' package providing a consistent set of functions that all return data frames. We introduce named concepts of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the 'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library itself with only the named concepts of 'variables', 'dimensions' and 'attributes'. 'ncmeta' provides a required framework for the in-development 'tidync' project <https://github.com/hypertidy/tidync>.
Author: Michael Sumner [aut, cre], Tomas Remenyi [ctb], Ben Raymond [ctb], David Blodgett [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>

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Package frailtySurv updated to version 1.3.6 with previous version 1.3.5 dated 2018-08-28

Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a wide range of frailty distributions using a consistent and asymptotically-normal estimator. Currently supports: gamma, power variance function, log-normal, and inverse Gaussian frailty models.
Author: Vinnie Monaco [aut, cre], Malka Gorfine [aut], Li Hsu [aut]
Maintainer: Vinnie Monaco <contact@vmonaco.com>

Diff between frailtySurv versions 1.3.5 dated 2018-08-28 and 1.3.6 dated 2019-04-19

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Package splusTimeDate updated to version 2.5.0-142 with previous version 2.5.0-141 dated 2018-05-30

Title: Times and Dates from S-PLUS
Description: A collection of classes and methods for working with times and dates. The code was originally available in S-PLUS.
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny <skaluzny@tibco.com>

Diff between splusTimeDate versions 2.5.0-141 dated 2018-05-30 and 2.5.0-142 dated 2019-04-19

 DESCRIPTION   |    8 ++++----
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Package rvinecopulib updated to version 0.3.1.1.0 with previous version 0.3.0.1.1 dated 2018-08-22

Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib' package implements the core features of the popular 'VineCopula' package, in particular inference algorithms for both vine copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker and more modern API, improved performances, especially in high dimensions, nonparametric and multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as header-only C++ library (currently version 0.3.1). Thus users do not need to install 'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre], Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>

Diff between rvinecopulib versions 0.3.0.1.1 dated 2018-08-22 and 0.3.1.1.0 dated 2019-04-19

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Package palasso updated to version 0.0.5 with previous version 0.0.4 dated 2019-03-08

Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al. 2019). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <a.rauschenberger@vumc.nl>

Diff between palasso versions 0.0.4 dated 2019-03-08 and 0.0.5 dated 2019-04-19

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Package memery updated to version 0.5.2 with previous version 0.5.0 dated 2018-05-17

Title: Internet Memes for Data Analysts
Description: Generates internet memes that optionally include a superimposed inset plot and other atypical features, combining the visual impact of an attention-grabbing meme with graphic results of data analysis. The package differs from related packages that focus on imitating and reproducing standard memes. Some packages do this by interfacing with online meme generators whereas others achieve this natively. This package takes the latter approach. It does not interface with online meme generators or require any authentication with external websites. It reads images directly from local files or via URL and meme generation is done by the package. While this is similar to the 'meme' package available on CRAN, it differs in that the focus is on allowing for non-standard meme layouts and hybrids of memes mixed with graphs. While this package can be used to make basic memes like an online meme generator would produce, it caters primarily to hybrid graph-meme plots where the meme presentation can be seen as a backdrop highlighting foreground graphs of data analysis results. The package also provides support for an arbitrary number of meme text labels with arbitrary size, position and other attributes rather than restricting to the standard top and/or bottom text placement. This is useful for proper aesthetic interleaving of plots of data between meme image backgrounds and overlain text labels. The package offers a selection of templates for graph placement and appearance with respect to the underlying meme. Graph templates also permit additional template-specific customization. Animated gif support is provided but this is optional and functional only if the 'magick' package is installed. 'magick' is not required unless gif functionality is desired.
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

Diff between memery versions 0.5.0 dated 2018-05-17 and 0.5.2 dated 2019-04-19

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Package funHDDC updated to version 2.3.0 with previous version 2.2.0 dated 2018-10-08

Title: Univariate and Multivariate Model-Based Clustering in Group-Specific Functional Subspaces
Description: The funHDDC algorithm allows to cluster functional univariate (Bouveyron and Jacques, 2011, <doi:10.1007/s11634-011-0095-6>) or multivariate data (Schmutz et al., 2018) by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

Diff between funHDDC versions 2.2.0 dated 2018-10-08 and 2.3.0 dated 2019-04-19

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Package Directional updated to version 3.7 with previous version 3.6 dated 2019-03-25

Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>, P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2019). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing (to appear). <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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Package chorrrds updated to version 0.1.9 with previous version 0.1.8 dated 2019-01-28

Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>. The package also has functions for cleaning the extracted data and feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>

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Package akmedoids updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-18

Title: Anchored Kmedoids for Longitudinal Data Clustering
Description: Advances a novel adaptation of longitudinal k-means clustering technique (Genolini et al. (2015) <doi:10.18637/jss.v065.i04>) for grouping trajectories based on the similarities of their long-term trends and determines the optimal solution based on the Calinski-Harabatz criterion (Calinski and Harabatz (1974) <doi:10.1080/03610927408827101>). Includes functions to extract descriptive statistics and generate a visualisation of the resulting groups, drawing methods from the 'ggplot2' library (Wickham H. (2016) <doi:10.1007/978-3-319-24277-4>). The package also includes a number of other useful functions for exploring and manipulating longitudinal data prior to the clustering process.
Author: Monsuru Adepeju [cre, aut], Samuel Langton [aut], Jon Bannister [aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>

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Package capm updated to version 0.13.10 with previous version 0.13.9 dated 2018-11-26

Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population management. Some functions assist survey sampling tasks (calculate sample size for simple and complex designs, select sampling units and estimate population parameters) while others assist the modelling of population dynamics. For demographic characterizations and population management evaluations see: "Baquero, et al." (2018), <doi:10.1016/j.prevetmed.2018.07.006>. For modelling of population dynamics see: "Baquero et al." (2016), <doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076"; "Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre], Marcos Amaku [ctb], Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>

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Package iMRMC updated to version 1.2.0 with previous version 1.1.0 dated 2017-12-12

Title: Multi-Reader, Multi-Case Analysis Methods (ROC, Agreement, and Other Metrics)
Description: Do Multi-Reader, Multi-Case (MRMC) analyses of data from imaging studies where clinicians (readers) evaluate patient images (cases). What does this mean? ... Many imaging studies are designed so that every reader reads every case in all modalities, a fully-crossed study. In this case, the data is cross-correlated, and we consider the readers and cases to be cross-correlated random effects. An MRMC analysis accounts for the variability and correlations from the readers and cases when estimating variances, confidence intervals, and p-values. The functions in this package can treat arbitrary study designs and studies with missing data, not just fully-crossed study designs. The initial package analyzes the reader-average area under the receiver operating characteristic (ROC) curve with U-statistics according to Gallas, Bandos, Samuelson, and Wagner 2009 <doi:10.1080/03610920802610084>. Additional functions analyze other endpoints with U-statistics (binary performance and score differences) following the work by Gallas, Pennello, and Myers 2007 <doi:10.1364/JOSAA.24.000B70>. Package development and documentation is at <https://github.com/DIDSR/iMRMC/tree/master>.
Author: Brandon Gallas
Maintainer: Brandon Gallas <Brandon.Gallas@fda.hhs.gov>

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Package forestChange updated to version 0.6 with previous version 0.5 dated 2019-03-26

Title: Computing Essential Biodiversity Variables from Global Forest Change Data
Description: Metrics of two Essential Biodiversity Variables: forest extents and forest fragmentation indices (O'connor et al., 2015) <doi:10.1002/rse2.4> are computed by processing Global Forest Change data (Hansen et al., 2013) <doi:10.1126/science.1244693>. The Forest Change Data are extracted using either Geographic Administrative Units, see <https://gadm.org/>, or user-defined polygons. Most of the procedures can be understood implementing two functions: FCPolygon() and EBVmetric().
Author: Wilson Lara <wilarhen@temple.edu>, Victor Gutierrez-Velez <victorhugo@temple.edu>
Maintainer: Wilson Lara <wilarhen@temple.edu>

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Package ecmwfr updated to version 1.2.0 with previous version 1.1.0 dated 2019-02-06

Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Climate Data Store (CDS; <https://cds.climate.copernicus.eu>). Allows for easy downloads of weather forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] (<https://orcid.org/0000-0002-5070-8109>), Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>), Elio Campitelli [ctb] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>

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Package rngtools updated to version 1.3.1.1 with previous version 1.3.1 dated 2018-05-15

Title: Utility Functions for Working with Random Number Generators
Description: Provides a set of functions for working with Random Number Generators (RNGs). In particular, a generic S4 framework is defined for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

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Package tint updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-01

Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'. A modern take on the 'Tufte' design for pdf and html vignettes, building on the 'tufte' package with additional contributions from the 'knitr' and 'ggtufte' package, and also acknowledging the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel and Jonathan Gilligan
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between tint versions 0.1.1 dated 2019-04-01 and 0.1.2 dated 2019-04-19

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Package Omisc updated to version 0.1.1 with previous version 0.1.0 dated 2018-10-14

Title: Univariate Bootstrapping and Other Things
Description: Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi.org/10.1037/1082-989X.12.4.414>.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>

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Package jsmodule updated to version 0.8.1 with previous version 0.8.0 dated 2019-04-07

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package FADA updated to version 1.3.4 with previous version 1.3.3 dated 2018-02-07

Title: Variable Selection for Supervised Classification in High Dimension
Description: The functions provided in the FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised classification of high-dimensional and correlated profiles. The procedure combines a decorrelation step based on a factor modeling of the dependence among covariates and a classification method. The available methods are Lasso regularized logistic model (see Friedman et al. (2010)), sparse linear discriminant analysis (see Clemmensen et al. (2011)), shrinkage linear and diagonal discriminant analysis (see M. Ahdesmaki et al. (2010)). More methods of classification can be used on the decorrelated data provided by the package FADA.
Author: Emeline Perthame (Institut Pasteur, Paris, France), Chloe Friguet (Universite de Bretagne Sud, Vannes, France) and David Causeur (Agrocampus Ouest, Rennes, France)
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>

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Package drake updated to version 7.2.0 with previous version 7.1.0 dated 2019-04-07

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://ropensci.github.io/drake/> and the online manual <https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>), Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>), Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>), Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package clickR updated to version 0.4.32 with previous version 0.4.20 dated 2018-10-17

Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis, fixing data errors in numerical, factor and date variables and creating report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

Diff between clickR versions 0.4.20 dated 2018-10-17 and 0.4.32 dated 2019-04-19

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Package madness updated to version 0.2.6 with previous version 0.2.5 dated 2018-08-29

Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>

Diff between madness versions 0.2.5 dated 2018-08-29 and 0.2.6 dated 2019-04-19

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Package gibble updated to version 0.2.0 with previous version 0.1.2 dated 2018-10-31

Title: Geometry Decomposition
Description: Build a map of path-based geometry, this is a simple description of the number of parts in an object and their basic structure. Translation and restructuring operations for planar shapes and other hierarchical types require a data model with a record of the underlying relationships between elements. The gibble() function creates a geometry map, a simple record of the underlying structure in path-based hierarchical types. There are methods for the planar shape types in the 'sf' and 'sp' packages and for types in the 'trip' and in-development 'silicate' packages.
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>)
Maintainer: Michael Sumner <mdsumner@gmail.com>

Diff between gibble versions 0.1.2 dated 2018-10-31 and 0.2.0 dated 2019-04-19

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Package ICAOD updated to version 0.9.9 with previous version 0.9.8 dated 2019-01-14

Title: Optimal Designs for Nonlinear Models
Description: Finds optimal designs for nonlinear models using a metaheuristic algorithm called imperialist competitive algorithm ICA. See, for details, Masoudi et al. (2017) <doi:10.1016/j.csda.2016.06.014> and Masoudi et al. (2019) <doi:10.1080/10618600.2019.1601097>.
Author: Ehsan Masoudi [aut, cre], Heinz Holling [aut], Weng Kee Wong [aut]
Maintainer: Ehsan Masoudi <ehsan.masoudi@wwu.de>

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Thu, 18 Apr 2019

Package StratigrapheR updated to version 0.0.4 with previous version 0.0.3 dated 2019-03-22

Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions based on R base graphics, interval management functions and svg importation functions among others. Also include stereographic projection functions, and other functions made to deal with large datasets while keeping options to get into the details of the data. When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, Litholog generation with the StratigrapheR package and signal decomposition for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21, EGU2019-5520, 2019, EGU General Assembly 2019. <http://hdl.handle.net/2268/234402> The palaeomagnetism functions are based on: Tauxe, L., 2010. Essentials of Paleomagnetism. University of California Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>; Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge University Press, 289 pp.; Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205, <doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>

Diff between StratigrapheR versions 0.0.3 dated 2019-03-22 and 0.0.4 dated 2019-04-18

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Package MetaCycle updated to version 1.2.0 with previous version 1.1.0 dated 2015-12-04

Title: Evaluate Periodicity in Large Scale Data
Description: There are two functions-meta2d and meta3d for detecting rhythmic signals from time-series datasets. For analyzing time-series datasets without individual information, 'meta2d' is suggested, which could incorporates multiple methods from ARSER, JTK_CYCLE and Lomb-Scargle in the detection of interested rhythms. For analyzing time-series datasets with individual information, 'meta3d' is suggested, which takes use of any one of these three methods to analyze time-series data individual by individual and gives out integrated values based on analysis result of each individual.
Author: Gang Wu [aut, cre], Ron Anafi [aut, ctb], John Hogenesch [aut, ctb], Michael Hughes [aut, ctb], Karl Kornacker [aut, ctb], Xavier Li [aut, ctb], Matthew Carlucci [aut, ctb]
Maintainer: Gang Wu <wggucas@gmail.com>

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Package CrossVA updated to version 0.9.6 with previous version 0.9.5 dated 2019-01-19

Title: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.
Author: Eungang Choi [aut], Sam Clark [aut], Zehang Li [aut], Jason Thomas [aut, cre]
Maintainer: Jason Thomas <jarathomas@gmail.com>

Diff between CrossVA versions 0.9.5 dated 2019-01-19 and 0.9.6 dated 2019-04-18

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Package caret updated to version 6.0-83 with previous version 6.0-82 dated 2019-03-26

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau, Andrew Ziem, Luca Scrucca, Yuan Tang, Can Candan, and Tyler Hunt.
Maintainer: Max Kuhn <mxkuhn@gmail.com>

Diff between caret versions 6.0-82 dated 2019-03-26 and 6.0-83 dated 2019-04-18

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Package blockseg updated to version 0.5.2 with previous version 0.5.0 dated 2018-07-03

Title: Two Dimensional Change-Points Detection
Description: Segments a matrix in blocks with constant values. BRAULT V, CHIQUET J. and LEVY-LEDUC C. (2017) <doi:10.1214/17-EJS1270>.
Author: Julien Chiquet [aut] (<https://orcid.org/0000-0002-3629-3429>), Vincent Brault [aut, cre] (<https://orcid.org/0000-0003-4228-6687>)
Maintainer: Vincent Brault <vincent.brault@univ-grenoble-alpes.fr>

Diff between blockseg versions 0.5.0 dated 2018-07-03 and 0.5.2 dated 2019-04-18

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Package akmedoids updated to version 0.1.1 with previous version 0.1.0 dated 2019-03-24

Title: Anchored Kmedoids for Longitudinal Data Clustering
Description: Advances a novel adaptation of longitudinal k-means clustering technique (Genolini et al. (2015) <doi:10.18637/jss.v065.i04>) for grouping trajectories based on the similarities of their long-term trends and determines the optimal solution based on the Calinski-Harabatz criterion (Calinski and Harabatz (1974) <doi:10.1080/03610927408827101>). Includes functions to extract descriptive statistics and generate a visualisation of the resulting groups, drawing methods from the 'ggplot2' library (Wickham H. (2016) <doi:10.1007/978-3-319-24277-4>). The package also includes a number of other useful functions for exploring and manipulating longitudinal data prior to the clustering process.
Author: Monsuru Adepeju [cre, aut], Samuel Langton [aut], Jon Bannister [aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>

Diff between akmedoids versions 0.1.0 dated 2019-03-24 and 0.1.1 dated 2019-04-18

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Package xtensor updated to version 0.11.0-0 with previous version 0.10.1-0 dated 2019-03-18

Title: Headers for the 'xtensor' Library
Description: The 'xtensor' C++ library for numerical analysis with multi-dimensional array expressions is provided as a header-only C++14 library. It offers an extensible expression system enabling lazy broadcasting; an API following the idioms of the C++ standard library; and tools to manipulate array expressions and build upon 'xtensor'.
Author: Johan Mabille, Sylvain Corlay and Wolf Vollprecht
Maintainer: Sylvain Corlay <sylvain.corlay@gmail.com>

Diff between xtensor versions 0.10.1-0 dated 2019-03-18 and 0.11.0-0 dated 2019-04-18

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Package textmineR updated to version 3.0.4 with previous version 3.0.3 dated 2019-03-22

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Author: Tommy Jones [aut, cre], William Doane [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>

Diff between textmineR versions 3.0.3 dated 2019-03-22 and 3.0.4 dated 2019-04-18

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Package SDMTools updated to version 1.1-221.1 with previous version 1.1-221 dated 2014-08-05

Title: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
Description: This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.. This package was made possible in part by financial support from the Australian Research Council & ARC Research Network for Earth System Science.
Author: Jeremy VanDerWal, Lorena Falconi, Stephanie Januchowski, Luke Shoo and Collin Storlie
Maintainer: ORPHANED

Diff between SDMTools versions 1.1-221 dated 2014-08-05 and 1.1-221.1 dated 2019-04-18

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Package plotGMM updated to version 0.2.0 with previous version 0.1.0 dated 2018-12-25

Title: Tools for Visualizing Gaussian Mixture Models
Description: The main function, plot_GMM, is used for plotting output from Gaussian mixture models, including both densities and overlaying mixture weight component curves from the fit GMM. The package includes another function, plot_mix_comps, which is used in the plot_GMM function, and can be used in any plot generated by the user for overlaying mixture component curves from Gaussian mixture models. For the plot_mix_comps function, usage most often will be specifying the "fun" argument within "stat_function" in a ggplot2 object.
Author: Philip Waggoner [aut, cre], Fong Chan [aut]
Maintainer: Philip Waggoner <philip.waggoner@gmail.com>

Diff between plotGMM versions 0.1.0 dated 2018-12-25 and 0.2.0 dated 2019-04-18

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Package PHEindicatormethods updated to version 1.1.1 with previous version 1.0.8 dated 2018-07-30

Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and their confidence intervals using methods approved for use in the production of Public Health England indicators such as those presented via Fingertips (<http://fingertips.phe.org.uk/>). It provides functions for the generation of proportions, crude rates, means, directly standardised rates, indirectly standardised rates, standardised mortality ratios, slope and relative index of inequality and life expectancy. Statistical methods are referenced in the following publications. Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>. Dobson et al (1991) <doi:10.1002/sim.4780100317>. Armitage P, Berry G (2002) <doi:10.1002/9780470773666>. Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>. Altman DG et al (2000, ISBN: 978-0-727-91375-3). Chiang CL. (1968, ISBN: 978-0-882-75200-6). Newell C. (1994, ISBN: 978-0-898-62451-9). Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>. Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>. Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
Author: Anderson Georgina [aut, cre], Fox Sebastian [ctb], Francis Matthew [ctb], Fryers Paul [ctb], Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>

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Package GerminaR updated to version 1.3 with previous version 1.2 dated 2017-10-25

Title: Germination Indices and Graphics for Seed Germination in Ecophysiological Studies
Description: The aim of GerminaR consists of the assessment of different seed germination indices and visualization techniques that provide a robust approach for germination data analysis.
Author: Flavio Lozano Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>), Omar Benites Alfaro [aut] (<https://orcid.org/0000-0002-6852-9598>), Denise Garcia de Santana [ctb], Marli A. Ranal [ctb], Marcelo F. Pompelli [aut, ths] (<https://orcid.org/0000-0002-4408-6374>), Federal University of Pernambuco [cph] (Register of application), Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano Isla <flavjack@gmail.com>

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Package GeneCycle updated to version 1.1.3 with previous version 1.1.2 dated 2012-04-16

Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert et al. (2004) <doi.org/10.1093/bioinformatics/btg364>, Ahdesmaki et al. (2005) <DOI:10.1186/1471-2105-6-117> and Ahdesmaki et al. (2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically expressed genes from gene expression time series data.
Author: Miika Ahdesmaki, Konstantinos Fokianos, and Korbinian Strimmer.
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>

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Package bzinb updated to version 1.0.1 with previous version 1.0.0 dated 2019-04-10

Title: Bivariate Zero-Inflated Negative Binomial Model Estimator
Description: Provides a maximum likelihood estimation of Bivariate Zero-Inflated Negative Binomial (BZINB) model or the nested model parameters. Also estimates the underlying correlation of the a pair of count data. See Cho, H., Preisser, J., Liu, C., and Wu, D. (In preparation) for details.
Author: Hunyong Cho, Chuwen Liu, Jinyoung Park, Di Wu
Maintainer: Hunyong Cho <hunycho@live.unc.edu>

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Package cba updated to version 0.2-21 with previous version 0.2-20 dated 2019-03-04

Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>

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Package PDFEstimator updated to version 0.1-3 with previous version 0.1-2 dated 2019-04-08

Title: Nonparametric Probability Density Estimator
Description: Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>

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Package MiDA updated to version 0.1.2 with previous version 0.1.0 dated 2019-03-04

Title: Microarray Data Analysis
Description: Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.
Author: Elena Filatova [aut, cre], Nikolai Sakharnov [dtc], Dmitry Knyazev [dtc], Oleg Utkin [dtc], Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia [fnd]
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Package expperm updated to version 1.1 with previous version 1.0 dated 2019-04-07

Title: Computing Expectations and Marginal Likelihoods for Permutations
Description: A set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper 'Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.
Author: Ben Powell
Maintainer: Ben Powell <ben.powell@york.ac.uk>

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Package deisotoper updated to version 0.0.7 with previous version 0.0.3 dated 2017-12-19

Title: Detection of Isotope Pattern of a Mass Spectrometric Measurement
Description: Provides a low-level interface for a deisotoper container implemented in the 'Java' programming language and means of S3 helper functions for plotting and debugging isotopes of mass spectrometric data. The deisotoper algorithm detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.
Author: Christian Panse [cre, aut] (<https://orcid.org/0000-0003-1975-3064>), Lucas Schmidt [ctb, aut] (<https://orcid.org/0000-0003-4496-0487>), Witold E. Wolski [ctb, aut] (<https://orcid.org/0000-0002-6468-120X>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

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Package UCSCXenaTools updated to version 1.2.1 with previous version 1.2.0 dated 2019-03-31

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between UCSCXenaTools versions 1.2.0 dated 2019-03-31 and 1.2.1 dated 2019-04-18

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Package pammtools updated to version 0.1.11 with previous version 0.1.9 dated 2019-03-14

Title: Piece-Wise Exponential Additive Mixed Modeling Tools
Description: The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and Scheipl (2018) <doi: 10.1177/1471082X17748083>) is a powerful model class for survival analysis, based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender et. al. (2018) <doi:10.1093/biostatistics/kxy003>. pammtools provides tidy workflow for survival analysis with PAMMs, including data transformation and other pre- and post-processing functions as well as visualization.
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>), Fabian Scheipl [aut]
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>

Diff between pammtools versions 0.1.9 dated 2019-03-14 and 0.1.11 dated 2019-04-18

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Package robustvarComp updated to version 0.1-5 with previous version 0.1-2 dated 2014-07-10

Title: Robust Estimation of Variance Component Models
Description: Robust Estimation of Variance Component Models by classic and composite robust procedures. The composite procedures are robust against outliers generated by the Independent Contamination Model.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it> and Victor J. Yohai <victoryohai@gmail.com>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>

Diff between robustvarComp versions 0.1-2 dated 2014-07-10 and 0.1-5 dated 2019-04-18

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Package Orcs updated to version 1.2.0 with previous version 1.1.1 dated 2019-02-28

Title: Omnidirectional R Code Snippets
Description: I tend to repeat the same code chunks over and over again. At first, this was fine for me and I paid little attention to such redundancies. A little later, when I got tired of manually replacing Linux filepaths with the referring Windows versions, and vice versa, I started to stuff some very frequently used work-steps into functions and, even later, into a proper R package. And that's what this package is - a hodgepodge of various R functions meant to simplify (my) everyday-life coding work without, at the same time, being devoted to a particular scope of application.
Author: Florian Detsch [cre, aut], Tim Appelhans [ctb], Baptiste Auguie [ctb], OpenStreetMap contributors [cph]
Maintainer: Florian Detsch <fdetsch@web.de>

Diff between Orcs versions 1.1.1 dated 2019-02-28 and 1.2.0 dated 2019-04-18

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Package R.filesets updated to version 2.13.0 with previous version 2.12.1 dated 2018-04-09

Title: Easy Handling of and Access to Files Organized in Structured Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.filesets versions 2.12.1 dated 2018-04-09 and 2.13.0 dated 2019-04-18

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Package nasapower updated to version 1.1.1 with previous version 1.1.0 dated 2019-04-10

Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>), Hazel Kavili [rev], Alison Boyer [rev]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

Diff between nasapower versions 1.1.0 dated 2019-04-10 and 1.1.1 dated 2019-04-18

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Package cOde updated to version 1.0.0 with previous version 0.4.1 dated 2018-08-08

Title: Automated C Code Generation for 'deSolve', 'bvpSolve'
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>

Diff between cOde versions 0.4.1 dated 2018-08-08 and 1.0.0 dated 2019-04-18

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Package clustree updated to version 0.4.0 with previous version 0.3.0 dated 2019-02-24

Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>), Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>), Andrea Rau [ctb], Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke.zappia@mcri.edu.au>

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Wed, 17 Apr 2019

Package wfe updated to version 1.9.1 with previous version 1.8 dated 2019-01-09

Title: Weighted Linear Fixed Effects Regression Models for Causal Inference
Description: Provides a computationally efficient way of fitting weighted linear fixed effects estimators for causal inference with various weighting schemes. Weighted linear fixed effects estimators can be used to estimate the average treatment effects under different identification strategies. This includes stratified randomized experiments, matching and stratification for observational studies, first differencing, and difference-in-differences. The package implements methods described in Imai and Kim (2017) "When should We Use Linear Fixed Effects Regression Models for Causal Inference with Longitudinal Data?", available at <https://imai.fas.harvard.edu/research/FEmatch.html>.
Author: In Song Kim [aut, cre], Kosuke Imai [aut]
Maintainer: In Song Kim <insong@mit.edu>

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Package hypergate updated to version 0.8.1 with previous version 0.8 dated 2018-08-31

Title: Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
Description: Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Author: Etienne Becht [cre, aut], Samuel Granjeaud [ctb]
Maintainer: Etienne Becht <etienne.becht@protonmail.com>

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Package Haplin updated to version 7.1.0 with previous version 7.0.0 dated 2018-05-27

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in Gjessing, HK and Lie, RT (2006) <doi:10.1111/j.1529-8817.2005.00218.x>.
Author: Hakon K. Gjessing [aut, cre], Miriam Gjerdevik [ctb] (functions 'lineByLine' and 'convertPed'), Julia Romanowska [ctb] (new data format, parallelisation, new documentation), Oivind Skare [ctb] (TDT tests)
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>

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Package cAIC4 updated to version 0.8 with previous version 0.7 dated 2019-02-02

Title: Conditional Akaike Information Criterion for 'lme4'
Description: Provides functions for the estimation of the conditional Akaike information in generalized mixed-effect models fitted with (g)lmer() from 'lme4'.
Author: Benjamin Saefken and David Ruegamer, with contributions from Sonja Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>

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Package taxotools updated to version 0.0.23 with previous version 0.0.20 dated 2019-04-08

Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>

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Package httk updated to version 1.9.1 with previous version 1.9 dated 2019-02-04

Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") as in Pearce et al. (2017) <doi:10.18637/jss.v079.i04>. Chemical-specific in vitro data have been obtained from relatively high throughput experiments. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and measurement limitations. Calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre], Robert Pearce [aut], Caroline Ring [aut], Greg Honda [aut], Jimena Davis [ctb], Nisha Sipes [ctb], Barbara Wetmore [ctb], Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>

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Package explor updated to version 0.3.5 with previous version 0.3.4 dated 2018-09-13

Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package transport updated to version 0.11-1 with previous version 0.11-0 dated 2019-02-04

Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre], Björn Bähre [aut] (aha and power diagrams), Carsten Gottschlich [aut] (simplex and shortlist), Valentin Hartmann [aut] (semidiscrete1), Florian Heinemann [aut] (transport_track), Bernhard Schmitzer [aut] (shielding), Jörn Schrieber [aut] (subsampling), Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>

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Package gjam updated to version 2.2.7 with previous version 2.2.6 dated 2018-09-22

Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>

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Package nzilbb.labbcat updated to version 0.2-0 with previous version 0.1-2 dated 2019-03-21

Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management system developed by the New Zealand Institute of Language, Brain and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>. This package defines functions for accessing corpus data in a 'LaBB-CAT' instance. For more information about 'LaBB-CAT', see Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142> or Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>

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Package gamCopula updated to version 0.0-5 with previous version 0.0-4 dated 2017-08-17

Title: Generalized Additive Models for Bivariate Conditional Dependence Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to apply generalized additive models to bivariate dependence structures and non-simplified vine copulas.
Author: Thomas Nagler [aut], Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>

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Package Map2NCBI updated to version 1.2 with previous version 1.1 dated 2015-11-13

Title: Mapping Markers to the Nearest Genomic Feature
Description: Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a current build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the current build used. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.
Author: Lauren L. Hulsman Hanna and David G. Riley
Maintainer: Lauren Hanna <Lauren.Hanna@ndsu.edu>

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Package reactR updated to version 0.4.0 with previous version 0.3.0 dated 2019-01-15

Title: React Helpers
Description: Make it easy to use 'React' in R with 'htmlwidget' scaffolds, helper dependency functions, an embedded 'Babel' 'transpiler', and examples.
Author: Facebook Inc [aut, cph] (React library in lib, https://facebook.github.io/react; see AUTHORS for full list of contributors), Kent Russell [aut, cre] (R interface), Alan Dipert [aut] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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Package geodist updated to version 0.0.3 with previous version 0.0.2 dated 2019-03-22

Title: Fast, Dependency-Free Geodesic Distance Calculations
Description: Dependency-free, ultra fast calculation of geodesic distances. Includes the reference nanometre-accuracy geodesic distances of Karney (2013) <doi:10.1007/s00190-012-0578-z>, as used by the 'sf' package, as well as Haversine and Vincenty distances. Default distance measure is the "Mapbox cheap ruler" which is generally more accurate than Haversine or Vincenty for distances out to a few hundred kilometres, and is considerably faster. The main function accepts one or two inputs in almost any generic rectangular form, and returns either matrices of pairwise distances, or vectors of sequential distances.
Author: Mark Padgham [aut, cre], Michael D. Sumner [aut], Charles F.F Karney [cph] (Original author of included code for geodesic distances)
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package filehash updated to version 2.4-2 with previous version 2.4-1 dated 2017-04-07

Title: Simple Key-Value Database
Description: Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.
Author: Roger D. Peng <rdpeng@jhu.edu>
Maintainer: Roger D. Peng <rdpeng@jhu.edu>

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Package EpiILMCT updated to version 1.1.3 with previous version 1.1.2 dated 2018-03-28

Title: Continuous Time Distance-Based and Network-Based Individual Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry, Vineetha Warriyar K. V. and Rob Deardon
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>

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Package eNetXplorer updated to version 1.0.2 with previous version 1.0.1 dated 2018-06-10

Title: Quantitative Exploration of Elastic Net Families for Generalized Linear Models
Description: Provides a quantitative toolkit to explore elastic net families and to uncover correlates contributing to prediction under a cross-validation framework. Fits linear, binomial (logistic) and multinomial models. Candia J and Tsang JS, BMC Bioinformatics (2019) 20:189 <doi:10.1186/s12859-019-2778-5>.
Author: Julian Candia and John S. Tsang
Maintainer: Julian Candia <julian.candia@nih.gov>

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Package worldmet updated to version 0.8.7 with previous version 0.8.4 dated 2018-02-27

Title: Import Surface Meteorological Data from NOAA Integrated Surface Database (ISD)
Description: Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package swdft updated to version 1.0.0 with previous version 0.0.1 dated 2018-07-30

Title: Sliding Window Discrete Fourier Transform (SWDFT)
Description: Implements the Sliding Window Discrete Fourier Transform (SWDFT). Also provides statistical methods based on the SWDFT, and graphical tools to display the outputs.
Author: Lee F. Richardson [aut, cre]
Maintainer: Lee F. Richardson <leerichardson2013@gmail.com>

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Tue, 16 Apr 2019

Package SPUTNIK updated to version 1.1.2 with previous version 1.1.1 dated 2018-10-25

Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>

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Package discSurv updated to version 1.4.0 with previous version 1.3.4 dated 2018-08-01

Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.
Author: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de> and Matthias Schmid <matthias.schmid@imbie.uni-bonn.de>
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>

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Package statVisual updated to version 1.0.9 with previous version 1.0.5 dated 2019-03-15

Title: Statistical Visualization Tools
Description: Visualization functions in the applications of translational medicine (TM) and biomarker (BM) development to compare groups by statistically visualizing data and/or results of analyses, such as visualizing data by displaying in one figure different groups' histograms, boxplots, densities, scatter plots, error-bar plots, or trajectory plots, by displaying scatter plots of top principal components or dendrograms with data points colored based on group information, or visualizing volcano plots to check the results of whole genome analyses for gene differential expression.
Author: Wenfei Zhang [aut, cre], Weiliang Qiu [aut, ctb], Xuan Lin [aut, ctb], Donghui Zhang [aut, ctb]
Maintainer: Wenfei Zhang <Wenfei.Zhang@sanofi.com>

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Package pct updated to version 0.1.2 with previous version 0.1.1 dated 2019-03-29

Title: Propensity to Cycle Tool
Description: Functions and example data to teach and increase the reproducibility of the methods and code underlying the Propensity to Cycle Tool (PCT), a research project and web application hosted at <https://www.pct.bike/>. For an academic paper on the methods, see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package tuneRanger updated to version 0.5 with previous version 0.4 dated 2019-01-22

Title: Tune Random Forest of the 'ranger' Package
Description: Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
Author: Philipp Probst [aut, cre], Simon Klau [ctb]
Maintainer: Philipp Probst <philipp_probst@gmx.de>

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Package traitdataform updated to version 0.5.3 with previous version 0.5.2 dated 2018-12-30

Title: Formatting and Harmonizing Ecological Trait-Data
Description: Assistance for handling ecological trait data and applying the Ecological Trait-Data Standard terminology (Schneider et al. 2018 <doi:10.1101/328302>). There are two major use cases: (1) preparation of own trait datasets for upload into public data bases, and (2) harmonizing trait datasets from different sources by re-formatting them into a unified format. See 'traitdataform' website for full documentation.
Author: Florian D. Schneider [aut, cre] (<https://orcid.org/0000-0002-1494-5684>), Caterina Penone [ctb] (<https://orcid.org/0000-0002-8170-6659>), Andreas Ostrowski [ctb] (<https://orcid.org/0000-0002-2033-779X>), Dennis Heimann [ctb], Felix Neff [ctb], Markus J. Ankenbrand [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>

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Package tidytransit updated to version 0.4.0 with previous version 0.3.8 dated 2019-03-04

Title: Read, Validate, Analyze, and Map Files in the General Transit Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre], Flavio Poletti [aut], Danton Noriega-Goodwin [aut], Mark Padgham [aut], Angela Li [ctb], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], Kearey Smith [ctb], Dave Vautin [ctb], Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>

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Package TCIApathfinder updated to version 1.0.5 with previous version 1.0.4 dated 2019-03-21

Title: Client for the Cancer Imaging Archive REST API
Description: A wrapper for The Cancer Imaging Archive's REST API. The Cancer Imaging Archive (TCIA) hosts de-identified medical images of cancer available for public download, as well as rich metadata for each image series. TCIA provides a REST API for programmatic access to the data. This package provides simple functions to access each API endpoint. For more information, see <https://github.com/pamelarussell/TCIApathfinder> and TCIA's website.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@gmail.com>

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Package radtools updated to version 1.0.5 with previous version 1.0.4 dated 2019-03-13

Title: Utilities for Convenient Extraction of Medical Image Metadata
Description: A collection of utilities for navigating medical image data. The DICOM and NIfTI formats are supported. Functions provide simple interfaces to the data and metadata contained in these formats. A particular emphasis on metadata allows simple conversion of image metadata to familiar R data structures such as lists and data frames. Where possible, generic functions can silently process either DICOM or NIfTI data. Additionally, image data can be extracted and viewed.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@gmail.com>

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Package geostatsp updated to version 1.7.8 with previous version 1.7.7 dated 2019-03-06

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>

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Package catnet updated to version 1.15.5 with previous version 1.15.3 dated 2017-10-26

Title: Categorical Bayesian Network Inference
Description: Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov <nhbalov@gmail.com>

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Package BART updated to version 2.4 with previous version 2.3 dated 2019-03-28

Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut], Rodney Sparapani [aut, cre], Robert Gramacy [aut], Charles Spanbauer [aut], Matthew Pratola [aut], Martyn Plummer [ctb], Nicky Best [ctb], Kate Cowles [ctb], Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>

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Package survtmle updated to version 1.1.1 with previous version 1.1.0 dated 2018-04-13

Title: Compute Targeted Minimum Loss-Based Estimates in Right-Censored Survival Settings
Description: Targeted estimates of marginal cumulative incidence in survival settings with and without competing risks, including estimators that respect bounds (Benkeser, Carone, and Gilbert. Statistics in Medicine, 2017. <doi:10.1002/sim.7337>).
Author: David Benkeser [aut, cre, cph] (<https://orcid.org/0000-0002-1019-8343>), Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>)
Maintainer: David Benkeser <benkeser@emory.edu>

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Package BMSC updated to version 0.2.0 with previous version 0.1.1 dated 2018-10-18

Title: Bayesian Model Selection under Constraints
Description: A Bayesian regression package supporting constrained coefficient estimation and variable selection using Stan. This includes a robust variable selection algorithm by a horseshoe prior (<doi:10.1093/biomet/asq017>) that finds the optimal model considering main effects, interactions as well as powers of given variables under potential parameter constraints.
Author: Marcus Groß [aut, cre], Ricardo Fernandes [aut], Mira Celine Klein [ctb]
Maintainer: Marcus Groß <marcus.gross@inwt-statistics.de>

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Package PTXQC updated to version 0.92.6 with previous version 0.92.5 dated 2019-03-15

Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite. Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'.
Author: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>

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Package tsfeatures updated to version 1.0.1 with previous version 1.0.0 dated 2019-02-06

Title: Time Series Feature Extraction
Description: Methods for extracting various features from time series data. The features provided are those from Hyndman, Wang and Laptev (2013) <doi:10.1109/ICDMW.2015.104>, Kang, Hyndman and Smith-Miles (2017) <doi:10.1016/j.ijforecast.2016.09.004> and from Fulcher, Little and Jones (2013) <doi:10.1098/rsif.2013.0048>. Features include spectral entropy, autocorrelations, measures of the strength of seasonality and trend, and so on. Users can also define their own feature functions.
Author: Rob Hyndman [aut, cre] (<https://orcid.org/0000-0002-2140-5352>), Yanfei Kang [aut] (<https://orcid.org/0000-0001-8769-6650>), Pablo Montero-Manso [aut], Thiyanga Talagala [aut] (<https://orcid.org/0000-0002-0656-9789>), Earo Wang [aut] (<https://orcid.org/0000-0001-6448-5260>), Yangzhuoran Yang [aut], Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Souhaib Ben Taieb [ctb], Cao Hanqing [ctb], D K Lake [ctb], Nikolay Laptev [ctb], J R Moorman [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

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Package forecast updated to version 8.6 with previous version 8.5 dated 2019-01-18

Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>), George Athanasopoulos [aut], Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>), Gabriel Caceres [aut], Leanne Chhay [aut], Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>), Slava Razbash [aut], Earo Wang [aut], Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>), R Core Team [ctb, cph], Ross Ihaka [ctb, cph], Daniel Reid [ctb], David Shaub [ctb], Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>), Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between forecast versions 8.5 dated 2019-01-18 and 8.6 dated 2019-04-16

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 NAMESPACE                   |    3 
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Package cdcsis updated to version 2.0.1 with previous version 2.0.0 dated 2019-01-09

Title: Conditional Distance Correlation Based Feature Screening and Conditional Independence Inference
Description: Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <doi:10.5705/ss.202014.0117>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.
Author: Wenhao Hu, Mian Huang, Wenliang Pan, Xueqin Wang, Canhong Wen, Yuan Tian, Heping Zhang, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>

Diff between cdcsis versions 2.0.0 dated 2019-01-09 and 2.0.1 dated 2019-04-16

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 24 files changed, 916 insertions(+), 140 deletions(-)

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Package BoolNet updated to version 2.1.5 with previous version 2.1.4 dated 2018-06-07

Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] (contributed PicoSAT code), Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>

Diff between BoolNet versions 2.1.4 dated 2018-06-07 and 2.1.5 dated 2019-04-16

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Package gllvm updated to version 1.1.3 with previous version 1.1.2 dated 2019-01-02

Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>). Details for gllvm, see Hui et al. (2015) <doi:10.1111/2041-210X.12236> and (2017) <doi:10.1080/10618600.2016.1164708> and Niku et al. (2017) <doi:10.1007/s13253-017-0304-7>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>

Diff between gllvm versions 1.1.2 dated 2019-01-02 and 1.1.3 dated 2019-04-16

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Package BIFIEsurvey updated to version 3.2-25 with previous version 3.1-33 dated 2019-03-20

Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational assessment) for datasets with replication designs (jackknife, bootstrap, replicate weights; see Kolenikov, 2010; Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>, <doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996, <doi:10.1080/02331889708802523>). Descriptive statistics, linear and logistic regression, path models for manifest variables with measurement error correction and two-level hierarchical regressions for weighted samples are included. Statistical inference can be conducted for multiply imputed datasets and nested multiply imputed datasets and is in particularly suited for the analysis of plausible values (for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016; Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham & Yanagida, 2016; <doi:10.17888/fdb-demo:bistE813I-16a>). The package development was supported by BIFIE (Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [aut, cre], Konrad Oberwimmer [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between BIFIEsurvey versions 3.1-33 dated 2019-03-20 and 3.2-25 dated 2019-04-16

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Package mdmb updated to version 1.3-18 with previous version 1.2-4 dated 2019-01-11

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>). The regression model can be nonlinear (e.g., interaction effects, quadratic effects or B-spline functions). Multilevel models with missing data in predictors are available for Bayesian estimation. Substantive-model compatible multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between mdmb versions 1.2-4 dated 2019-01-11 and 1.3-18 dated 2019-04-16

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Package fastNaiveBayes updated to version 1.1.2 with previous version 1.1.1 dated 2019-03-31

Title: Extremely Fast Implementation of a Naive Bayes Classifier
Description: This is an extremely fast implementation of a Naive Bayes classifier. This package is currently the only package that supports a Bernoulli distribution, a Multinomial distribution, and a Gaussian distribution, making it suitable for both binary features, frequency counts, and numerical features. Another feature is the support of a mix of different event models. Only numerical variables are allowed, however, categorical variables can be transformed into dummies and used with the Bernoulli distribution. This implementation offers a huge performance gain compared to other implementations in R. The execution times were compared on a data set of tweets and this package was found to be around 283 to 34,841 times faster for the Bernoulli event models and 17 to 60 times faster for the Multinomial model. See the vignette for more details. For the Gaussian distribution this package was found to be between 2.8 and 1679 times faster. The implementation is largely based on the paper "A comparison of event models for Naive Bayes anti-spam e-mail filtering" written by K.M. Schneider (2003) <doi:10.3115/1067807>. Any issues can be submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
Author: Martin Skogholt
Maintainer: Martin Skogholt <m.skogholt@gmail.com>

Diff between fastNaiveBayes versions 1.1.1 dated 2019-03-31 and 1.1.2 dated 2019-04-16

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Package scatterD3 updated to version 0.9 with previous version 0.8.2 dated 2018-03-10

Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre], Kent Russell [aut, ctb], Mike Bostock [aut, cph] (d3.js library, http://d3js.org), Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/), Speros Kokenes [aut, cph] (d3-lasso-plugin library, https://github.com/skokenes/D3-Lasso-Plugin), Evan Wang [aut, cph] (d3-labeler plugin, https://github.com/tinker10/D3-Labeler)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

Diff between scatterD3 versions 0.8.2 dated 2018-03-10 and 0.9 dated 2019-04-16

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Package fpeek updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-22

Title: Check Text Files Content at a Glance
Description: Tools to help text files importation. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files. This package provides an alternative to a simple use of the 'head', 'tail', 'wc' and 'iconv' programs that are not always available on machine where R is installed.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between fpeek versions 0.1.0 dated 2018-07-22 and 0.1.1 dated 2019-04-16

 DESCRIPTION                 |   10 ++++++----
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Package arulesSequences updated to version 0.2-22 with previous version 0.2-21 dated 2019-03-04

Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>

Diff between arulesSequences versions 0.2-21 dated 2019-03-04 and 0.2-22 dated 2019-04-16

 CHANGELOG        |    4 ++++
 DESCRIPTION      |    6 +++---
 MD5              |   10 +++++-----
 data/zaki.rda    |binary
 src/similarity.c |    4 ++--
 tests/ptree.R    |    4 ++++
 6 files changed, 18 insertions(+), 10 deletions(-)

More information about arulesSequences at CRAN
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Package RJDemetra updated to version 0.1.2 with previous version 0.1.1 dated 2019-03-04

Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially recommended to the members of the European Statistical System (ESS) and the European System of Central Banks. It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre], Anna Michalek [aut], Jean Palate [aut], Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>

Diff between RJDemetra versions 0.1.1 dated 2019-03-04 and 0.1.2 dated 2019-04-16

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More information about RJDemetra at CRAN
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