Thu, 16 Dec 2021

Package spatstat.sparse updated to version 2.1-0 with previous version 2.0-0 dated 2021-03-16

Title: Sparse Three-Dimensional Arrays and Linear Algebra Utilities
Description: Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.
Author: Adrian Baddeley [aut, cre, cph] (<https://orcid.org/0000-0001-9499-8382>), Rolf Turner [aut, cph] (<https://orcid.org/0000-0001-5521-5218>), Ege Rubak [aut, cph] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.sparse versions 2.0-0 dated 2021-03-16 and 2.1-0 dated 2021-12-16

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Package spatstat.data updated to version 2.1-2 with previous version 2.1-0 dated 2021-03-21

Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>), Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>), Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.data versions 2.1-0 dated 2021-03-21 and 2.1-2 dated 2021-12-16

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Package ks updated to version 1.13.3 with previous version 1.13.2 dated 2021-07-01

Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] (<https://orcid.org/0000-0002-1198-3482>), Matt Wand [ctb] (<https://orcid.org/0000-0003-2555-896X>), Jose Chacon [ctb], Artur Gramacki [ctb] (<https://orcid.org/0000-0002-1610-9743>)
Maintainer: Tarn Duong <tarn.duong@gmail.com>

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Package parallelly updated to version 1.30.0 with previous version 1.29.0 dated 2021-11-21

Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between parallelly versions 1.29.0 dated 2021-11-21 and 1.30.0 dated 2021-12-16

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Package readabs updated to version 0.4.11 with previous version 0.4.10 dated 2021-10-28

Title: Download and Tidy Time Series Data from the Australian Bureau of Statistics
Description: Downloads, imports, and tidies time series data from the Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre] (<https://orcid.org/0000-0003-0422-3300>), Zoe Meers [aut], Jaron Lee [aut], David Diviny [aut], Hugh Parsonage [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>

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Package medfate updated to version 2.3.7 with previous version 2.2.3 dated 2021-06-18

Title: Mediterranean Forest Simulation
Description: Functions to simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Cáceres [aut, cre], Shengli Huang [aut], Víctor Granda [aut], Antoine Cabon [aut], Jordi Martínez-Vilalta [ctb], Maurizio Mencuccini [ctb], Nicolas Martin-StPaul [ctb]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>

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New package viewpoly with initial version 0.1.0
Package: viewpoly
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
Version: 0.1.0
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Description: Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly' and 'polyqtlR' packages.
License: GPL-3
Depends: R (>= 4.0)
Imports: shiny (>= 1.6.0), shinyjs, shinythemes, shinyWidgets, shinydashboard, config (>= 0.3.1), golem (>= 0.3.1), JBrowseR, dplyr, tidyr, DT, ggplot2, ggpubr, plotly, vroom, abind, reshape2, markdown, stats, rlang
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Language: en-US
NeedsCompilation: no
Packaged: 2021-12-16 15:10:49 UTC; chtan
Author: Cristiane Taniguti [aut, cre], Gabriel Gesteira [aut], Jeekin Lau [ctb], Guilherme Pereira [ctb], David Byrne [ctb], Zhao-Bang Zeng [ctb], Oscar Riera-Lizarau [ctb], Marcelo Mollinari [aut]
Repository: CRAN
Date/Publication: 2021-12-16 21:00:02 UTC

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New package thewitcher with initial version 1.0.0
Package: thewitcher
Title: Palettes Inspired by the TV Show "The Witcher"
Version: 1.0.0
Description: Plot your data using color palettes for 'ggplot2' inspired by the TV show, book series and video games "The Witcher".
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: ggplot2 (>= 1.0.1), dplyr, tidyverse, usethis, gridExtra, MASS, magrittr, grDevices, readr
Suggests: covr
LazyData: true
NeedsCompilation: no
Packaged: 2021-12-16 12:25:27 UTC; grafluca
Author: Lukas Graf [aut, cre] (<https://orcid.org/0000-0001-9630-5615>)
Maintainer: Lukas Graf <graflukas57@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-16 21:00:05 UTC

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New package SOAs with initial version 1.0-1
Package: SOAs
Title: Creation of Stratum Orthogonal Arrays
Version: 1.0-1
Description: Creates stratum orthogonal arrays (also known as strong orthogonal arrays). These are arrays with more levels per column than the typical orthogonal array, and whose low order projections behave like orthogonal arrays, when collapsing levels to coarser strata. Details are described in Groemping (2021) "A unified implementation of stratum (aka strong) orthogonal arrays" <http://www1.bht-berlin.de/FB_II/reports/Report-2021-001.pdf>.
Depends: R (>= 3.6.0), DoE.base (>= 1.2)
Imports: stats, combinat, FrF2, igraph, lhs (>= 1.1.3), conf.design
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/bertcarnell/SOAs
BugReports: https://github.com/bertcarnell/SOAs/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-12-16 15:33:20 UTC; Grömping
Author: Ulrike Groemping [aut, cre], Rob Carnell [ctb]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Repository: CRAN
Date/Publication: 2021-12-16 21:00:11 UTC

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New package skewsamp with initial version 1.0.0
Package: skewsamp
Title: Estimate Sample Sizes for Group Comparisons with Skewed Distributions
Version: 1.0.0
Description: Estimate necessary sample sizes for comparing the location of data from two groups or categories when the distribution of the data is skewed. The package offers a non-parametric method for a Wilcoxon Mann-Whitney test of location shift as well as methods for several generalized linear models, for instance, Gamma regression.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-12-16 15:57:31 UTC; jobrachem
Author: Johannes Brachem [cre, aut], Dominik Strache [aut]
Maintainer: Johannes Brachem <jbrachem@posteo.de>
Repository: CRAN
Date/Publication: 2021-12-16 21:00:08 UTC

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New package covid19srilanka with initial version 1.0.0
Package: covid19srilanka
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Data in Sri Lanka
Version: 1.0.0
Description: Provides a daily counts of the Coronavirus (COVID19) cases by districts and country. Data source: Epidemiological Unit, Ministry of Health, Sri Lanka <https://www.epid.gov.lk/web/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: tidyverse
NeedsCompilation: no
Packaged: 2021-12-16 11:28:26 UTC; thiyangashaminitalagala
Author: Thiyanga S. Talagala [aut, cre] (<https://orcid.org/0000-0002-5058-7503>)
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Repository: CRAN
Date/Publication: 2021-12-16 20:50:02 UTC

More information about covid19srilanka at CRAN
Permanent link

New package aba with initial version 0.0.9
Package: aba
Title: Automated Biomarker Analysis
Version: 0.0.9
Description: A tool to fit clinical prediction models and plan clinical trials using biomarker data across multiple analysis factors (groups, outcomes, predictors).
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: covr, knitr, plotly, rmarkdown, testthat (>= 3.0.0), methods, tidyselect, nlme, yardstick, pins, Matrix, MuMIn, broom.mixed, emmeans, ggpubr, pROC, progress, OptimalCutpoints, tableone, longpower, withr, reactable, psychometric, readr, writexl
Imports: purrr, dplyr, broom, tibble, ggplot2, glue, magrittr, stringr, rlang, tidyr, stats, generics
VignetteBuilder: knitr
Depends: R (>= 2.10)
URL: https://github.com/ncullen93/abaR/, https://ncullen93.github.io/abaR/
NeedsCompilation: no
Packaged: 2021-12-16 11:21:48 UTC; ni5875cu
Author: Nicholas Cullen [aut, cre]
Maintainer: Nicholas Cullen <nickcullen31@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-16 20:50:05 UTC

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Package Rfssa updated to version 2.0.0 with previous version 1.0.0 dated 2019-09-12

Title: Functional Singular Spectrum Analysis
Description: Methods and tools for implementing univariate and multivariate functional singular spectrum analysis for functional time series whose variables might be observed over different dimensional domains. The univariate fssa algorithm is described in Haghbin H., Najibi, S.M., Mahmoudvand R., Trinka J., Maadooliat M. (2021) and the multivariate fssa over different dimensional domains technique may be found in Trinka J., Haghbin H., and Maadooliat M. (Accepted). In addition, one may perform forecasting of univariate and multivariate fts whose variables are observed over one-dimensional domains as described in the dissertation of Trinka J. (2021) and the manuscript of Trinka J., Haghbin H., Maadooliat M. (2020) where the manuscript is to be submitted to a journal for publication.
Author: Hossein Haghbin [aut, cre], Jordan Trinka [aut], Seyed Morteza Najibi [aut], Mehdi Maadooliat [aut]
Maintainer: Hossein Haghbin <haghbinh@gmail.com>

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More information about Rfssa at CRAN
Permanent link

Package knitr updated to version 1.37 with previous version 1.36 dated 2021-09-29

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>), Abhraneel Sarma [ctb], 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], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [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], Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>), 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>

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Package Seurat updated to version 4.0.6 with previous version 4.0.5 dated 2021-10-17

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat@nygenome.org>

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Package sendgridr updated to version 0.4.2 with previous version 0.3.3 dated 2021-10-06

Title: Mail Sender Using 'Sendgrid' Service
Description: Send email using 'Sendgrid' <https://sendgrid.com/> mail API(v3) <https://docs.sendgrid.com/api-reference/how-to-use-the-sendgrid-v3-api/authentication>.
Author: Chanyub Park [aut, cre] (<https://orcid.org/0000-0001-6474-2570>)
Maintainer: Chanyub Park <mrchypark@gmail.com>

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Package SteppedPower updated to version 0.3.1 with previous version 0.2.0 dated 2021-07-07

Title: Power Calculation for Stepped Wedge Designs
Description: Tools for power and sample size calculation as well as design diagnostics for longitudinal mixed model settings, with a focus on stepped wedge designs. All calculations are oracle estimates i.e. assume random effect variances to be known (or guessed) in advance. The method is introduced in Hussey and Hughes (2007) <doi:10.1016/j.cct.2006.05.007>, extensions are discussed in Li et al. (2020) <doi:10.1177/0962280220932962>.
Author: Philipp Mildenberger [aut, cre] (<https://orcid.org/0000-0002-7367-1708>), Federico Marini [ctb] (<https://orcid.org/0000-0003-3252-7758>)
Maintainer: Philipp Mildenberger <pmildenb@uni-mainz.de>

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Package metap updated to version 1.7 with previous version 1.6 dated 2021-11-05

Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and routines for graphical display.
Author: Michael Dewey [aut, cre] (<https://orcid.org/0000-0002-7522-3677>)
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>

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Package fusen updated to version 0.3.0 with previous version 0.2.4 dated 2021-08-04

Title: Build a Package from Rmarkdown File
Description: Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.
Author: Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>), ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>

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Package rpact updated to version 3.2.0 with previous version 3.1.1 dated 2021-08-27

Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut], Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>

Diff between rpact versions 3.1.1 dated 2021-08-27 and 3.2.0 dated 2021-12-16

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Package gausscov updated to version 0.1.2 with previous version 0.1.1 dated 2021-04-30

Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the web site below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Assumption -free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>

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Package umx updated to version 4.10.50 with previous version 4.10.10 dated 2021-11-29

Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>), Gillespie Nathan [wit], Michael Zakharin [wit], Brenton Wiernik [ctb], Luis De Araujo [ctb], Joshua N. Pritikin [ctb], Michael C. Neale [ctb], Hermine Maes [ctb]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>

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Package ClusTorus updated to version 0.2.0 with previous version 0.1.3 dated 2021-07-26

Title: Prediction and Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular data on the torus. The package provides angular adaptations of usual clustering methods such as the k-means clustering, pairwise angular distances, which can be used as an input for distance-based clustering algorithms, and implements clustering based on the conformal prediction framework. Options for the conformal scores include scores based on a kernel density estimate, multivariate von Mises mixtures, and naive k-means clusters. Moreover, the package provides some basic data handling tools for angular data.
Author: Sungkyu Jung [aut, cph], Seungki Hong [aut, cre], Kiho Park [ctb], Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>

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Package rfacebookstat updated to version 2.5.0 with previous version 2.4.0 dated 2021-07-27

Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package pegas updated to version 1.1 with previous version 1.0-1 dated 2021-05-17

Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>

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Package mlt.docreg updated to version 1.1-2 with previous version 1.1-1 dated 2021-12-07

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package yorkr updated to version 0.0.30 with previous version 0.0.29 dated 2021-12-13

Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>

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Package rtmpt updated to version 0.2-3 with previous version 0.2-2 dated 2021-10-11

Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it to estimate process completion times and encoding plus motor execution times next to the process probabilities of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre], Karl C. Klauer [cph, aut, ctb, ths], Henrik Singmann [ctb, aut], Jean Marie Linhart [ctb], Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>

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Package WordR updated to version 0.3.2 with previous version 0.3.1 dated 2018-07-23

Title: Rendering Word Documents with R Inline Code
Description: Serves for rendering MS Word documents with R inline code and inserting tables and plots.
Author: Tomas Hovorka
Maintainer: Tomas Hovorka <tomashovorka@seznam.cz>

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New package WINS with initial version 1.0
Package: WINS
Title: The R WINS Package
Version: 1.0
Maintainer: Ying Cui <cuiyingbeicheng@gmail.com>
Description: Calculate the win statistics (win ratio, net benefit and win odds) for prioritized multiple endpoints, plot the win statistics and win proportions over study time if at least one time-to-event endpoint is analyzed, and simulate datasets with dependent endpoints. The package can handle any type of outcomes (continuous, ordinal, binary, time-to-event) and allow users to perform stratified analysis and inverse probability of censoring weighting (IPCW) analysis.
Depends: R (>= 3.5.0)
Imports: copula,ggplot2,ggpubr,reshape2,survival,stringr,viridis
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-12-15 23:49:37 UTC; ycui
Author: Ying Cui [aut, cre], Bo Huang [aut]
Repository: CRAN
Date/Publication: 2021-12-16 10:20:08 UTC

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Package spatialwarnings updated to version 3.0.2 with previous version 3.0.0 dated 2021-05-19

Title: Spatial Early Warning Signals of Ecosystem Degradation
Description: Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are metrics derived from the observed spatial structure of an ecosystem -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Author: Alain Danet, Alexandre Genin, Vishwesha Guttal, Sonia Kefi, Sabiha Majumder, Sumithra Sankaran, Florian Schneider
Maintainer: Alexandre Genin <a.a.h.genin@uu.nl>

Diff between spatialwarnings versions 3.0.0 dated 2021-05-19 and 3.0.2 dated 2021-12-16

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New package rasterbc with initial version 1.0.0
Package: rasterbc
Title: Access Forest Ecology Layers for British Columbia in 2001-2018
Version: 1.0.0
Description: R-based access to a large set of data variables relevant to forest ecology in British Columbia (BC), Canada. Layers are in raster format at 100m resolution in the BC Albers projection, hosted at the Federated Research Data Repository (FRDR) with <doi:10.20383/101.0283>. The collection includes: elevation; biogeoclimatic zone; wildfire; cutblocks; forest attributes from Hansen et al. (2013) <doi:10.1139/cjfr-2013-0401> and Beaudoin et al. (2017) <doi:10.1139/cjfr-2017-0184>; and rasterized Forest Insect and Disease Survey (FIDS) maps for a number of insect pest species, all covering the period 2001-2018. Users supply a polygon or point location in the province of BC, and 'rasterbc' will download the overlapping raster tiles hosted at FRDR, merging them as needed and returning the result in R as a 'SpatRaster' object. Metadata associated with these layers, and code for downloading them from their original sources can be found in the 'github' repository <https://github.com/deankoch/rasterbc_src>.
License: MIT + file LICENSE
URL: https://github.com/deankoch/rasterbc, https://github.com/deankoch/rasterbc_src
BugReports: https://github.com/deankoch/rasterbc/issues
Encoding: UTF-8
LazyData: true
Imports: sf, methods, terra
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, bcmaps, units
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-15 22:16:29 UTC; deank
Author: Dean Koch [aut, cre] (<https://orcid.org/0000-0002-8849-859X>)
Maintainer: Dean Koch <dkoch@ualberta.ca>
Repository: CRAN
Date/Publication: 2021-12-16 10:20:02 UTC

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New package midas2 with initial version 0.1.0
Package: midas2
Title: Bayesian Drug-Combination Platform Design(MIDAS-2)
Version: 0.1.0
Author: Su Liwen
Maintainer: Su Liwen <cpusullivan@163.com>
Description: Implementation of Bayesian drug-combination platform design. More and more immuno-oncology drug combinations make the traditional two-arm phase II trials inefficient, which stimulate the emerge of platform trials. In the case of multiple trial objectives such as candidates screening and subgroup analysis, we propose an information borrowing drug-combination Bayesian design for platform trials with subgroup exploration. MIDAS-2 consists of one control arm and several experimental agents. We use Bayesian spike and slab prior to identify factors that should be included in regression model and borrow information between combinations in the existence of subgroup interaction. Promising drug combinations are allowed to graduated early to move to next stage and new combination strategies can be added accordingly. Catch-up rule, curtail rule and early stopping rules are also applied to accelerate the trial process.
License: GPL-3
Encoding: UTF-8
Imports: MCMCpack,coda,R2jags
NeedsCompilation: no
Packaged: 2021-12-16 06:06:57 UTC; sama
Repository: CRAN
Date/Publication: 2021-12-16 10:50:02 UTC

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New package miceafter with initial version 0.1.0
Package: miceafter
Depends: R (>= 4.0.0),
Imports: survival (>= 3.1-12), pROC (>= 1.16.2), rms (>= 6.1-0), mice (>= 3.12.0), mitml (>= 0.3-7), mitools (>= 2.4), dplyr (>= 1.0.2), purrr (>= 0.3.4), tidyr (>= 1.1.2), tibble (>= 3.0.4), stringr (>= 1.4.0), car (>= 3.0-10), rlang, magrittr
Suggests: foreign (>= 0.8-80), knitr, rmarkdown, testthat (>= 3.0.0), bookdown, readr
Title: Data and Statistical Analyses after Multiple Imputation
Version: 0.1.0
Description: Statistical Analyses and Pooling after Multiple Imputation. A large variety of repeated statistical analysis can be performed and finally pooled. Statistical analysis that are available are, among others, Levene's test, Odds and Risk Ratios, One sample proportions, difference between proportions and linear and logistic regression models. Functions can also be used in combination with the Pipe operator. More and more statistical analyses and pooling functions will be added over time. Heymans (2007) <doi:10.1186/1471-2288-7-33>. Eekhout (2017) <doi:10.1186/s12874-017-0404-7>. Wiel (2009) <doi:10.1093/biostatistics/kxp011>. Marshall (2009) <doi:10.1186/1471-2288-9-57>. Sidi (2021) <doi:10.1080/00031305.2021.1898468>. Lott (2018) <doi:10.1080/00031305.2018.1473796>. Grund (2021) <doi:10.31234/osf.io/d459g>.
Encoding: UTF-8
LazyData: true
License: GPL (>= 2)
URL: https://mwheymans.github.io/miceafter/
BugReports: https://github.com/mwheymans/miceafter/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-15 20:41:40 UTC; mwhey
Author: Martijn Heymans [cre, aut] (<https://orcid.org/0000-0002-3889-0921>), Jaap Brand [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>
Repository: CRAN
Date/Publication: 2021-12-16 10:10:02 UTC

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Package mFD updated to version 1.0.1 with previous version 1.0.0 dated 2021-11-05

Title: Compute and Illustrate the Multiple Facets of Functional Diversity
Description: Computing functional traits-based distances between pairs of species for species gathered in assemblages allowing to build several functional spaces. The package allows to compute functional diversity indices assessing the distribution of species (and of their dominance) in a given functional space for each assemblage and the overlap between assemblages in a given functional space, see: Chao et al. (2018) <doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>, Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al. (2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009) <doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included. Visit the 'mFD' website for more information, documentation and examples.
Author: Camille Magneville [aut, cre, cph] (<https://orcid.org/0000-0003-0489-3822>), Nicolas Loiseau [aut] (<https://orcid.org/0000-0002-2469-1980>), Camille Albouy [aut] (<https://orcid.org/0000-0003-1629-2389>), Nicolas Casajus [aut] (<https://orcid.org/0000-0002-5537-5294>), Thomas Claverie [aut] (<https://orcid.org/0000-0002-6258-4991>), Arthur Escalas [aut] (<https://orcid.org/0000-0002-6450-5716>), Fabien Leprieur [aut] (<https://orcid.org/0000-0001-6869-342X>), Eva Maire [aut] (<https://orcid.org/0000-0002-1032-3394>), David Mouillot [aut] (<https://orcid.org/0000-0003-0402-2605>), Sebastien Villeger [aut] (<https://orcid.org/0000-0002-2362-7178>)
Maintainer: Camille Magneville <camille.magneville@gmail.com>

Diff between mFD versions 1.0.0 dated 2021-11-05 and 1.0.1 dated 2021-12-16

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New package InflectSSP with initial version 1.4.3
Package: InflectSSP
Title: Melt Curve Fitting and Melt Shift Analysis
Version: 1.4.3
Description: Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. McCracken (2021) <doi:10.1021/acs.jproteome.0c00872>.
License: GPL-2
Encoding: UTF-8
Imports: readxl, data.table, plotrix, tidyr, ggplot2, xlsx, httr, jsonlite, GGally, network, stats, RColorBrewer, svglite
Suggests: knitr, rmarkdown,
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-15 19:27:50 UTC; namccrac
Author: Neil McCracken [aut], Hao Liu [ctb], Amber Mosley [cre]
Maintainer: Amber Mosley <almosley@iu.edu>
Repository: CRAN
Date/Publication: 2021-12-16 10:12:12 UTC

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New package CLA with initial version 0.96-2
Package: CLA
Version: 0.96-2
Date: 2021-12-14
Title: Critical Line Algorithm in Pure R
Author: Yanhao Shi <syhelena@163.com>, Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Depends: R (>= 3.6.0)
Imports: stats, grDevices, graphics, utils
Suggests: fGarch, FRAPO, Matrix, sfsmisc
Description: Implements 'Markowitz' Critical Line Algorithm ('CLA') for classical mean-variance portfolio optimization, see Markowitz (1952) <doi:10.2307/2975974>. Care has been taken for correctness in light of previous buggy implementations.
License: GPL (>= 3) | file LICENSE
Encoding: UTF-8
URL: https://gitlab.math.ethz.ch/maechler/CLA/
NeedsCompilation: no
Packaged: 2021-12-15 10:10:49 UTC; maechler
Repository: CRAN
Date/Publication: 2021-12-16 10:42:03 UTC

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New package brmsmargins with initial version 0.1.1
Package: brmsmargins
Title: Bayesian Marginal Effects for 'brms' Models
Version: 0.1.1
URL: https://joshuawiley.com/brmsmargins/, https://github.com/JWiley/brmsmargins
BugReports: https://github.com/JWiley/brmsmargins/issues
Description: Calculate Bayesian marginal effects and average marginal effects for models fit using the 'brms' package including fixed effects, mixed effects, and location scale models. These are based on marginal predictions that integrate out random effects if necessary (see for example <doi:10.1186/s12874-015-0046-6>).
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: methods, stats, data.table (>= 1.12.0), extraoperators (>= 0.1.1), brms, bayestestR, Rcpp, posterior
Suggests: testthat (>= 3.0.0), covr, withr, knitr, rmarkdown, margins, betareg
Config/testthat/parallel: true
LinkingTo: RcppArmadillo, Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-12-15 21:39:03 UTC; jwile
Author: Joshua F. Wiley [aut, cre] (<https://orcid.org/0000-0002-0271-6702>)
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-16 10:20:05 UTC

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New package bayMDS with initial version 1.6
Package: bayMDS
Title: Bayesian Multidimensional Scaling and Choice of Dimension
Version: 1.6
Date: 2021-12-13
Description: Bayesian approach to multidimensional scaling. The package consists of implementations of the methods of Oh and Raftery (2001) <doi:10.1198/016214501753208690>.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 1.0.7), progress, ggplot2, shinythemes, shiny, gridExtra, rgl, ggpubr
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-12-14 10:40:29 UTC; EKLee
Author: Man-Suk Oh [aut, cre], Eun-Kyung Lee [aut]
Maintainer: Man-Suk Oh <msoh@ewha.ac.kr>
Repository: CRAN
Date/Publication: 2021-12-16 10:00:06 UTC

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Package midasml updated to version 0.1.8 with previous version 0.1.7 dated 2021-12-08

Title: Estimation and Prediction Methods for High-Dimensional Mixed Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut], Andrii Babii [aut], Eric Ghysels [aut], Alex Kostrov [ctb] (Contributions to analytical gradients for non-linear low-dimensional MIDAS estimation code)
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>

Diff between midasml versions 0.1.7 dated 2021-12-08 and 0.1.8 dated 2021-12-16

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Package googleCloudStorageR updated to version 0.7.0 with previous version 0.6.0 dated 2021-01-05

Title: Interface with Google Cloud Storage API
Description: Interact with Google Cloud Storage <https://cloud.google.com/storage/> API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>)
Maintainer: Mark Edmondson <r@sunholo.com>

Diff between googleCloudStorageR versions 0.6.0 dated 2021-01-05 and 0.7.0 dated 2021-12-16

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Package RProtoBuf updated to version 0.4.18 with previous version 0.4.17 dated 2020-03-28

Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the 'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RProtoBuf versions 0.4.17 dated 2020-03-28 and 0.4.18 dated 2021-12-16

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Package permutes updated to version 2.3.2 with previous version 2.2 dated 2021-10-13

Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007) <doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints where significance of an effect begins and ends, and the results can be plotted in various types of heatmap for reporting. Mixed-effects models are supported using an implementation of the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>

Diff between permutes versions 2.2 dated 2021-10-13 and 2.3.2 dated 2021-12-16

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Package gld updated to version 2.6.4 with previous version 2.6.3 dated 2021-11-24

Title: Estimation and Use of the Generalised (Tukey) Lambda Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form. This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different types of the distribution, the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden and Loots 2009) and FM5 - see documentation for details. It provides the density function, distribution function, and Quantile-Quantile plots. It implements a variety of estimation methods for the distribution, including diagnostic plots. Estimation methods include the starship (all 4 types), method of L-Moments for the GPD and FKML types, and a number of methods for only the FKML type. These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King [aut, cre] (<https://orcid.org/0000-0001-7495-6599>), Benjamin Dean [aut], Sigbert Klinke [aut], Paul van Staden [aut] (<https://orcid.org/0000-0002-5710-5984>)
Maintainer: Robert King <Robert.King.Newcastle@gmail.com>

Diff between gld versions 2.6.3 dated 2021-11-24 and 2.6.4 dated 2021-12-16

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 16 files changed, 59 insertions(+), 34 deletions(-)

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Package geneExpressionFromGEO updated to version 0.9 with previous version 0.8 dated 2021-11-06

Title: Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Author: Davide Chicco [aut, cre] (<https://orcid.org/0000-0001-9655-7142>)
Maintainer: Davide Chicco <davidechicco@davidechicco.it>

Diff between geneExpressionFromGEO versions 0.8 dated 2021-11-06 and 0.9 dated 2021-12-16

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Package crctStepdown updated to version 0.2.1 with previous version 0.1 dated 2021-08-03

Title: Univariate Analysis of Cluster Trials with Multiple Outcomes
Description: Frequentist statistical inference for cluster randomised trials with multiple outcomes that controls the family-wise error rate and provides nominal coverage of confidence sets. A full description of the methods can be found in Watson et al. (2021) <arXiv:2107.10017>.
Author: Sam Watson [aut, cre] (<https://orcid.org/0000-0002-8972-769X>)
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>

Diff between crctStepdown versions 0.1 dated 2021-08-03 and 0.2.1 dated 2021-12-16

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Package TileManager (with last version 0.4.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-05-08 0.4.0
2018-10-04 0.3.0
2017-09-07 0.2.0
2017-01-28 0.1.11
2017-01-16 0.1.0

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Package MRPC updated to version 3.0.0 with previous version 2.3.1 dated 2021-05-02

Title: PC Algorithm with the Principle of Mendelian Randomization
Description: A PC Algorithm with the Principle of Mendelian Randomization. This package implements the MRPC (PC with the principle of Mendelian randomization) algorithm to infer causal graphs. It also contains functions to simulate data under a certain topology, to visualize a graph in different ways, and to compare graphs and quantify the differences. See Badsha and Fu (2019) <doi:10.3389/fgene.2019.00460>; Badsha, Martin and Fu (2021) <doi:10.3389/fgene.2021.651812>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mbbadshar@gmail.com>

Diff between MRPC versions 2.3.1 dated 2021-05-02 and 3.0.0 dated 2021-12-16

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 42 files changed, 1060 insertions(+), 381 deletions(-)

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