Tue, 12 Nov 2019

Package metR updated to version 0.5.0 with previous version 0.4.0 dated 2019-07-08

Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>

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Package ctrdata updated to version 1.1 with previous version 1.0.1 dated 2019-10-23

Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analysing protocol- and results-related information on clinical trials from two public registers, the European Union Clinical Trials Register (EUCTR, <https://www.clinicaltrialsregister.eu/>) and ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The information is transformed and then stored in a database (nodbi). Functions are provided for accessing and analysing the locally stored information on the clinical trials, as well as for identifying duplicate records. The package is motivated by the need for aggregating and trend-analysing the design, conduct and outcomes across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

Diff between ctrdata versions 1.0.1 dated 2019-10-23 and 1.1 dated 2019-11-12

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Package R6 updated to version 2.4.1 with previous version 2.4.0 dated 2019-02-14

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

Diff between R6 versions 2.4.0 dated 2019-02-14 and 2.4.1 dated 2019-11-12

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Package eq5d updated to version 0.4.0 with previous version 0.3.0 dated 2019-09-13

Title: Methods for Calculating 'EQ-5D' Utility Index Scores
Description: EQ-5D is a popular health related quality of life instrument used in the clinical and economic evaluation of health care. Developed by the EuroQol group <https://www.euroqol.org>, the instrument consists of two components: health state description and evaluation. For the description component a subject self-rates their health in terms of five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression using either a three-level (EQ-5D-3L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-3l-about>) or a five-level (EQ-5D-5L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-5l-about>) scale. Frequently the scores on these five dimensions are converted to a single utility index using country specific value sets, which can be used in the clinical and economic evaluation of health care as well as in population health surveys. The eq5d package provides methods to calculate index scores from a subject's dimension scores. 25 TTO and 11 VAS EQ-5D-3L value sets including those for countries in Szende et al (2007) <doi:10.1007/1-4020-5511-0> and Szende et al (2014) <doi:10.1007/978-94-007-7596-1>, 18 EQ-5D-5L EQ-VT value sets from the EuroQol website, and the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008> are included. Additionally, a shiny web tool is included to enable the calculation and visualisation of EQ-5D index values via a web browser using EQ-5D dimension scores stored in CSV or Excel files.
Author: Fraser Morton [aut, cre], Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>

Diff between eq5d versions 0.3.0 dated 2019-09-13 and 0.4.0 dated 2019-11-12

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Package schoRsch updated to version 1.7 with previous version 1.6 dated 2019-05-02

Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>

Diff between schoRsch versions 1.6 dated 2019-05-02 and 1.7 dated 2019-11-12

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Package knitr updated to version 1.26 with previous version 1.25 dated 2019-09-18

Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between knitr versions 1.25 dated 2019-09-18 and 1.26 dated 2019-11-12

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Package ehelp updated to version 1.1 with previous version 1.0 dated 2019-10-18

Title: Enhanced Help to Enable "Docstring"-Comments in Users Functions
Description: By overloading the R help() function, this package allows users to use "docstring" style comments within their own defined functions.
Author: Marcelo Ponce [aut, cre]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>

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Package unmarked updated to version 0.13-0 with previous version 0.12-3 dated 2019-02-05

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson, Adam Smith, Ken Kellner
Maintainer: Andy Royle <aroyle@usgs.gov>

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Package rqdatatable updated to version 1.2.4 with previous version 1.2.3 dated 2019-10-24

Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between rqdatatable versions 1.2.3 dated 2019-10-24 and 1.2.4 dated 2019-11-12

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Package imagefx updated to version 0.3.0 with previous version 0.2.0 dated 2019-09-13

Title: Extract Features from Images
Description: Synthesize images into characteristic features for time-series analysis or machine learning applications. The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity. However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.
Author: Alex J.C. Witsil
Maintainer: Alex J.C. Witsil <alexjcwitsil@gmail.com>

Diff between imagefx versions 0.2.0 dated 2019-09-13 and 0.3.0 dated 2019-11-12

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Package BIGDAWG updated to version 2.3 with previous version 2.1 dated 2018-02-08

Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>

Diff between BIGDAWG versions 2.1 dated 2018-02-08 and 2.3 dated 2019-11-12

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Package readJDX updated to version 0.4.29 with previous version 0.3.250 dated 2018-10-15

Title: Import Data in the JCAMP-DX Format
Description: Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package freesurferformats updated to version 0.1.5 with previous version 0.1.4 dated 2019-11-06

Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>

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Package flextable updated to version 0.5.6 with previous version 0.5.5 dated 2019-06-25

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents. Functions are provided to let users create tables, modify and format their content. It extends package 'officer' that does not contain any feature for customized tabular reporting and can be used within R markdown documents.
Author: David Gohel [aut, cre], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] (rmarkdown for docx output), Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package DT updated to version 0.10 with previous version 0.9 dated 2019-09-17

Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre], Joe Cheng [aut], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib), SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between DT versions 0.9 dated 2019-09-17 and 0.10 dated 2019-11-12

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Package DiffXTables updated to version 0.0.2 with previous version 0.0.1 dated 2019-11-04

Title: Pattern Heterogeneity via Distributional Differences Across Contingency Tables
Description: Statistical hypothesis testing of pattern heterogeneity via differences in underlying distributions across two or more contingency tables. Three tests are included: the comparative chi-squared test (Song et al, 2014) <doi:10.1093/nar/gku086> (Zhang et al, 2015) <doi:10.1093/nar/gkv358>, the Sharma-Song test, and the heterogeneity test. Under the null hypothesis that row and column variables are statistically independent and joint distributions are equal, their test statistics all follow an asymptotically chi-squared distribution. These options test for heterogeneous patterns that differ in either the first order (marginal) or the second order (joint distribution deviation from product of marginals). Second-order differences may reveal more fundamental changes than first-order differences across heterogeneous patterns.
Author: Ruby Sharma [aut], Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package deTestSet updated to version 1.1.7 with previous version 1.1.6 dated 2019-08-21

Title: Test Set for Differential Equations
Description: Solvers and test set for stiff and non-stiff differential equations, and differential algebraic equations. 'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
Author: Karline Soetaert [aut, cre], Jeff Cash [aut], Francesca Mazzia [aut], Ernst Hairer [ctb] (files dopri8.f, dopri6.f), Gerard Wanner [ctb] (files dopri8.f, dopri6.f), T. Abdulla [ctb] (file mebdfi.f), Cecilia Magherini [ctb] (files bimd.f, bimda.f), Luigi Brugnano [ctb] (files bimd.f, bimda.f), Cleve Moler [ctb] (file bimda.f)
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

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Package bookdown updated to version 0.15 with previous version 0.14 dated 2019-10-01

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>), Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Ellis Valentiner [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Noam Ross [ctb], Peter Hickey [ctb], Romain Lesur [ctb] (<https://orcid.org/0000-0002-0721-5595>), Sahir Bhatnagar [ctb], Steve Simpson [ctb], Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), Zeno Rocha [cph] (clipboard.js library), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

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Package xfun updated to version 0.11 with previous version 0.10 dated 2019-10-01

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package sen2r updated to version 1.2.1 with previous version 1.1.0 dated 2019-10-21

Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images and perform preliminary processing operations. 'sen2r' provides the instruments required to easily perform (and eventually automate) the steps necessary to build a complete Sentinel-2 processing chain. A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>), Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>

Diff between sen2r versions 1.1.0 dated 2019-10-21 and 1.2.1 dated 2019-11-12

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Package rticles updated to version 0.12 with previous version 0.11 dated 2019-10-01

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph] (<https://orcid.org/0000-0002-8319-7624>), Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>), MDPI [aut, cph], Taylor and Francis [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>), Petter Uvesten [aut, cph], Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>), John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package roxygen2 updated to version 7.0.0 with previous version 6.1.1 dated 2018-11-07

Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and collation field using specially formatted comments. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. 'Roxygen2' is inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph] (<https://orcid.org/0000-0003-4757-117X>), Peter Danenberg [aut, cph], Gábor Csárdi [aut], Manuel Eugster [aut, cph], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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New package Rmst with initial version 0.0.3
Package: Rmst
Type: Package
Title: Computerized Adaptive Multistage Testing
Version: 0.0.3
Date: 2019-11-12
Authors@R: c(person("Xiao", "Luo", role=c("aut","cre"), email="xluo1986@gmail.com"))
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Description: Assemble the panels of computerized adaptive multistage testing by the bottom-up and the top-down approach, and simulate the administration of the assembled panels. The full documentation and tutorials are at <https://github.com/xluo11/Rmst>. Reference: Luo and Kim (2018) <doi:10.1111/jedm.12174>.
License: GPL (>= 3)
Depends: R (>= 3.6.0)
URL: https://github.com/xluo11/Rmst
BugReports: https://github.com/xluo11/Rmst/issues
Imports: ggplot2, Rata, reshape2, Rirt, stats
Suggests: testthat
RoxygenNote: 6.1.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-11-12 16:40:10 UTC; Luo.Xiao
Repository: CRAN
Date/Publication: 2019-11-12 17:30:15 UTC

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Package rFIA updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-28

Title: Space-Time Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatio-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson (2005) <doi:10.2737/SRS-GTR-80>, and has been validated against estimates and sampling errors produced by FIA 'EVALIDator'. Current development is focused on the implementation of spatially-enabled model-assisted estimators to improve population, change, and ratio estimates.
Author: Hunter Stanke [aut, cre], Andrew Finley [aut]
Maintainer: Hunter Stanke <stankehu@msu.edu>

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Package ows4R updated to version 0.1-4 with previous version 0.1-3 dated 2019-11-05

Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service (WFS) for vector data, Catalogue Service (CSW) for ISO/OGC metadata and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. The long-term purpose is to add support for additional OGC service standards such as Web Coverage Service (WCS) and Web Processing Service (WPS).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>), Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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New package bujar with initial version 0.2-7
Package: bujar
Type: Package
Title: Buckley-James Regression for Survival Data with High-Dimensional Covariates
Version: 0.2-7
Date: 2019-11-12
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <wangz1@uthscsa.edu>
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.
Imports: mda, mpath, mboost, gbm, earth, elasticnet, rms, methods, modeltools, bst, parallel, survival
Depends: R (>= 2.10)
Suggests: TH.data, R.rsp, gridExtra
VignetteBuilder: R.rsp
License: GPL-2
LazyLoad: yes
Packaged: 2019-11-12 17:40:08 UTC; zhu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2019-11-12 18:00:02 UTC

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Package testit updated to version 0.11 with previous version 0.10 dated 2019-10-01

Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package Rmagic updated to version 2.0.0 with previous version 1.4.0 dated 2018-11-24

Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.
Author: David van Dijk [aut], Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>

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Package pagedown updated to version 0.6 with previous version 0.5 dated 2019-10-01

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>), Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), RStudio, Inc. [cph], Adam Hyde [ctb] (paged.js in resources/js/), Min-Zhong Lu [ctb] (resume.css in resources/css/), Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>

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Package RxODE updated to version 0.9.1-8 with previous version 0.9.1-7 dated 2019-10-27

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>), Melissa Hallow [aut], Wenping Wang [aut, cre], Zufar Mulyukov [ctb], Justin Wilkins [ctb] (<https://orcid.org/0000-0002-7099-9396>), Simon Frost [ctb], Goro Fuji [ctb], Morwenn [ctb], Heng Li [ctb], Yu Feng [ctb], Alan Hindmarsh [ctb], Linda Petzold [ctb], Ernst Hairer [ctb], Gerhard Wanner [ctb], J Colinge [ctb], Hadley Wickham [ctb], G Grothendieck [ctb], Robert Gentleman [ctb], Daniel C. Dillon [ctb], Ross Ihaka [ctb], Cleve Moler [ctb], Jack Dongarra [ctb], R core team [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>

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Package palasso updated to version 0.0.6 with previous version 0.0.5 dated 2019-04-19

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 <armin.rauschenberger@uni.lu>

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Package FuzzyR updated to version 2.2 with previous version 2.1 dated 2017-03-24

Title: Fuzzy Logic Toolkit for R
Description: Design and simulate fuzzy logic systems using Type-1 and Interval Type-2 Fuzzy Logic. This toolkit includes with graphical user interface (GUI) and an adaptive neuro- fuzzy inference system (ANFIS). This toolkit is a continuation from the previous package ('FuzzyToolkitUoN'). Produced by the Intelligent Modelling & Analysis Group (IMA) and Lab for UnCertainty In Data and decision making (LUCID), University of Nottingham.
Author: Chao Chen, Jon Garibaldi, Tajul Razak
Maintainer: Chao Chen <fuzzyr@cs.nott.ac.uk>

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New package RAINBOWR with initial version 0.1.13
Package: RAINBOWR
Type: Package
Title: Genome-Wide Association Study with SNP-Set Methods
Version: 0.1.13
Authors@R: c( person("Kosuke", "Hamazaki", email = "hamazaki@ut-biomet.org", role = c("aut", "cre")), person("Hiroyoshi", "Iwata", email = "aiwata@mail.ecc.u-tokyo.ac.jp", role = c("aut", "ctb")) )
Maintainer: Kosuke Hamazaki <hamazaki@ut-biomet.org>
Description: By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our preprint on bioRxiv: Kosuke Hamazaki and Hiroyoshi Iwata (2019) <doi:10.1101/612028>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: Rcpp, rrBLUP, rgl, tcltk, Matrix, cluster, MASS, pbmcapply, optimx, methods
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-11-08 08:34:30 UTC; hamazaki
Author: Kosuke Hamazaki [aut, cre], Hiroyoshi Iwata [aut, ctb]
Repository: CRAN
Date/Publication: 2019-11-12 12:30:02 UTC

More information about RAINBOWR at CRAN
Permanent link

New package AzureCognitive with initial version 1.0.0
Package: AzureCognitive
Title: Interface to Azure Cognitive Services
Version: 1.0.0
Authors@R: c( person("Hong", "Ooi", , "hongooi@microsoft.com", role = c("aut", "cre")), person("Microsoft", role="cph") )
Description: An interface to Azure Cognitive Services <https://docs.microsoft.com/azure/cognitive-services/welcome>. Both an 'Azure Resource Manager' interface, for deploying Cognitive Services resources, and a client framework are supplied. While 'AzureCognitive' can be called by the end-user, it is meant to provide a foundation for other packages that will support specific services, like Computer Vision, Custom Vision, language translation, and so on. Part of the 'AzureR' family of packages.
URL: https://github.com/Azure/AzureCognitive https://github.com/Azure/AzureR
BugReports: https://github.com/Azure/AzureCognitive/issues
License: MIT + file LICENSE
Depends: R (>= 3.3)
Imports: AzureAuth (>= 1.2.0), AzureRMR, jsonlite, httr (>= 1.3),
Suggests: knitr, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-11-10 16:09:59 UTC; hongo
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Repository: CRAN
Date/Publication: 2019-11-12 12:50:02 UTC

More information about AzureCognitive at CRAN
Permanent link

Package rsimsum updated to version 0.7.0 with previous version 0.6.1 dated 2019-09-12

Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (White I.R., 2010 <http://www.stata-journal.com/article.html?article=st0200>), further extending it with additional functionality.
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Ian R. White [aut]
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

Diff between rsimsum versions 0.6.1 dated 2019-09-12 and 0.7.0 dated 2019-11-12

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Permanent link

Package RcppAnnoy updated to version 0.0.14 with previous version 0.0.13 dated 2019-09-23

Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppAnnoy versions 0.0.13 dated 2019-09-23 and 0.0.14 dated 2019-11-12

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New package Jaya with initial version 0.1.9
Package: Jaya
Type: Package
Title: Jaya, a Gradient-Free Optimization Algorithm
Version: 0.1.9
Authors@R: c(person(given = "Mayur", family = "Shende", role = c("aut")), person(given = "Neeraj", family = "Bokde", role = c("aut", "cre"), email = "neerajdhanraj@gmail.com", comment = c(ORCID = "0000-0002-3493-9302")))
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Description: Maximization or Minimization of a fitness function using Jaya Algorithm (JA). A population based method which repeatedly modifies a population of individual solutions. Capable of solving both constrained and unconstrained optimization problems. It does not contain any hyperparameters. For further details: R.V. Rao (2016) <doi:10.5267/j.ijiec.2015.8.004> .
License: GPL (>= 2)
Suggests: knitr, rmarkdown, evaluate, testthat
Imports: GA
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-11-08 13:19:57 UTC; au644200
Author: Mayur Shende [aut], Neeraj Bokde [aut, cre] (<https://orcid.org/0000-0002-3493-9302>)
Repository: CRAN
Date/Publication: 2019-11-12 11:20:02 UTC

More information about Jaya at CRAN
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Package gtsummary updated to version 1.2.3 with previous version 1.2.2 dated 2019-11-10

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers. The package is enhanced when the 'gt' package is installed. Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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More information about gtsummary at CRAN
Permanent link

New package DealGPL570 with initial version 0.0.1
Package: DealGPL570
Title: Dealing GPL570 RAW.tar file
Version: 0.0.1
Authors@R: c(person("Nan", "Zhang", email = "15776658849@163.com", role = "cre"), person("YaKun", "Zhang", email = "15776452861@163.com", role = "aut"))
Description: Dealing GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array) RAW.tar file using the robust multi-array average expression measure and returning expression profile.
Depends: R (>= 3.5.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Imports: dplyr, stringr, GEOquery, affy, tibble
Suggests: BiocGenerics, knitr, rmarkdown, spelling
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2019-11-08 14:11:35 UTC; ZN
Author: Nan Zhang [cre], YaKun Zhang [aut]
Maintainer: Nan Zhang <15776658849@163.com>
Repository: CRAN
Date/Publication: 2019-11-12 11:10:02 UTC

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New package marindicators with initial version 1.0.0
Package: marindicators
Title: Marine Ecosystem and Fishing Pressure Indicators
Version: 1.0.0
Date: 2019-11-06
Authors@R: c(person("Danielle", "Dempsey", email="Danielle.Dempsey@dfo-mpo.gc.ca", role = c("aut", "cre")), person("Adam", "Cook", email="Adam.Cook@dfo-mpo.gc.ca", role= "aut"), person("Catalina", "Gomez", email="Catalina.Gomez@dfo-mpo.gc.ca", role= "aut"), person("Alida", "Bundy", email="Alida.Bundy@dfo-mpo.gc.ca", role= c("aut")))
Maintainer: Danielle Dempsey <Danielle.Dempsey@dfo-mpo.gc.ca>
Description: Provides functions to calculate indicators for four marine ecosystem attributes (Biodiversity, Ecosystem Structure and Functioning, Ecosystem Stability and Resistance to Perturbations, Resource Potential) and one marine ecosystem pressure (Fishing Pressure) from fishery independent trawl survey data and commercial landings data. All indicators were selected and evaluated using the “Indicator Selection Guidance Framework” developed by Bundy, Gomez, and Cook (2017, ISBN: 978-0-660-23573-8).
Depends: R (>= 3.6.0)
Imports: stats
License: GPL-3 | file LICENSE
LazyData: true
RoxygenNote: 6.1.1
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-11-07 12:30:47 UTC; dempseyd
Author: Danielle Dempsey [aut, cre], Adam Cook [aut], Catalina Gomez [aut], Alida Bundy [aut]
Repository: CRAN
Date/Publication: 2019-11-12 10:40:02 UTC

More information about marindicators at CRAN
Permanent link

Package dtplyr updated to version 1.0.0 with previous version 0.0.3 dated 2019-02-25

Title: Data Table Back-End for 'dplyr'
Description: Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.
Author: Lionel Henry [aut], Hadley Wickham [cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package comat updated to version 0.7.2 with previous version 0.7.0 dated 2019-10-10

Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data. It includes creation of weighted co-occurrence matrices (wecoma) and integrated co-occurrence matrices (incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>), Maximillian H.K. Hesselbarth [ctb] (Co-author of underlying C++ code for get_class_index_map(), get_unique_values(), and rcpp_get_coma() functions), Marco Sciaini [ctb] (Co-author of underlying C++ code for get_class_index_map(), get_unique_values(), and rcpp_get_coma() functions), Sebastian Hanss [ctb] (Co-author of underlying C++ code for get_class_index_map(), get_unique_values(), and rcpp_get_coma() functions)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

Diff between comat versions 0.7.0 dated 2019-10-10 and 0.7.2 dated 2019-11-12

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Package lime updated to version 0.5.1 with previous version 0.5.0 dated 2019-06-24

Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to explain why the model should be trusted. While global measures such as accuracy are useful, they cannot be used for explaining why a model made a specific prediction. 'lime' (a port of the 'lime' 'Python' package) is a method for explaining the outcome of black box models by fitting a local model around the point in question an perturbations of this point. The approach is described in more detail in the article by Ribeiro et al. (2016) <arXiv:1602.04938>.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), Michaël Benesty [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between lime versions 0.5.0 dated 2019-06-24 and 0.5.1 dated 2019-11-12

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Package creditmodel updated to version 1.1.6 with previous version 1.1.5 dated 2019-10-23

Title: Toolkit for Credit Modeling
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>

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Package bestglm updated to version 0.37.1 with previous version 0.37 dated 2018-05-27

Title: Best Subset GLM and Regression Utilities
Description: Best subset glm using information criteria or cross-validation. Implements PCR and PLS using AIC/BIC. Implements one-standard deviation rule for use with the `caret` package.
Author: A.I. McLeod and Changjiang Xu
Maintainer: A.I. McLeod <aimcleod@uwo.ca>

Diff between bestglm versions 0.37 dated 2018-05-27 and 0.37.1 dated 2019-11-12

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Package kernlab updated to version 0.9-29 with previous version 0.9-28 dated 2019-11-09

Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre], Alex Smola [aut], Kurt Hornik [aut], National ICT Australia (NICTA) [cph], Michael A. Maniscalco [ctb, cph], Choon Hui Teo [ctb]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>

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Package surveillance updated to version 1.17.2 with previous version 1.17.1 dated 2019-09-13

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by H<f6>hle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>), Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>), Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Saban<e9>s Bov<e9> [ctb], Ma<eb>lle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>

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Package rayshader updated to version 0.13.1 with previous version 0.11.5 dated 2019-07-11

Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package qgcomp updated to version 1.2.0 with previous version 1.1.0 dated 2019-07-13

Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with quantile-based basis functions, possibly under linearity and homogeneity assumptions. This approach estimates a regression line corresponding to the expected change in the outcome (on the link basis) given a simultaneous increase in the quantile-based category for all exposures. Works with continuous, binary, and right-censored time-to-event outcomes. Reference: Alexander P. Keil, Jessie P. Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao Alexandra J. White (2019) A quantile-based g-computation approach to addressing the effects of exposure mixtures; <arXiv:1902.04200> [stat.ME].
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>

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Package plotKML updated to version 0.6-0 with previous version 0.5-9 dated 2019-01-09

Title: Visualization of Spatial and Spatio-Temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@opengeohub.org>

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Package CondIndTests updated to version 0.1.5 with previous version 0.1.4 dated 2018-05-07

Title: Nonlinear Conditional Independence Tests
Description: Code for a variety of nonlinear conditional independence tests: Kernel conditional independence test (Zhang et al., UAI 2011, <arXiv:1202.3775>), Residual Prediction test (based on Shah and Buehlmann, <arXiv:1511.03334>), Invariant environment prediction, Invariant target prediction, Invariant residual distribution test, Invariant conditional quantile prediction (all from Heinze-Deml et al., <arXiv:1706.08576>).
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>, Jonas Peters <jonas.peters@math.ku.dk>, Asbjoern Marco Sinius Munk <fgp998@alumni.ku.dk>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>

Diff between CondIndTests versions 0.1.4 dated 2018-05-07 and 0.1.5 dated 2019-11-12

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Package AzureAuth updated to version 1.2.3 with previous version 1.2.2 dated 2019-09-13

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. Part of the 'AzureR' family of packages.
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>

Diff between AzureAuth versions 1.2.2 dated 2019-09-13 and 1.2.3 dated 2019-11-12

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Package RCPmod updated to version 2.190 with previous version 2.186 dated 2017-09-29

Title: Regions of Common Profiles Modelling with Mixtures-of-Experts
Description: Identifies regions of common (species) profiles (RCPs), possibly when sampling artefacts are present. Within a region the probability of sampling all species remains approximately constant. This is performed using mixtures-of-experts models. The package also contains associated methods, such as diagnostics.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>

Diff between RCPmod versions 2.186 dated 2017-09-29 and 2.190 dated 2019-11-12

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Package enveomics.R updated to version 1.6.0 with previous version 1.5.0 dated 2019-10-27

Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>

Diff between enveomics.R versions 1.5.0 dated 2019-10-27 and 1.6.0 dated 2019-11-12

 DESCRIPTION                            |    6 
 MD5                                    |   22 -
 R/recplot2.R                           |  520 +++++++++++++++++----------------
 README.md                              |    4 
 man/enve.recplot2.Rd                   |    4 
 man/enve.recplot2.__counts.Rd          |    2 
 man/enve.recplot2.compareIdentities.Rd |    2 
 man/enve.recplot2.extractWindows.Rd    |    8 
 man/enve.recplot2.findPeaks.Rd         |    2 
 man/enve.recplot2.findPeaks.em.Rd      |    4 
 man/enve.recplot2.findPeaks.mower.Rd   |    8 
 man/plot.enve.RecPlot2.Rd              |    4 
 12 files changed, 314 insertions(+), 272 deletions(-)

More information about enveomics.R at CRAN
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Package arulesCBA updated to version 1.1.5 with previous version 1.1.4 dated 2018-12-16

Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph], Michael Hahsler [aut, cph], Tyler Giallanza [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

Diff between arulesCBA versions 1.1.4 dated 2018-12-16 and 1.1.5 dated 2019-11-12

 arulesCBA-1.1.4/arulesCBA/tests/testthat/tests.R            |only
 arulesCBA-1.1.5/arulesCBA/DESCRIPTION                       |   19 
 arulesCBA-1.1.5/arulesCBA/MD5                               |   28 
 arulesCBA-1.1.5/arulesCBA/NAMESPACE                         |    7 
 arulesCBA-1.1.5/arulesCBA/NEWS.md                           |    7 
 arulesCBA-1.1.5/arulesCBA/R/CBA.R                           |  382 +++++++-----
 arulesCBA-1.1.5/arulesCBA/R/CBA.internal.R                  |only
 arulesCBA-1.1.5/arulesCBA/R/CBA.object.R                    |   86 +-
 arulesCBA-1.1.5/arulesCBA/R/RCAR.R                          |only
 arulesCBA-1.1.5/arulesCBA/R/mineCARs.R                      |   43 -
 arulesCBA-1.1.5/arulesCBA/inst/doc/arulesCBA.pdf            |binary
 arulesCBA-1.1.5/arulesCBA/man/CBA.Rd                        |   36 -
 arulesCBA-1.1.5/arulesCBA/man/CBA.object.Rd                 |   10 
 arulesCBA-1.1.5/arulesCBA/man/RCAR.Rd                       |only
 arulesCBA-1.1.5/arulesCBA/man/mineCARs.Rd                   |    9 
 arulesCBA-1.1.5/arulesCBA/tests/testthat/test-CBA.R         |only
 arulesCBA-1.1.5/arulesCBA/tests/testthat/test-CBA_ruleset.R |only
 arulesCBA-1.1.5/arulesCBA/tests/testthat/test-RCAR.R        |only
 arulesCBA-1.1.5/arulesCBA/tests/testthat/test-discretize.R  |only
 19 files changed, 376 insertions(+), 251 deletions(-)

More information about arulesCBA at CRAN
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