Tue, 24 Apr 2018

Package sourcetools updated to version 0.1.7 with previous version 0.1.6 dated 2017-04-05

Title: Tools for Reading, Tokenizing and Parsing R Code
Description: Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>

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Package edpclient updated to version 0.5.1 with previous version 0.3.1 dated 2018-03-05

Title: Empirical Data Platform Client
Description: R client for Empirical Data Platform. More information is at <https://empirical.com>. For support, contact support@empirical.com.
Author: Empirical Engineering
Maintainer: Madeleine Thompson <madeleine@empirical.com>

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Package sjlabelled updated to version 1.0.9 with previous version 1.0.8 dated 2018-02-26

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package robustbase updated to version 0.93-0 with previous version 0.92-8 dated 2017-11-01

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre], Peter Rousseeuw [ctb] (Qn and Sn), Christophe Croux [ctb] (Qn and Sn), Valentin Todorov [aut] (most robust Cov), Andreas Ruckstuhl [aut] (nlrob, anova, glmrob), Matias Salibian-Barrera [aut] (lmrob orig.), Tobias Verbeke [ctb, fnd] (mc, adjbox), Manuel Koller [aut] (lmrob, psi-func.), Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package rly updated to version 1.6.1 with previous version 1.5 dated 2018-03-26

Title: 'Lex' and 'Yacc'
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph], Yasutaka Tanaka [ctb], Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>

Diff between rly versions 1.5 dated 2018-03-26 and 1.6.1 dated 2018-04-24

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Package sigr updated to version 0.2.5 with previous version 0.2.4 dated 2018-03-13

Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting and planning of experimental results, working around issue such as the difficulty of extracting model summary facts (such as with 'lm'/'glm'). This package also includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between sigr versions 0.2.4 dated 2018-03-13 and 0.2.5 dated 2018-04-24

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New package mleap with initial version 0.1.0
Package: mleap
Type: Package
Title: Interface to 'MLeap'
Version: 0.1.0
Authors@R: c( person("Kevin", "Kuo", role = c("aut", "cre"), email = "kevin.kuo@rstudio.com", comment = c(ORCID = "0000-0001-7803-7901")) )
Description: A 'sparklyr' <https://spark.rstudio.com> extension that provides an interface to 'MLeap' <https://github.com/combust/mleap>, an open source library that enables exporting and serving of 'Apache Spark' pipelines.
URL: https://github.com/rstudio/mleap
BugReports: https://github.com/rstudio/mleap/issues
License: Apache License (>= 2.0)
SystemRequirements: Apache Spark 2.0+, Apache Maven 3.5+, Java JDK 8, MLeap Runtime 0.9.6+
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.2)
Imports: sparklyr, jsonlite, purrr, fs, tibble, rJava, digest
RoxygenNote: 6.0.1
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2018-04-24 21:12:57 UTC; kevinykuo
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>
Repository: CRAN
Date/Publication: 2018-04-24 21:32:19 UTC

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Package languageserver updated to version 0.2.1 with previous version 0.2.0 dated 2018-04-24

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between languageserver versions 0.2.0 dated 2018-04-24 and 0.2.1 dated 2018-04-24

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Package water updated to version 0.8 with previous version 0.7 dated 2017-10-15

Title: Actual Evapotranspiration with Energy Balance Models
Description: Tools and functions to calculate actual Evapotranspiration using surface energy balance models.
Author: Guillermo Federico Olmedo [aut, cre], Samuel Ortega-Farías [aut], David Fonseca-Luengo [aut], Daniel de la Fuente-Sáiz [aut], Fernando Fuentes Peñailillo [aut], María Victoria Munafó [ctb]
Maintainer: Guillermo Federico Olmedo <guillermo.olmedo@gmail.com>

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Package sn updated to version 1.5-2 with previous version 1.5-1 dated 2017-11-22

Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package PieceExpIntensity updated to version 1.0.4 with previous version 1.0.2 dated 2018-03-28

Title: Bayesian Model to Find Changepoints Based on Rates and Count Data
Description: This function fits a reversible jump Bayesian piecewise exponential model that also includes the intensity of each event considered along with the rate of events.
Author: Andrew G. Chapple
Maintainer: Andrew G. Chapple <agc6@rice.edu>

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Package MARX updated to version 0.2 with previous version 0.1 dated 2017-06-16

Title: Simulation, Estimation, Model Selection and Forecasting for MARX Models
Description: Simulate, estimate (by t-MLE), select and forecast mixed causal-noncausal autoregressive models with possibly exogenous regressors, using methods proposed in Lanne and Saikkonen (2011) <doi:10.2202/1941-1928.1080> and Hecq et al. (2016) <doi:10.15609/annaeconstat2009.123-124.0307>.
Author: Sean Telg [aut, cre, cph], Alain Hecq [ctb], Lenard Lieb [ctb]
Maintainer: Sean Telg <j.telg@maastrichtuniversity.nl>

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Package mdmb updated to version 0.7-19 with previous version 0.6-17 dated 2018-02-16

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., including interaction or quadratic effects). Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package hrbrthemes updated to version 0.5.0 with previous version 0.1.0 dated 2017-02-26

Title: Additional Themes, Theme Components and Utilities for 'ggplot2'
Description: A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/> is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type> and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts are also included to support their respective typography-oriented themes.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Patrick Kennedy [ctb], Philipp Reiner [ctb], Dan Wilson [ctb] (Secondary axis support), Xavier Adam [ctb], Google [cph] (Roboto Condensed & Titillium Web Fonts), IBM [cph] (Plex Sans Font), Jacob Barnett [ctb], Thomas J. Leeper [ctb] (<https://orcid.org/0000-0003-4097-6326>)
Maintainer: Bob Rudis <bob@rud.is>

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Package bigrquery updated to version 1.0.0 with previous version 0.4.1 dated 2017-06-26

Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre], Kungliga Tekniska Högskolan [ctb] (strptime implementation), The NetBSD Foundation, Inc. [ctb] (gmtime implementation), RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package textclean updated to version 0.7.3 with previous version 0.7.2 dated 2018-04-19

Title: Text Cleaning Tools
Description: Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) <doi:10.1006/csla.2001.0169>) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The 'replace_emoticon()' function replaces emoticons with word equivalents.
Author: Tyler Rinker [aut, cre], ctwheels StackOverflow [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between textclean versions 0.7.2 dated 2018-04-19 and 0.7.3 dated 2018-04-24

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Package SNFtool updated to version 2.3.0 with previous version 2.2.1 dated 2017-11-24

Title: Similarity Network Fusion
Description: Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.
Author: Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg
Maintainer: Daniel Cole <goldenberglab@gmail.com>

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Permanent link

New package support with initial version 0.1.1
Package: support
Type: Package
Title: Support Points
Version: 0.1.1
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Description: Provides the function sp() for generating the support points proposed in Mak and Joseph (2017) <arXiv:1609.01811>. Support points are representative points of a possibly non-uniform distribution, and can be used as optimal sampling or integration points for a distribution of choice. The provided function sp() can be used to generate support points for standard distributions or for reducing big data (e.g., from Markov-chain Monte Carlo methods). A detailed description of the algorithm is found in Mak and Joseph (2017).
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.12.4), randtoolbox, matrixStats, doParallel, nloptr, MHadaptive
LinkingTo: Rcpp, RcppArmadillo, BH
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-04-24 05:40:31 UTC; Simon
X-CRAN-Comment: Archived on 2018-01-25 as requirement of OpenMP was not corrected despite reminders.
Repository: CRAN
Date/Publication: 2018-04-24 15:56:39 UTC

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Package sentimentr updated to version 2.3.2 with previous version 2.2.3 dated 2018-01-16

Title: Calculate Text Polarity Sentiment
Description: Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s).
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between sentimentr versions 2.2.3 dated 2018-01-16 and 2.3.2 dated 2018-04-24

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New package pmultinom with initial version 1.0.0
Package: pmultinom
Type: Package
Title: One-Sided Multinomial Probabilities
Version: 1.0.0
Author: Alexander Davis
Maintainer: Alexander Davis <ajdavis2@mdanderson.org>
Description: Implements multinomial CDF (P(N1<=n1, ..., Nk<=nk)) and tail probabilities (P(N1>n1, ..., Nk>nk)), as well as probabilities with both constraints (P(l1<N1<=u1, ..., lk<Nk<=uk)). Uses a method suggested by Bruce Levin (1981) <doi:10.1214/aos/1176345593>.
License: AGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: fftw
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-04-24 13:44:53 UTC; ajdavis2
Repository: CRAN
Date/Publication: 2018-04-24 15:42:54 UTC

More information about pmultinom at CRAN
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New package ivtools with initial version 1.0.0
Package: ivtools
Type: Package
Title: Instrumental Variables
Version: 1.0.0
Date: 2018-04-18
Author: Arvid Sjolander
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>
Description: Contains tools for instrumental variables estimation. Currently, only non-parametric bounds and two-stage least squares are implemented, but more methods will be added in the future. Balke, A. and Pearl, J. (1997) <doi:10.2307/2965583>, Vansteelandt S., Bowden J., Babanezhad M., Goetghebeur E. (2011) <doi:10.1214/11-STS360>.
License: LGPL (>= 3)
Imports: stats, data.table, numDeriv
NeedsCompilation: no
RoxygenNote: 6.0.1
Packaged: 2018-04-24 13:49:11 UTC; arvsjo
Repository: CRAN
Date/Publication: 2018-04-24 15:38:03 UTC

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Package epitrix updated to version 0.2.0 with previous version 0.1.2 dated 2018-03-01

Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymise data, and fitting discretised Gamma distributions.
Author: Thibaut Jombart [aut, cre], Anne Cori [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

Diff between epitrix versions 0.1.2 dated 2018-03-01 and 0.2.0 dated 2018-04-24

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More information about epitrix at CRAN
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New package diffeqr with initial version 0.1.0
Package: diffeqr
Type: Package
Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Version: 0.1.0
Authors@R: person("Christopher", "Rackauckas", email = "me@chrisrackauckas.com", role = c("aut", "cre"))
Description: An interface to 'DifferentialEquations.jl' from the R programming language. It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE), delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality, including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods. 'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users.
Depends: R (>= 3.4.0)
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: true
SystemRequirements: Julia (>= 0.6.0), DifferentialEquations.jl
Imports: JuliaCall, stringr
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-04-24 15:10:52 UTC; Chris
Author: Christopher Rackauckas [aut, cre]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>
Repository: CRAN
Date/Publication: 2018-04-24 15:52:33 UTC

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Package detrendr updated to version 0.5.1 with previous version 0.5.0 dated 2018-04-19

Title: Detrend Images
Description: Image series affected by bleaching must be corrected by 'detrending' prior to the performance of quantitative analysis. 'detrendr' is for correctly detrending images. It uses Nolan's algorithm (Nolan et al., 2017 <doi:10.1093/bioinformatics/btx434>).
Author: Rory Nolan [aut, cre, cph], Sergi Padilla-Parra [ths, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between detrendr versions 0.5.0 dated 2018-04-19 and 0.5.1 dated 2018-04-24

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Package nmfem updated to version 1.0.3 with previous version 1.0.2 dated 2018-04-23

Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for mix-models, reducing the numbers of parameters to estimate using Non-negative Matrix Factorization methods. For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>

Diff between nmfem versions 1.0.2 dated 2018-04-23 and 1.0.3 dated 2018-04-24

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Package VarReg updated to version 1.0.2 with previous version 1.0.1 dated 2017-05-30

Title: Semi-Parametric Variance Regression
Description: Methods for fitting semi-parametric mean and variance models, with normal or censored data. Also extended to allow a regression in the location, scale and shape parameters.
Author: Kristy Robledo [aut, cre], Ian Marschner [ths]
Maintainer: Kristy Robledo <robledo.kristy@gmail.com>

Diff between VarReg versions 1.0.1 dated 2017-05-30 and 1.0.2 dated 2018-04-24

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Package tstools updated to version 0.3.6.1 with previous version 0.3.6 dated 2018-03-13

Title: A Time Series Toolbox for Official Statistics
Description: Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
Author: Matthias Bannert [aut, cre], Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>

Diff between tstools versions 0.3.6 dated 2018-03-13 and 0.3.6.1 dated 2018-04-24

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Package provenance updated to version 2.0 with previous version 1.9 dated 2018-01-02

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances, and point-counting data with the chi-square distance. Also included are tools to plot compositional and point-counting data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between provenance versions 1.9 dated 2018-01-02 and 2.0 dated 2018-04-24

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New package ggplotify with initial version 0.0.2
Package: ggplotify
Title: Convert Plot to 'grob' or 'ggplot' Object
Version: 0.0.2
Authors@R: c(person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")))
Description: Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'grid', 'lattice', 'vcd' etc. by converting them to 'ggplot' objects.
Depends: R (>= 3.4.0)
Imports: ggplot2, graphics, grDevices, grid, gridGraphics, rvcheck
Suggests: colorspace, cowplot, ggimage, knitr, lattice, prettydoc, vcd
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
URL: https://github.com/GuangchuangYu/ggplotify
BugReports: https://github.com/GuangchuangYu/ggplotify/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-24 11:23:24 UTC; guangchuangyu
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Repository: CRAN
Date/Publication: 2018-04-24 12:13:50 UTC

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New package QTL.gCIMapping with initial version 1.0
Package: QTL.gCIMapping
Type: Package
Title: QTL Genome-Wide Composite Interval Mapping
Version: 1.0
Date: 2018-4-11
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo,Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Description: Conduct multi-Quantitative Trait Locus (QTL) mapping under the framework of random-QTL-effect mixed linear model. First, each position on the genome is detected in order to construct a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid or by adaptive lasso in F2, and true QTL are identified by likelihood radio test. Wang S-B, Wen Y-J, Ren W-L, Ni Y-L, Zhang J, Feng J-Y, Zhang Y-M (2016) <doi:10.1038/srep29951>.
Depends: MASS,qtl,doParallel,foreach,parallel
Imports: methods,openxlsx,stringr,data.table,parcor
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-04-24 09:21:52 UTC; abc
Repository: CRAN
Date/Publication: 2018-04-24 11:44:21 UTC

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Package survival updated to version 2.42-3.1 with previous version 2.42-3 dated 2018-04-16

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

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Package upwaver updated to version 1.1.0 with previous version 1.0.1 dated 2018-01-22

Title: Access 'Upwave' API
Description: 'Upwave' <https://www.upwave.io/> is a task management app organising tasks on boards and cards. 'upwaver' is a wrapper around the 'Upwave' API <https://upwavehq.github.io/api/> that allows listing and updating those boards and cards.
Author: Adrian Staempfli, Christoph Strauss, Fabian Leuthold, Michael Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>

Diff between upwaver versions 1.0.1 dated 2018-01-22 and 1.1.0 dated 2018-04-24

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Package RSMET updated to version 1.3.8 with previous version 1.2.9 dated 2016-03-17

Title: Get Real-Time Meteorological Data in SMET Format
Description: It manages snow and weather local time series as provided by MeteoIO (<http://models.slf.ch/docserver/meteoio/html/index.html>, <http:// www.slf.ch/ueber/organisation/schnee_permafrost/projekte/MeteoIO/index_EN>, <https://www.openhub.net/p/MeteoIO>). MeteoIO is a C/C++ Open Source library which has been designed to settle both the needs of carefully crafted simulations for a specific purpose/study and for the needs of operational simulations that run automatically and unattended". It is integrated in physical spatially-distributed models and tackles several issues with weather input/ output data. Here a SMET S4 class object is defined and can be imported from/ exported to a SMET ini files of MeteoIO , allowing interoperability from R to MeteoIO and other SMET-compliant software.
Author: Emanuele Cordano
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>

Diff between RSMET versions 1.2.9 dated 2016-03-17 and 1.3.8 dated 2018-04-24

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Package margins updated to version 0.3.20 with previous version 0.3.0 dated 2017-03-22

Title: Marginal Effects for Model Objects
Description: An R port of Stata's 'margins' command, which can be used to calculate marginal (or partial) effects from model objects.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>), Jeffrey Arnold [ctb], Vincent Arel-Bundock [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between margins versions 0.3.0 dated 2017-03-22 and 0.3.20 dated 2018-04-24

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Package immer updated to version 1.0-138 with previous version 0.8-5 dated 2017-04-27

Title: Item Response Models for Multiple Ratings
Description: Implements some item response models for multiple ratings, including the hierarchical rater model, conditional maximum likelihood estimation of linear logistic partial credit model and a wrapper function to the commercial FACETS program. See Robitzsch and Steinfeld (2018) for a description of the functionality of the package.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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New package fuzzyreg with initial version 0.2
Package: fuzzyreg
Title: Fuzzy Linear Regression
Version: 0.2
Date: 2018-04-23
Authors@R: c(person(given = "Pavel", family = "Skrabanek", email = "pavel.skrabanek@upce.cz", role = c("aut", "cph")), person(given = "Natalia", family = "Martinkova", email = "martinkova@ivb.cz", role = c("aut", "cre", "cph")))
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Description: Estimators for fuzzy linear regression. The functions estimates parameters of fuzzy linear regression models with crisp or fuzzy independent variables (triangular fuzzy numbers are supported). Implements multiple methods for parameter estimation and algebraic operations with triangular fuzzy numbers. Includes functions for summarising, printing and plotting the model fit. Calculates predictions from the model. Diamond (1988) <doi:10.1016/0020-0255(88)90047-3> Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004> Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98> Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008> Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: quadprog, limSolve, stats, graphics, grDevices
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-24 09:49:39 UTC; martinkova
Author: Pavel Skrabanek [aut, cph], Natalia Martinkova [aut, cre, cph]
Repository: CRAN
Date/Publication: 2018-04-24 10:30:00 UTC

More information about fuzzyreg at CRAN
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Package EpiCurve updated to version 2.1-1 with previous version 2.0-1 dated 2017-08-24

Title: Plot an Epidemic Curve
Description: Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>

Diff between EpiCurve versions 2.0-1 dated 2017-08-24 and 2.1-1 dated 2018-04-24

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Permanent link

New package cultevo with initial version 1.0.2
Package: cultevo
Title: Tools, Measures and Statistical Tests for Cultural Evolution
Version: 1.0.2
Date: 2018-04-24
Authors@R: person("Kevin Stadler", role=c("aut", "cre"), email="a00425926@unet.univie.ac.at")
Description: Provides tools for measuring the compositionality of signalling systems (in particular the information-theoretic measure due to Spike (2016) <http://hdl.handle.net/1842/25930> and the Mantel test for distance matrix correlation (after Dietz 1983) <doi:10.1093/sysbio/32.1.21>), functions for computing string and meaning distance matrices as well as an implementation of the Page test for monotonicity of ranks (Page 1963) <doi:10.1080/01621459.1963.10500843> with exact p-values up to k = 22.
URL: https://kevinstadler.github.io/cultevo/
BugReports: https://github.com/kevinstadler/cultevo/issues
Encoding: UTF-8
License: MIT + file LICENSE
Imports: combinat, grDevices, graphics, Hmisc, pspearman, stats, stringi, utils
Suggests: memoise, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-04-24 09:50:38 UTC; kevin
Author: Kevin Stadler [aut, cre]
Maintainer: Kevin Stadler <a00425926@unet.univie.ac.at>
Repository: CRAN
Date/Publication: 2018-04-24 10:28:19 UTC

More information about cultevo at CRAN
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Package BayesXsrc updated to version 3.0-1 with previous version 3.0-0 dated 2018-02-22

Title: R Package Distribution of the BayesX C++ Sources
Description: BayesX performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the BayesX command line tool for easy installation. A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre], Daniel Adler [aut], Thomas Kneib [aut], Stefan Lang [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tlinklst.cpp                            |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tpremat.cpp                             |   74 -
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/adjacency.cpp                           |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_dag.h                          |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_dag_ia.cpp                     |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_rj.cpp                         |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_rj_ia.cpp                      |  264 +--
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/main.cpp                                    |   17 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/distribution.cpp                       |  122 -
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/distribution_glasgow.cpp               |   84 -
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond.cpp                           |   10 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond_merror.cpp                    |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond_nonp_gaussian.cpp             |   10 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/gaussian_heteroskedastic.cpp           |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/hrandom.cpp                            |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmc_nonp.cpp                          |    8 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmc_nonpbasis.cpp                     |    7 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmcsimul2.cpp                         |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmcsimul2_multi.cpp                   |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect.cpp                       |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect_alt.cpp                   |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect_alt2.cpp                  |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/remlest_multi.h                        |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/remlest_multi2.h                       |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/tvariance.cpp                          |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/variance_nonp.cpp                      |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/IWLS_pspline.cpp                   |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/bsplinemat.cpp                     |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/fullcond_pspline_surf_gaussian.cpp |    3 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/mcmc_pspline.cpp                   |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/mcmc_pspline_surf.cpp              |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/spline_basis.cpp                   |   15 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/samson/multgaussian.cpp                     |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC.cpp                            |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC.h                              |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom.cpp                    |    5 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance.cpp           |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance_vec.cpp       |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance_vec_nmig.cpp  |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_linear.cpp                     |   12 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_mult.cpp                       |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_mult.h                         |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp.cpp                       |   96 +
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp.h                         |    9 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp_variance.cpp              |    5 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_predict.cpp                    |    3 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_variance_pen_vector.cpp        |   21 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design.cpp                        |   95 +
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design.h                          |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_kriging.cpp                |    3 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_userdefined.cpp            |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_userdefined.h              |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr.cpp                         |  703 +++++++++-
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr.h                           |  171 ++
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical.cpp             |   16 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical.h               |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical_mult.cpp        |   11 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical_mult.h          |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss.cpp                  |   27 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss.h                    |    2 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss_copula.cpp           |    8 
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss_nadja.cpp            |  180 +-
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/mcmcsim.cpp                       |   75 -
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/superbayesreg.cpp                 |  167 +-
 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/superbayesreg.h                   |    4 
 BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile                                          |    6 
 BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile.inner.win                                |only
 BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile.win                                      |  172 --
 BayesXsrc-3.0-1/BayesXsrc/src/install.libs.R                                        |    1 
 BayesXsrc-3.0-1/BayesXsrc/src/rel-Makefile                                          |    7 
 BayesXsrc-3.0-1/BayesXsrc/src/rel-Makefile.win                                      |    4 
 94 files changed, 1897 insertions(+), 1264 deletions(-)

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Package archivist updated to version 2.3.1 with previous version 2.3 dated 2018-02-19

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut], Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between archivist versions 2.3 dated 2018-02-19 and 2.3.1 dated 2018-04-24

 archivist-2.3.1/archivist/DESCRIPTION       |    9 ++----
 archivist-2.3.1/archivist/MD5               |   41 +++++-----------------------
 archivist-2.3.1/archivist/NAMESPACE         |    1 
 archivist-2.3.1/archivist/NEWS.md           |    4 ++
 archivist-2.3.1/archivist/R/alink.R         |    3 ++
 archivist-2.3.1/archivist/R/cache.R         |    4 +-
 archivist-2.3.1/archivist/R/saveToRepo.R    |   28 +++++++++++++++++--
 archivist-2.3.1/archivist/man/alink.Rd      |    3 ++
 archivist-2.3.1/archivist/man/saveToRepo.Rd |   16 ++++++----
 archivist-2.3/archivist/build               |only
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 13 files changed, 60 insertions(+), 49 deletions(-)

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New package CJAMP with initial version 0.1.0
Package: CJAMP
Type: Package
Title: Copula-Based Joint Analysis of Multiple Phenotypes
Version: 0.1.0
Authors@R: c( person("Stefan", "Konigorski", email = "stefan.konigorski@gmail.com", role = c("aut", "cre")), person("Yildiz E.", "Yilmaz", email = "yyilmaz@mun.ca", role = c("ctb", "ths")))
Description: We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2018, submitted). C-JAMP allows estimating and testing the association of one or multiple predictors on multiple outcomes in a joint model, and is implemented here with a focus on large-scale genome-wide association studies with two phenotypes. The use of copula functions allows modeling a wide range of multivariate dependencies between the phenotypes, and previous results are supporting that C-JAMP can increase the power of association studies to identify associated genetic variants in comparison to existing methods (Konigorski, Yilmaz, Pischon, 2016, <DOI:10.1186/s12919-016-0045-6>; Konigorski, Yilmaz, Bull, 2014, <DOI:10.1186/1753-6561-8-S1-S72>). In addition to the C-JAMP functions, functions are available to generate genetic and phenotypic data, to compute the minor allele frequency (MAF) of genetic markers, and to estimate the phenotypic variance explained by genetic markers.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Imports: stats, optimx
Suggests: MASS, knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-24 09:40:12 UTC; skonigor
Author: Stefan Konigorski [aut, cre], Yildiz E. Yilmaz [ctb, ths]
Maintainer: Stefan Konigorski <stefan.konigorski@gmail.com>
Repository: CRAN
Date/Publication: 2018-04-24 10:00:42 UTC

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Package SourceSet updated to version 0.1.1 with previous version 0.1.0 dated 2018-02-28

Title: A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways
Description: The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')').
Author: Elisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>

Diff between SourceSet versions 0.1.0 dated 2018-02-28 and 0.1.1 dated 2018-04-24

 DESCRIPTION             |    8 ++++----
 MD5                     |   12 ++++++------
 R/mainFunctions.R       |    6 ++++++
 inst/doc/SourceSet.R    |    8 +++++++-
 inst/doc/SourceSet.Rmd  |    8 +++++++-
 inst/doc/SourceSet.html |   24 ++++++++++++++++--------
 vignettes/SourceSet.Rmd |    8 +++++++-
 7 files changed, 53 insertions(+), 21 deletions(-)

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New package panelView with initial version 1.0.1
Package: panelView
Type: Package
Title: Visualizing Panel Data with Dichotomous Treatments
Version: 1.0.1
Date: 2018-04-23
Author: Licheng Liu, Yiqing Xu
Maintainer: Yiqing Xu <yiqingxu@ucsd.edu>
Description: Visualizes panel data with dichotomous treatments. 'panelView' has two main functionalities: (1) it visualizes the treatment and missing-value statuses of each observation in a panel/time-series-cross-sectional (TSCS) dataset; and (2) it plots the outcome variable (either continuous or discrete) in a time-series fashion.
URL: http://yiqingxu.org/software/panelView/panelView.html
License: GPL-2
Imports: ggplot2 (>= 2.1.0), gridExtra, grid
Depends: R (>= 2.10)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-23 17:17:44 UTC; xyq
Repository: CRAN
Date/Publication: 2018-04-24 08:33:49 UTC

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New package imdbapi with initial version 0.1.0
Package: imdbapi
Title: Get Movie, Television Data from the 'imdb' Database
Version: 0.1.0
Author: Daxuan Deng Yuan Li
Maintainer: Yuan Li <851277048@qq.com>
Description: Provides API access to the <http://imdbapi.net> which maintains metadata about movies, games and television shows through a public API.
Depends: R (>= 3.1.1)
License: GPL-3
Imports: httr, dplyr, stringr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-23 11:49:25 UTC; Kevin
Repository: CRAN
Date/Publication: 2018-04-24 08:11:08 UTC

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New package frambgrowth with initial version 0.1.0
Package: frambgrowth
Version: 0.1.0
Title: Simulation of the Growth of Framboidal and Sunflower Pyrite
Authors@R: c(person(given = "Raul", family = "Merinero", role = c("aut","cre"), email = "rmeriner@ucm.es"), person(given = "Victor", family = "Cardenes", role = "aut"))
Description: Generation of theoretical size distributions of framboidal or sunflower pyrite. The growth mechanisms used are surface and supply controlled and dependent or independent of size. The algorithms are fully described in the published work in Mineralogy and Petrology journal: "Theoretical growth of framboidal and sunflower pyrite using the R-package frambgrowth" The authors Merinero, R., and Cardenes, V. (2018). <DOI:10.1007/s00710-017-0535-x>.
LazyLoad: yes
LazyData: yes
License: GPL-2
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-04-23 16:55:06 UTC; Raul
Maintainer: Raul Merinero <rmeriner@ucm.es>
Author: Raul Merinero [aut, cre], Victor Cardenes [aut]
Repository: CRAN
Date/Publication: 2018-04-24 08:27:02 UTC

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New package EMVS with initial version 1.0
Package: EMVS
Type: Package
Title: The Expectation-Maximization Approach to Bayesian Variable Selection
Version: 1.0
Date: 2018-04-23
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gmoran@wharton.upenn.edu>
Description: An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization paths for linear regression. Rockova and George (2014) <doi:10.1080/01621459.2013.869223>.
License: GPL-3
URL: https://doi.org/10.1080/01621459.2013.869223
Imports: Rcpp (>= 0.12.16)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-04-23 12:02:47 UTC; gem
Repository: CRAN
Date/Publication: 2018-04-24 08:13:33 UTC

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Package DDD updated to version 3.7 with previous version 3.6 dated 2018-02-07

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>

Diff between DDD versions 3.6 dated 2018-02-07 and 3.7 dated 2018-04-24

 DESCRIPTION          |   12 -
 MD5                  |   39 +++---
 NAMESPACE            |    5 
 R/dd_KI_loglik.R     |    6 
 R/dd_LR.R            |   16 +-
 R/dd_ML.R            |    1 
 R/dd_SR_loglik.R     |   24 ---
 R/dd_loglik.R        |  102 +++++++++++++--
 R/dd_loglik_M.R      |   12 +
 R/dd_loglik_bw_rhs.R |   83 ++----------
 R/dd_loglik_rhs.R    |  149 +++++++++++++----------
 R/dd_utils.R         |   17 ++
 R/td_sim.R           |  328 +++++++++++++++++++++++++--------------------------
 man/DDD-internal.Rd  |    8 +
 man/DDD-package.Rd   |    8 -
 man/dd_KI_ML.Rd      |    5 
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 21 files changed, 454 insertions(+), 375 deletions(-)

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Package aroma.core updated to version 3.1.2 with previous version 3.1.1 dated 2017-09-13

Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between aroma.core versions 3.1.1 dated 2017-09-13 and 3.1.2 dated 2018-04-24

 DESCRIPTION                                                 |   12 
 MD5                                                         |  389 
 NAMESPACE                                                   |    3 
 NEWS                                                        | 6001 ++++++------
 R/006.fixVarArgs.R                                          |   46 
 R/008.BioC.R                                                |   32 
 R/009.setup.R                                               |   66 
 R/998.AromaPackage.R                                        |   70 
 R/999.AromaCore.R                                           |   19 
 R/999.DEPRECATED.R                                          |   52 
 R/999.NonDocumentedObjects.R                                |    6 
 R/AbstractCNData.R                                          |   99 
 R/AbstractPSCNData.R                                        |  105 
 R/Arguments.EXTRAS.R                                        |   26 
 R/AromaCellCpgFile.R                                        |  101 
 R/AromaCellPositionFile.R                                   |  324 
 R/AromaCellSequenceFile.R                                   | 1842 +--
 R/AromaCellSequenceFile.REPEATS.R                           |  310 
 R/AromaCellSequenceFile.SNPs.R                              |  728 -
 R/AromaCellTabularBinaryFile.R                              |   58 
 R/AromaGenomeTextFile.R                                     |  115 
 R/AromaMicroarrayDataFile.ATTRS.R                           |  137 
 R/AromaMicroarrayDataFile.PLOT.R                            |   48 
 R/AromaMicroarrayDataFile.R                                 |   23 
 R/AromaMicroarrayDataSet.ATTRS.R                            |  204 
 R/AromaMicroarrayDataSet.EXT.R                              |   42 
 R/AromaMicroarrayDataSet.R                                  |   30 
 R/AromaMicroarrayDataSetTuple.R                             |  165 
 R/AromaMicroarrayTabularBinaryFile.R                        |  433 
 R/AromaNnn.getRootName.R                                    |   21 
 R/AromaPlatform.R                                           |   13 
 R/AromaPlatformInterface.R                                  |  202 
 R/AromaRepository.R                                         | 1202 +-
 R/AromaSettings.R                                           |  163 
 R/AromaTabularBinaryFile.R                                  | 2723 ++---
 R/AromaTabularBinarySet.ATTRS.R                             |  257 
 R/AromaTabularBinarySet.R                                   |   17 
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 R/AromaUcscGenomeTextFile.R                                 |   16 
 R/AromaUflFile.R                                            |  534 -
 R/AromaUgpFile.R                                            |  475 
 R/AromaUgpFile.plotCoverageMap.R                            |   62 
 R/AromaUnitCallFile.R                                       |  283 
 R/AromaUnitCallSet.R                                        |   37 
 R/AromaUnitChromosomeTabularBinaryFile.R                    |  392 
 R/AromaUnitFracBCnBinaryFile.R                              |   14 
 R/AromaUnitFracBCnBinarySet.R                               |   28 
 R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R            |  374 
 R/AromaUnitGcContentFile.R                                  |   73 
 R/AromaUnitGenotypeCallFile.R                               |  898 -
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 R/AromaUnitTotalCnBinaryFile.R                              |  168 
 R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R             |   89 
 R/AromaUnitTotalCnBinaryFile.xam.R                          |  183 
 R/AromaUnitTotalCnBinaryFileList.R                          |  448 
 R/AromaUnitTotalCnBinarySet.R                               |  710 -
 R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R  |  204 
 R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R         |  524 -
 R/AromaUnitTotalCnBinarySetTuple.R                          |   19 
 R/AromaUnitTypesFile.R                                      |   49 
 R/BasicObject.asThis.R                                      |   23 
 R/BinnedScatter.R                                           |  454 
 R/CacheKeyInterface.R                                       |   13 
 R/CbsModel.R                                                |   36 
 R/CbsSegmentationDataFile.R                                 |   16 
 R/CbsSegmentationDataSet.R                                  |   22 
 R/ChromosomalModel.R                                        | 1563 +--
 R/ChromosomalModel.drawCytoband.R                           |  177 
 R/ChromosomeExplorer.LAYERS.R                               |  250 
 R/ChromosomeExplorer.R                                      | 1318 +-
 R/CopyNumberChromosomalModel.R                              | 2507 ++---
 R/CopyNumberChromosomalModel.newPlot.R                      |   44 
 R/CopyNumberChromosomalModel.plotChromosomesLayers.R        |  610 -
 R/CopyNumberChromosomalModel.plotFitLayers.R                |  436 
 R/CopyNumberChromosomalModel.plotRawCopyNumbers.R           |  223 
 R/CopyNumberChromosomalModel.plotSampleLayers.R             |  468 
 R/CopyNumberDataSetTuple.R                                  |   68 
 R/CopyNumberOutliers.FOREIGN.R                              |   47 
 R/CopyNumberOutliers.R                                      |   68 
 R/CopyNumberRegions.EXT.R                                   |  186 
 R/CopyNumberRegions.EXT2.R                                  |   36 
 R/CopyNumberRegions.PLOT.R                                  |   12 
 R/CopyNumberRegions.R                                       |  197 
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More information about aroma.core at CRAN
Permanent link

Package FRegSigCom updated to version 0.2.1 with previous version 0.1.0 dated 2017-09-06

Title: Functional Regression using Signal Compression Approach
Description: Signal compression methods for function-on-function (FOF) regression with functional response and functional predictors, including linear models with both scalar and functional predictors for a small number of functional predictors, linear models with functional predictors for a large number of functional predictors, stepwise selection for FOF models with two-way interactions, and nonlinear models. References are linked to via the URL below.
Author: Ruiyan Luo, Xin Qi
Maintainer: Ruiyan Luo <rluo@gsu.edu>

Diff between FRegSigCom versions 0.1.0 dated 2017-09-06 and 0.2.1 dated 2018-04-24

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Permanent link

Package dglars updated to version 2.0.1 with previous version 2.0.0 dated 2017-02-28

Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

Diff between dglars versions 2.0.0 dated 2017-02-28 and 2.0.1 dated 2018-04-24

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Permanent link

Package lexicon updated to version 1.0.0 with previous version 0.7.4 dated 2018-01-13

Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre, cph], University of Notre Dame [dtc, cph], Department of Knowledge Technologies [dtc, cph], Unicode, Inc. [dtc, cph], John Higgins [dtc, cph], Grady Ward [dtc], Heiko Possel [dtc], Michal Boleslav Mechura [dtc, cph], Bing Liu [dtc], Minqing Hu [dtc], Saif M. Mohammad [dtc], Peter Turney [dtc], Erik Cambria [dtc], Soujanya Poria [dtc], Rajiv Bajpai [dtc], Bjoern Schuller [dtc], SentiWordNet [dtc, cph], Liang Wu [dtc, cph], Fred Morstatter [dtc, cph], Huan Liu [dtc, cph], Grammar Revolution [dtc, cph], Vidar Holen [dtc, cph], Alejandro U. Alvarez [dtc, cph], Stackoverflow User user2592414 [dtc, cph], BannedWordList.com [dtc, cph], Apache Software Foundation [dtc, cph], Andrew Kachites McCallum [dtc, cph], Alireza Savand [dtc, cph]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between lexicon versions 0.7.4 dated 2018-01-13 and 1.0.0 dated 2018-04-24

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More information about lexicon at CRAN
Permanent link

Package languageserver updated to version 0.2.0 with previous version 0.1.0 dated 2018-03-01

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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 languageserver-0.2.0/languageserver/R/handlers-langfeatures.R   |    9 
 languageserver-0.2.0/languageserver/R/handlers-textsync.R       |   18 -
 languageserver-0.2.0/languageserver/R/handlers-workspace.R      |    8 
 languageserver-0.2.0/languageserver/R/languageserver.R          |  138 +++++----
 languageserver-0.2.0/languageserver/R/signature.R               |    2 
 languageserver-0.2.0/languageserver/R/utils.R                   |   37 ++
 languageserver-0.2.0/languageserver/R/workspace.R               |  140 +++++-----
 languageserver-0.2.0/languageserver/README.md                   |   25 +
 languageserver-0.2.0/languageserver/man/workspace_sync.Rd       |    6 
 languageserver-0.2.0/languageserver/src/languageserver.c        |    9 
 languageserver-0.2.0/languageserver/tests/testthat/test_queue.R |   23 -
 21 files changed, 318 insertions(+), 200 deletions(-)

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Package iterpc updated to version 0.4.0 with previous version 0.3.4 dated 2017-12-06

Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They can be either drawn with or without replacement, or with distinct/ non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer being maintained. Users are recommended to switch to 'arrangements'.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between iterpc versions 0.3.4 dated 2017-12-06 and 0.4.0 dated 2018-04-24

 iterpc-0.3.4/iterpc/R/RcppExports.R            |only
 iterpc-0.3.4/iterpc/src                        |only
 iterpc-0.4.0/iterpc/DESCRIPTION                |   16 -
 iterpc-0.4.0/iterpc/MD5                        |   35 --
 iterpc-0.4.0/iterpc/NAMESPACE                  |    4 
 iterpc-0.4.0/iterpc/R/combination.R            |   53 ---
 iterpc-0.4.0/iterpc/R/iterpc.R                 |   84 ++----
 iterpc-0.4.0/iterpc/R/permutation.R            |   53 ---
 iterpc-0.4.0/iterpc/README.md                  |    4 
 iterpc-0.4.0/iterpc/build/vignette.rds         |binary
 iterpc-0.4.0/iterpc/inst/doc/combinations.html |  336 +++++++++++++++++++-----
 iterpc-0.4.0/iterpc/inst/doc/permutations.html |  349 ++++++++++++++++++++-----
 12 files changed, 618 insertions(+), 316 deletions(-)

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Package arulesViz updated to version 1.3-1 with previous version 1.3-0 dated 2017-09-09

Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler [aut, cre, cph], Giallanza Tyler [ctb], Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between arulesViz versions 1.3-0 dated 2017-09-09 and 1.3-1 dated 2018-04-24

 DESCRIPTION             |   24 ++-
 MD5                     |   38 +++--
 NAMESPACE               |   22 +--
 NEWS.md                 |   16 ++
 R/AAAhelpers.R          |    8 -
 R/graph.R               |    2 
 R/matrix.R              |   25 +++
 R/plot.R                |   20 ++-
 R/plotly.R              |   64 +++++++--
 R/scatterplot.R         |    6 
 R/shiny.R               |only
 README.md               |   10 -
 build/vignette.rds      |binary
 inst/doc/arulesViz.R    |  125 ++++++------------
 inst/doc/arulesViz.Rnw  |  317 ++++++++++++++++++++----------------------------
 inst/doc/arulesViz.pdf  |binary
 man/plot.Rd             |   20 +--
 man/plotly_arules.Rd    |    2 
 man/shiny.Rd            |only
 vignettes/arulesViz.Rnw |  317 ++++++++++++++++++++----------------------------
 vignettes/arulesViz.bib |   24 +++
 21 files changed, 522 insertions(+), 518 deletions(-)

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