Tue, 30 Nov 2021

Package table.express updated to version 0.3.2 with previous version 0.3.1 dated 2019-09-07

Title: Build 'data.table' Expressions with Data Manipulation Verbs
Description: A specialization of 'dplyr' data manipulation verbs that parse and build expressions which are ultimately evaluated by 'data.table', letting it handle all optimizations. A set of additional verbs is also provided to facilitate some common operations on a subset of the data.
Author: Alexis Sarda-Espinosa [cre, aut]
Maintainer: Alexis Sarda-Espinosa <alexis.sarda@gmail.com>

Diff between table.express versions 0.3.1 dated 2019-09-07 and 0.3.2 dated 2021-11-30

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Package pvaluefunctions updated to version 1.6.2 with previous version 1.6.1 dated 2020-12-09

Title: Creates and Plots P-Value Functions, S-Value Functions, Confidence Distributions and Confidence Densities
Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Infanger D, Schmidt-Trucksäss A. (2019) <doi:10.1002/sim.8293>; Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; Greenland S. (2019) <doi:10.1080/00031305.2018.1529625> and Rafi Z, Greenland S. (2020) <doi:10.1186/s12874-020-01105-9>.
Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
Maintainer: Denis Infanger <denis.infanger@unibas.ch>

Diff between pvaluefunctions versions 1.6.1 dated 2020-12-09 and 1.6.2 dated 2021-11-30

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Package PostcodesioR updated to version 0.3.1 with previous version 0.3.0 dated 2021-01-07

Title: API Wrapper Around 'Postcodes.io'
Description: Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.
Author: Eryk Walczak [aut, cre] (<https://orcid.org/0000-0001-8724-462X>), Claudia Vitolo [rev] (<https://orcid.org/0000-0002-4252-1176>), Robin Lovelace [rev] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Eryk Walczak <erykjwalczak@gmail.com>

Diff between PostcodesioR versions 0.3.0 dated 2021-01-07 and 0.3.1 dated 2021-11-30

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More information about PostcodesioR at CRAN
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Package activegp updated to version 1.0.6 with previous version 1.0.5 dated 2020-10-27

Title: Gaussian Process Based Design and Analysis for the Active Subspace Method
Description: The active subspace method is a sensitivity analysis technique that finds important linear combinations of input variables for a simulator. This package provides functions allowing estimation of the active subspace without gradient information using Gaussian processes as well as sequential experimental design tools to minimize the amount of data required to do so. Implements Wycoff et al. (2019) <arXiv:1907.11572>.
Author: Nathan Wycoff, Mickael Binois
Maintainer: Nathan Wycoff <nathan.wycoff@georgetown.edu>

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Package datefixR updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-05

Title: Fix Really Messy Dates
Description: Fixes messy dates in data frames such as those entered via text boxes. Standardizes / - and whitespace separation, month abbreviations, and year first or day first by converting to R's built-in Date class. Imputes missing date or month using user-provided values.
Author: Nathan Constantine-Cooke [aut, cre] (<https://orcid.org/0000-0002-4437-8713>)
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>

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New package Wcompo with initial version 1.0
Package: Wcompo
Title: Semiparametric Proportional Means Regression of Weighted Composite Endpoint
Version: 1.0
Author: Lu Mao
Maintainer: Lu Mao <lmao@biostat.wisc.edu>
URL: https://sites.google.com/view/lmaowisc/
Description: Implements inferential and graphic procedures for the semiparametric proportional means regression of weighted composite endpoint of recurrent event and death (Mao and Lin, 2016, <doi:10.1093/biostatistics/kxv050>).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: survival
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-11-29 21:30:23 UTC; lmao
Repository: CRAN
Date/Publication: 2021-11-30 21:30:02 UTC

More information about Wcompo at CRAN
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Package RobStatTM updated to version 1.0.3 with previous version 1.0.2 dated 2020-03-02

Title: Robust Statistics: Theory and Methods
Description: Companion package for the book: "Robust Statistics: Theory and Methods, second edition", <http://www.wiley.com/go/maronna/robust>. This package contains code that implements the robust estimators discussed in the recent second edition of the book above, as well as the scripts reproducing all the examples in the book.
Author: Matias Salibian-Barrera [cre], Victor Yohai [aut], Ricardo Maronna [aut], Doug Martin [aut], Gregory Brownson [aut] (ShinyUI), Kjell Konis [aut], Kjell Konis [cph] (erfi), Christophe Croux [ctb] (WBYlogreg, BYlogreg), Gentiane Haesbroeck [ctb] (WBYlogreg, BYlogreg), Martin Maechler [cph] (lmrob.fit, lmrob..M..fit, lmrob.S), Manuel Koller [cph] (lmrob.fit, .vcov.avar1, lmrob.S, lmrob.lar), Matias Salibian-Barrera [aut]
Maintainer: Matias Salibian-Barrera <matias@stat.ubc.ca>

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Package pkgdown updated to version 2.0.0 with previous version 1.6.1 dated 2020-09-12

Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>), Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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New package FourWayHMM with initial version 1.0.0
Package: FourWayHMM
Title: Parsimonious Hidden Markov Models for Four-Way Data
Version: 1.0.0
Description: Implements parsimonious hidden Markov models for four-way data via expectation- conditional maximization algorithm, as described in Tomarchio et al. (2020) <arXiv:2107.04330>. The matrix-variate normal distribution is used as emission distribution. For each hidden state, parsimony is reached via the eigen-decomposition of the covariance matrices of the emission distribution. This produces a family of 98 parsimonious hidden Markov models.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: withr, snow, doSNOW, foreach, mclust, tensor, tidyr, data.table, LaplacesDemon
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-11-29 17:24:17 UTC; Daniele
Author: Salvatore D. Tomarchio [aut, cre], Antonio Punzo [aut], Antonello Maruotti [aut]
Maintainer: Salvatore D. Tomarchio <daniele.tomarchio@unict.it>
Repository: CRAN
Date/Publication: 2021-11-30 21:20:02 UTC

More information about FourWayHMM at CRAN
Permanent link

Package diyar updated to version 0.4.0 with previous version 0.3.1 dated 2021-08-09

Title: Record Linkage and Epidemiological Case Definitions in R
Description: An R package for record linkage and implementing epidemiological case definitions in R. Record linkage is implemented either through a multistage deterministic approach or a probabilistic approach. Matching records are assigned to unique groups. There are mechanisms to address missing data and conflicting matches across linkage stages. Track and assign events (e.g. sample collection) and periods (e.g. hospital admission) to unique groups based on a case definition. The tracking process permits several options such as episode lengths and recurrence. Duplicate events or records can then be identified for removal or further analyses.
Author: Olisaeloka Nsonwu
Maintainer: Olisaeloka Nsonwu <olisa.nsonwu@gmail.com>

Diff between diyar versions 0.3.1 dated 2021-08-09 and 0.4.0 dated 2021-11-30

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New package AustralianPoliticians with initial version 0.1.0
Package: AustralianPoliticians
Title: Provides Datasets About Australian Politicians
Version: 0.1.0
Description: Provides access to biographical and political data about Australian federal politicians who served between 1901 and 2021. This enhances how reproducible research is that uses this data.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
URL: https://github.com/RohanAlexander/AustralianPoliticians
BugReports: https://github.com/RohanAlexander/AustralianPoliticians/issues
Imports: dplyr, readr, purrr, utils, tibble
Suggests: rmarkdown, knitr, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-29 20:57:22 UTC; rohanalexander
Author: Rohan Alexander [aut, cre] (<https://orcid.org/0000-0001-6759-7276>), Paul A. Hodgetts [aut]
Maintainer: Rohan Alexander <rohan.alexander@utoronto.ca>
Repository: CRAN
Date/Publication: 2021-11-30 21:30:04 UTC

More information about AustralianPoliticians at CRAN
Permanent link

Package ActiveDriverWGS updated to version 1.1.2 with previous version 1.1.1 dated 2020-09-17

Title: A Driver Discovery Tool for Cancer Whole Genomes
Description: A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.
Author: Juri Reimand [aut, cre], Helen Zhu [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>

Diff between ActiveDriverWGS versions 1.1.1 dated 2020-09-17 and 1.1.2 dated 2021-11-30

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Permanent link

Package text2sdg updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-07

Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications.
Author: Dirk U. Wulff [aut] (<https://orcid.org/0000-0002-4008-8022>), Dominik S. Meier [aut, cre] (<https://orcid.org/0000-0002-3999-1388>), Rui Mata [ctb] (<https://orcid.org/0000-0002-1679-906X>)
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>

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Package readr updated to version 2.1.1 with previous version 2.1.0 dated 2021-11-11

Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
Author: Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package LWFBrook90R updated to version 0.4.5 with previous version 0.4.4 dated 2021-02-24

Title: Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre] (<https://orcid.org/0000-0003-2699-0893>), Volodymyr Trotsiuk [aut] (<https://orcid.org/0000-0002-8363-656X>), Klaus Hammel [aut], Martin Kennel [aut], Anthony Federer [aut], Robert Nuske [ctb] (<https://orcid.org/0000-0001-9773-2061>), Bavarian State Institute of Forestry (LWF) [cph, fnd], Northwest German Forest Research Institute (NW-FVA) [cph, fnd]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>

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Package xml2 updated to version 1.3.3 with previous version 1.3.2 dated 2020-04-23

Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], RStudio [cph], R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package withr updated to version 2.4.3 with previous version 2.4.2 dated 2021-04-18

Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
Author: Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package vroom updated to version 1.5.7 with previous version 1.5.6 dated 2021-11-10

Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between vroom versions 1.5.6 dated 2021-11-10 and 1.5.7 dated 2021-11-30

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Package SIPDIBGE updated to version 0.1.6 with previous version 0.1.5 dated 2021-10-05

Title: Collection of Household Survey Packages Conducted by IBGE
Description: Provides access to packages developed for downloading, reading and analyzing microdata from household surveys conducted by Brazilian Institute of Geography and Statistics - IBGE. More information can be obtained from the official website <https://www.ibge.gov.br/>.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package quanteda updated to version 3.2.0 with previous version 3.1.0 dated 2021-08-17

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and ngrams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] (<https://orcid.org/0000-0002-0797-564X>), Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>), Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>), Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>), Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>), Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>), Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>), William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>), Christian Müller [ctb], European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package POFIBGE updated to version 0.1.5 with previous version 0.1.4 dated 2021-10-15

Title: Downloading, Reading and Analyzing POF Microdata
Description: Provides tools for downloading, reading and analyzing the POF, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNSIBGE updated to version 0.1.6 with previous version 0.1.5 dated 2021-10-15

Title: Downloading, Reading and Analyzing PNS Microdata
Description: Provides tools for downloading, reading and analyzing the PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNADcIBGE updated to version 0.7.0 with previous version 0.6.5 dated 2021-06-24

Title: Downloading, Reading and Analyzing PNADC Microdata
Description: Provides tools for downloading, reading and analyzing the PNADC, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut], Gabriel Assuncao [aut, cre], Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package pkgload updated to version 1.2.4 with previous version 1.2.3 dated 2021-10-13

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], Lionel Henry [aut, cre], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package midasml updated to version 0.1.6 with previous version 0.1.5-1 dated 2021-05-20

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>

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New package EpiSignalDetection with initial version 0.1.2
Package: EpiSignalDetection
Title: Signal Detection Analysis
Version: 0.1.2
Date: 2021-10-27
Description: Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon (2016) <doi:10.18637/jss.v070.i10>. The package includes: - Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see 'Population' variable). This project was funded by the European Centre for Disease Prevention and Control.
Depends: R (>= 3.4.0)
License: EUPL
Encoding: UTF-8
LazyData: true
Imports: dplyr, graphics, ISOweek, rmarkdown, shiny, surveillance, utils
Suggests: DT, ggplot2, knitr (>= 1.20), pander
VignetteBuilder: knitr
SystemRequirements: pandoc (>= 1.12.3)
URL: https://github.com/EU-ECDC/EpiSignalDetection
NeedsCompilation: no
Packaged: 2021-10-27 16:20:04 UTC; LMC
Author: Lore Merdrignac [aut, ctr, cre] (Author of the package and original code), Joana Gomes Dias [aut, fnd] (Project manager), Esther Kissling [aut, ctr], Tommi Karki [aut, fnd], Margot Einoder-Moreno [ctb, fnd]
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>
Repository: CRAN
Date/Publication: 2021-11-30 15:00:02 UTC

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Package COVIDIBGE updated to version 0.1.8 with previous version 0.1.7 dated 2021-11-03

Title: Downloading, Reading and Analyzing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analyzing the PNAD COVID19, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

Diff between COVIDIBGE versions 0.1.7 dated 2021-11-03 and 0.1.8 dated 2021-11-30

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New package AgroR with initial version 1.2.4
Package: AgroR
Title: Experimental Statistics and Graphics for Agricultural Sciences
Version: 1.2.4
Date: 2021-10-13
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), ANOVA of aligned ranks (Wobbrock, J.O., Findlater, L., Gergle, D., Higgins, JJ (2011), <doi:10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Encoding: UTF-8
Imports: ggplot2, nortest, ScottKnott, lme4, crayon, lmtest, stringr, Hmisc, emmeans, ARTool, multcomp, ggrepel, reshape2, MASS, cowplot, multcompView, RColorBrewer, drc, dunn.test
Suggests: DT, knitr, rmarkdown, roxygen2
Depends: R (>= 3.6.0)
License: GPL (>= 2)
URL: https://agronomiar.github.io/AgroR_package/index.html
NeedsCompilation: no
Packaged: 2021-10-13 14:34:58 UTC; Gabriel
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Rodrigo Yudi Palhaci Marubayashi [aut, ctb] (<https://orcid.org/0000-0003-2778-8654>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Repository: CRAN
Date/Publication: 2021-11-30 15:00:06 UTC

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Package urlchecker updated to version 1.0.1 with previous version 1.0.0 dated 2021-03-04

Title: Run CRAN URL Checks from Older R Versions
Description: Provide the URL checking tools available in R 4.1+ as a package for earlier versions of R. Also uses concurrent requests so can be much faster than the serial versions.
Author: R Core team [aut] (The code in urltools.R adapted from the tools package), Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between urlchecker versions 1.0.0 dated 2021-03-04 and 1.0.1 dated 2021-11-30

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Package remotes updated to version 2.4.2 with previous version 2.4.1 dated 2021-09-29

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Jim Hester [aut], Hadley Wickham [aut], Winston Chang [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package pkgbuild updated to version 1.2.1 with previous version 1.2.0 dated 2020-12-15

Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut], Jim Hester [aut], Gábor Csárdi [aut, cre], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between pkgbuild versions 1.2.0 dated 2020-12-15 and 1.2.1 dated 2021-11-30

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Package fs updated to version 1.5.1 with previous version 1.5.0 dated 2020-07-31

Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on top of the 'libuv' C library.
Author: Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between fs versions 1.5.0 dated 2020-07-31 and 1.5.1 dated 2021-11-30

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Package brio updated to version 1.1.3 with previous version 1.1.2 dated 2021-04-23

Title: Basic R Input Output
Description: Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package bpp updated to version 1.0.3 with previous version 1.0.2 dated 2021-05-20

Title: Computations Around Bayesian Predictive Power
Description: Implements functions to update Bayesian Predictive Power Computations after not stopping a clinical trial at an interim analysis. Such an interim analysis can either be blinded or unblinded. Code is provided for Normally distributed endpoints with known variance, with a prominent example being the hazard ratio.
Author: Kaspar Rufibach, Paul Jordan, Markus Abt
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>

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Package available updated to version 1.0.5 with previous version 1.0.4 dated 2019-07-19

Title: Check if the Title of a Package is Available, Appropriate and Interesting
Description: Check if a given package name is available to use. It checks the name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks for unintended meanings by querying Urban Dictionary, 'Wiktionary' and Wikipedia.
Author: Carl Ganz [aut], Gábor Csárdi [aut, cre], Jim Hester [aut], Molly Lewis [aut], Rachael Tatman [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between available versions 1.0.4 dated 2019-07-19 and 1.0.5 dated 2021-11-30

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Package archive updated to version 1.1.3 with previous version 1.1.2 dated 2021-10-25

Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], Ondrej Holy [cph] (archive_write_add_filter implementation), RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between archive versions 1.1.2 dated 2021-10-25 and 1.1.3 dated 2021-11-30

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Package sparklyr updated to version 1.7.3 with previous version 1.7.2 dated 2021-09-16

Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data processing, see <http://spark.apache.org>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), Kevin Ushey [aut], JJ Allaire [aut], Samuel Macedo [ctb], Hossein Falaki [aut], Lu Wang [aut], Andy Zhang [aut], Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>), Jozef Hajnala [ctb], Maciej Szymkiewicz [ctb] (<https://orcid.org/0000-0003-1469-9396>), Wil Davis [ctb], RStudio [cph], The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>

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Package GeoFIS updated to version 1.0.2 with previous version 1.0.1 dated 2021-07-22

Title: Spatial Data Processing for Decision Making
Description: Methods for processing spatial data for decision-making. This package is an R implementation of methods provided by the open source software GeoFIS <https://www.geofis.org> (Leroux et al. 2018) <doi:10.3390/agriculture8060073>. The main functionalities are the management zone delineation (Pedroso et al. 2010) <doi:10.1016/j.compag.2009.10.007> and data aggregation (Mora-Herrera et al. 2020) <doi:10.1016/j.compag.2020.105624>.
Author: Serge Guillaume [aut], Jean-Luc Lablée [aut, cre], INRAE [cph] (National Research Institute for Agriculture, Food and Environment, France)
Maintainer: Jean-Luc Lablée <jean-luc.lablee@inrae.fr>

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New package tsentiment with initial version 1.0.4
Package: tsentiment
Title: Fetching Tweet Data for Sentiment Analysis
Version: 1.0.4
Author: Hakki Sabah <hakkisabah@hotmail.com>
Maintainer: Hakki Sabah <hakkisabah@hotmail.com>
Description: Which uses Twitter APIs for the necessary data in sentiment analysis, acts as a middleware with the approved Twitter Application. A special access key is given to users who subscribe to the application with their Twitter account. With this special access key, the user defined keyword for sentiment analysis can be searched in twitter recent searches and results can be obtained( more information <https://github.com/hakkisabah/tsentiment> ). In addition, a service named tsentiment-services has been developed to provide all these operations ( for more information <https://github.com/hakkisabah/tsentiment-services> ). After the successful results obtained and in line with the permissions given by the user, the results of the analysis of the word cloud and bar graph saved in the user folder directory can be seen. In each analysis performed, the previous analysis visual result is deleted and this is the basic information you need to know as a practice rule. 'tsentiment' package provides a free service that acts as a middleware for easy data extraction from Twitter, and in return, the user rate limit is reduced by 30 requests from the total limit and the remaining requests are used. These 30 requests are reserved for use in application analytics. For information about endpoints, you can refer to the limit information in the "GET search/tweets" row in the Endpoints column in the list at <https://developer.twitter.com/en/docs/twitter-api/v1/rate-limits>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/hakkisabah/tsentiment, https://www.tsentiment.com
BugReports: https://github.com/hakkisabah/tsentiment/issues
Depends: R (>= 4.0)
Imports: reshape2,wordcloud,wordcloud2,ggplot2,httr,syuzhet,tidytext,dplyr,tibble,progress,stringi
NeedsCompilation: no
Packaged: 2021-11-27 18:13:35 UTC; hakki
Repository: CRAN
Date/Publication: 2021-11-30 11:30:02 UTC

More information about tsentiment at CRAN
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Package BayesCTDesign updated to version 0.6.1 with previous version 0.6.0 dated 2019-08-02

Title: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data
Description: A set of functions to help clinical trial researchers calculate power and sample size for two-arm Bayesian randomized clinical trials that do or do not incorporate historical control data. At some point during the design process, a clinical trial researcher who is designing a basic two-arm Bayesian randomized clinical trial needs to make decisions about power and sample size within the context of hypothesized treatment effects. Through simulation, the simple_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about treatment effect,control group characteristics, and outcome. If the clinical trial researcher has access to historical control data, then the researcher can design a two-arm Bayesian randomized clinical trial that incorporates the historical data. In such a case, the researcher needs to work through the potential consequences of historical and randomized control differences on trial characteristics, in addition to working through issues regarding power in the context of sample size, treatment effect size, and outcome. If a researcher designs a clinical trial that will incorporate historical control data, the researcher needs the randomized controls to be from the same population as the historical controls. What if this is not the case when the designed trial is implemented? During the design phase, the researcher needs to investigate the negative effects of possible historic/randomized control differences on power, type one error, and other trial characteristics. Using this information, the researcher should design the trial to mitigate these negative effects. Through simulation, the historic_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about historical and randomized control differences as well as treatment effects and outcomes. The results from historic_sim() and simple_sim() can be printed with print_table() and graphed with plot_table() methods. Outcomes considered are Gaussian, Poisson, Bernoulli, Lognormal, Weibull, and Piecewise Exponential. The methods are described in Eggleston et al. (2021) <doi:10.18637/jss.v100.i21>.
Author: Barry Eggleston [cre, aut], Doug Wilson [aut], Becky McNeil [aut], Joseph Ibrahim [aut], Diane Catellier [fnd, rth, aut]
Maintainer: Barry Eggleston <beggleston@rti.org>

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Package meta4diag updated to version 2.1.1 with previous version 2.0.8 dated 2018-07-23

Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <https://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE).
Author: Jingyi Guo <jingyi.guo@ntnu.no> and Andrea Riebler <andrea.riebler@ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@ntnu.no>

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Package DDIwR updated to version 0.9 with previous version 0.8 dated 2021-09-02

Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative) related inputs and outputs. Converts data files to and from SPSS, Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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New package soilphysics with initial version 4.1
Package: soilphysics
Title: Soil Physical Analysis
Version: 4.1
Date: 2021-11-21
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva [aut, cre] (<https://orcid.org/0000-0003-2518-542X>), Renato Paiva de Lima [aut] (<https://orcid.org/0000-0003-0524-439X>)
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
URL: https://arsilva87.github.io/soilphysics/
Imports: utils, stats, graphics, boot, grDevices, datasets, MASS, shiny, shinydashboard, fields
Suggests: knitr, rmarkdown, rpanel, tcltk
VignetteBuilder: knitr
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-11-21 11:41:00 UTC; User
Repository: CRAN
Date/Publication: 2021-11-30 09:50:02 UTC

More information about soilphysics at CRAN
Permanent link

Package rethnicity updated to version 0.2.2 with previous version 0.1.2 dated 2021-10-07

Title: Predicting Ethnic Group from Names
Description: Implementation of the ethnicity prediction method, described in "Rethnicity: Predicting Ethnicity from Names" by Fangzhou Xie (2021) <arXiv:2109.09228>.
Author: Fangzhou Xie [aut, cre] (<https://orcid.org/0000-0001-7702-093X>)
Maintainer: Fangzhou Xie <fangzhou.xie@rutgers.edu>

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Package odbc updated to version 1.3.3 with previous version 1.3.2 dated 2021-04-03

Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut], Hadley Wickham [aut, cre], Oliver Gjoneski [ctb] (detule), lexicalunit [cph] (nanodbc library), Google Inc. [cph] (cctz library), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package glue updated to version 1.5.1 with previous version 1.5.0 dated 2021-11-06

Title: Interpreted String Literals
Description: An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package cpp11 updated to version 0.4.2 with previous version 0.4.1 dated 2021-11-03

Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Romain François [aut, cre], Benjamin Kietzman [ctb], RStudio [cph, fnd]
Maintainer: Romain François <romain@rstudio.com>

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Package ubms updated to version 1.1.0 with previous version 1.0.2 dated 2021-02-01

Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence via the 'rstan' package, the R interface to the 'Stan' C++ library. Supported models include single-season occupancy, dynamic occupancy, and N-mixture abundance models. Covariates on model parameters are specified using a formula-based interface similar to package 'unmarked', while also allowing for estimation of random slope and intercept terms. References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>

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 ubms-1.1.0/ubms/tests/testthat/test_missing.R                     |   26 -
 ubms-1.1.0/ubms/tests/testthat/test_multinomPois.R                |   47 +-
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 ubms-1.1.0/ubms/tests/testthat/test_occuRN.R                      |   42 +-
 ubms-1.1.0/ubms/tests/testthat/test_occuTTD.R                     |   38 +
 ubms-1.1.0/ubms/tests/testthat/test_pcount.R                      |   63 ++-
 ubms-1.1.0/ubms/tests/testthat/test_plot_effects.R                |only
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 ubms-1.1.0/ubms/tests/testthat/test_priors.R                      |only
 ubms-1.1.0/ubms/tests/testthat/test_ranef.R                       |    4 
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 ubms-1.1.0/ubms/tests/testthat/test_submodel.R                    |  168 ++++++--
 ubms-1.1.0/ubms/tests/testthat/test_ubmsFit_methods.R             |   51 ++
 ubms-1.1.0/ubms/tests/testthat/test_utils.R                       |   13 
 ubms-1.1.0/ubms/vignettes/JAGS-comparison.Rmd                     |    5 
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Permanent link

New package PhaseTypeR with initial version 1.0.0
Package: PhaseTypeR
Title: General-Purpose Phase-Type Functions
Version: 1.0.0
Maintainer: Iker Rivas-González <ikerrivas96@gmail.com>
Description: General implementation of core function from phase-type theory. 'PhaseTypeR' can be used to model continuous and discrete phase-type distributions, both univariate and multivariate. The package includes functions for outputting the mean and (co)variance of phase-type distributions; their density, probability and quantile functions; functions for random draws; functions for reward-transformation; and functions for plotting the distributions as networks. For more information on these functions please refer to Bladt and Nielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro (2019) <https://orbit.dtu.dk/en/publications/order-statistics-and-multivariate-discrete-phase-type-distributio>.
License: GPL-3
URL: https://rivasiker.github.io/PhaseTypeR/, https://github.com/rivasiker/PhaseTypeR
BugReports: https://github.com/rivasiker/PhaseTypeR/issues
Depends: expm, igraph, methods
Suggests: knitr, partitions, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-29 16:29:11 UTC; au595587
Author: Iker Rivas-González [aut, cre] (<https://orcid.org/0000-0002-0515-0628>), Colin Guetemme [aut], Asger Hobolth [aut], Lars Nørvang Andersen [aut]
Repository: CRAN
Date/Publication: 2021-11-30 09:00:06 UTC

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Package gmailr updated to version 1.0.1 with previous version 1.0.0 dated 2019-08-23

Title: Access the 'Gmail' 'RESTful' API
Description: An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.
Author: Jim Hester [aut], Jennifer Bryan [aut, cre], RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between gmailr versions 1.0.0 dated 2019-08-23 and 1.0.1 dated 2021-11-30

 DESCRIPTION                      |   27 -
 MD5                              |  142 +++----
 NAMESPACE                        |  284 +++++++--------
 NEWS.md                          |    6 
 R/aaa.R                          |    8 
 R/draft.R                        |   10 
 R/gm-auth.R                      |   11 
 R/history.R                      |    2 
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 README.md                        |   16 
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 inst/doc/sending_messages.R      |  166 ++++----
 inst/doc/sending_messages.html   |  732 +++++++++++++++------------------------
 inst/secret/rpkgtester@gmail.com |binary
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 man/gm_create_label.Rd           |   67 +--
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 man/gm_delete_draft.Rd           |   60 +--
 man/gm_delete_label.Rd           |   52 +-
 man/gm_delete_message.Rd         |   76 ++--
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 man/gm_has_token.Rd              |   36 -
 man/gm_history.Rd                |   67 +--
 man/gm_id.Rd                     |   55 +-
 man/gm_import_message.Rd         |  100 ++---
 man/gm_insert_message.Rd         |  100 ++---
 man/gm_label.Rd                  |   52 +-
 man/gm_labels.Rd                 |   58 +--
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 man/gm_modify_message.Rd         |   93 ++--
 man/gm_modify_thread.Rd          |   84 ++--
 man/gm_profile.Rd                |   70 +--
 man/gm_save_attachment.Rd        |   78 ++--
 man/gm_save_attachments.Rd       |   91 ++--
 man/gm_send_draft.Rd             |   64 +--
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 man/gm_thread.Rd                 |   64 +--
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 man/gm_trash_thread.Rd           |   63 +--
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 man/gm_untrash_thread.Rd         |   63 +--
 man/gm_update_label.Rd           |   76 ++--
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 man/gmailr.Rd                    |   19 -
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 man/quoted_printable_encode.Rd   |   36 -
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 tests/testthat.R                 |    6 
 tests/testthat/helper.R          |    2 
 vignettes/gmailr.Rmd             |    2 
 72 files changed, 2839 insertions(+), 3019 deletions(-)

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New package diffudist with initial version 1.0.0
Package: diffudist
Title: Diffusion Distance for Complex Networks
Version: 1.0.0
URL: https://gbertagnolli.github.io/diffudist/
BugReports: https://github.com/gbertagnolli/diffudist/issues/
Description: Enables the evaluation of diffusion distances for complex single-layer networks. Given a network one can define different types of Laplacian (or transition) matrices corresponding to different continuous-time random walks dynamics on the network. This package enables the evaluation of Laplacians, stochastic matrices, and the corresponding diffusion distance matrices. The metric structure induced by the network-driven process is richer and more robust than the one given by shortest-paths and allows to study the geometry induced by different types of diffusion-like communication mechanisms taking place on complex networks. For more details see: De Domenico, M. (2017) <doi:10.1103/physrevlett.118.168301> and Bertagnolli, G. and De Domenico, M. (2021) <doi:10.1103/PhysRevE.103.042301>.
Depends: R (>= 3.5.0)
Imports: expm, ggdendro, ggplot2, grid, igraph, Matrix, stats, Rcpp (>= 1.0.7), reshape2, rlang, viridis
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, cowplot, parallelDist, strex, tidyr, rmarkdown
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-11-29 09:47:25 UTC; giulia
Author: Giulia Bertagnolli [aut, cre] (<https://orcid.org/0000-0001-8637-0632>), Manlio De Domenico [aut] (<https://orcid.org/0000-0001-5158-8594>)
Maintainer: Giulia Bertagnolli <giulia.bertagnolli@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-30 08:20:06 UTC

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Package devtools updated to version 2.4.3 with previous version 2.4.2 dated 2021-06-07

Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut], Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between devtools versions 2.4.2 dated 2021-06-07 and 2.4.3 dated 2021-11-30

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 devtools-2.4.3/devtools/NEWS.md                          |    9 +++
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 devtools-2.4.3/devtools/tests/testthat/test-run-source.R |   13 +++--
 devtools-2.4.3/devtools/vignettes/dependencies.Rmd       |    6 +-
 22 files changed, 102 insertions(+), 74 deletions(-)

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New package d4storagehub4R with initial version 0.1
Package: d4storagehub4R
Version: 0.1
Date: 2021-11-29
Title: Interface to 'D4Science' 'StorageHub' API
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Depends: R (>= 3.3.0), methods
Imports: R6, httr, jsonlite, XML, keyring, tools
Suggests: testthat, parallel
Description: Provides an interface to 'D4Science' 'StorageHub' API (<https://dev.d4science.org/>). Allows to get user profile, and perform actions over the 'StorageHub' (workspace) including creation of folders, files management (upload/update/deletion/sharing), and listing of stored resources.
License: MIT + file LICENSE
URL: https://github.com/eblondel/d4storagehub4R, https://www.d4science.org/, https://dev.d4science.org/
BugReports: https://github.com/eblondel/d4storagehub4R/issues
LazyLoad: yes
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-29 08:40:28 UTC; manub
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Repository: CRAN
Date/Publication: 2021-11-30 08:20:09 UTC

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Package COINr updated to version 0.6.1 with previous version 0.6.0 dated 2021-11-26

Title: Composite Indicator Construction and Analysis
Description: A comprehensive high-level package for composite indicator construction and analysis. It is a "development environment" for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation, data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single hierarchical list called a "COIN". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons. It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results (maps, bar charts, radar charts, and more). Finally, three Shiny apps are available which enable fast data exploration, results presentation, and checking the effects of altering weights. Full documentation is found in the online book at <https://bluefoxr.github.io/COINrDoc/>, as well as the vignette.
Author: William Becker [aut, cre, cph] (<https://orcid.org/0000-0002-6467-4472>)
Maintainer: William Becker <william.becker@bluefoxdata.eu>

Diff between COINr versions 0.6.0 dated 2021-11-26 and 0.6.1 dated 2021-11-30

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 R/coin_assemble.R     |    4 ++--
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 9 files changed, 41 insertions(+), 40 deletions(-)

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New package cthist with initial version 0.1.1
Package: cthist
Title: Clinical Trial Registry History
Version: 0.1.1
Description: Retrieves historical versions of clinical trial registry entries.
License: AGPL (>= 3)
URL: https://github.com/bgcarlisle/cthist
BugReports: https://github.com/bgcarlisle/cthist/issues
Imports: dplyr, httr, jsonlite, magrittr, readr, rlang, rvest, selectr, stringr, tibble
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-29 10:09:42 UTC; bgcarlisle
Author: Benjamin Gregory Carlisle [aut, cre] (<https://orcid.org/0000-0001-8975-0649>)
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Repository: CRAN
Date/Publication: 2021-11-30 08:30:02 UTC

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Package canvasXpress updated to version 1.37.0-1 with previous version 1.37.0 dated 2021-11-26

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut], Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>

Diff between canvasXpress versions 1.37.0 dated 2021-11-26 and 1.37.0-1 dated 2021-11-30

 DESCRIPTION                            |    6 +++---
 MD5                                    |   14 +++++++-------
 NEWS.md                                |    2 ++
 R/html_functionality.R                 |    2 ++
 inst/doc/additional_examples.html      |    4 ++--
 inst/doc/getting_started.html          |    4 ++--
 man/cxHtmlPage.Rd                      |    2 ++
 tests/testthat/test-other-cxHtmlPage.R |    4 ++++
 8 files changed, 24 insertions(+), 14 deletions(-)

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Package bs4cards updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-03

Title: Generate Bootstrap Cards
Description: Allows the user to generate bootstrap cards within R markdown documents. Intended for use in conjunction with R markdown HTML outputs and other formats that support the bootstrap 4 library.
Author: Danielle Navarro [aut, cre] (<https://orcid.org/0000-0001-7648-6578>)
Maintainer: Danielle Navarro <djnavarro@protonmail.com>

Diff between bs4cards versions 0.1.0 dated 2021-09-03 and 0.1.1 dated 2021-11-30

 DESCRIPTION                 |   14 +++++++-------
 MD5                         |   25 +++++++++++++------------
 NEWS.md                     |only
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 R/build-tag-list.R          |    8 +++++---
 R/card-pieces.R             |    2 +-
 R/cards.R                   |   23 +++++++++++++++++++----
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 README.md                   |    5 +++--
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 tests/testthat/test-cards.R |   26 ++++++++++++++++++++++++++
 14 files changed, 102 insertions(+), 43 deletions(-)

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New package abstr with initial version 0.4.1
Package: abstr
Title: R Interface to the A/B Street Transport System Simulation Software
Version: 0.4.1
Description: Provides functions to convert origin-destination data, represented as straight 'desire lines' in the 'sf' Simple Features class system, into JSON files that can be directly imported into A/B Street <https://www.abstreet.org>, a free and open source tool for simulating urban transport systems and scenarios of change <doi:10.1007/s10109-020-00342-2>.
License: Apache License (>= 2)
URL: https://github.com/a-b-street/abstr, https://a-b-street.github.io/abstr/
BugReports: https://github.com/a-b-street/abstr/issues
Depends: R (>= 4.0.0)
Imports: jsonlite (>= 1.7.2), lwgeom (>= 0.2.5), magrittr (>= 2.0.1), methods, od (>= 0.3.1), sf (>= 1.0.1), tibble (>= 3.0.6), tidyr (>= 1.1.3)
Suggests: knitr, dplyr (>= 1.0.0), rmarkdown, tmap, pct, foreign
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-26 21:32:54 UTC; natha
Author: Nathanael Sheehan [aut, cre] (<https://orcid.org/0000-0002-2779-0976>), Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>), Trevor Nederlof [aut], Lucas Dias [ctb], Dustin Carlino [aut]
Maintainer: Nathanael Sheehan <nathanaelsheehan@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-30 08:10:05 UTC

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New package sigora with initial version 3.1.1
Package: sigora
Title: Signature Overrepresentation Analysis
Version: 3.1.1
Date: 2021-11-29
Depends: R (>= 3.0.0)
URL: https://github.com/wolski/sigora
BugReports: https://github.com/wolski/sigora/issues
Imports: stats, slam
Suggests: knitr
Description: Pathway Analysis is statistically linking observations on the molecular level to biological processes or pathways on the systems(i.e., organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. However, this can lead to identifying spurious pathways as statistically significant since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse datasets. In addition, it contains pre-computed Pathway-GPS data for pathways in the KEGG and Reactome pathway repositories and mechanisms for extracting GPS for user-supplied repositories.
License: GPL-3
NeedsCompilation: no
biocViews: GeneSetEnrichment, GO, Software, Pathways, KEGG
VignetteBuilder: knitr
Packaged: 2021-11-29 12:47:12 UTC; wolski
Author: Amir Foroushani [aut] (<https://orcid.org/0000-0003-2748-3009>), Fiona Brinkman [aut], David Lynn [aut], Witold Wolski [cre] (<https://orcid.org/0000-0002-6468-120X>)
Maintainer: Witold Wolski <wew@fgcz.ethz.ch>
Repository: CRAN
Date/Publication: 2021-11-30 07:50:02 UTC

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Package rsparse updated to version 0.5.0 with previous version 0.4.0 dated 2020-04-01

Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on sparse matrices - matrix factorizations, matrix completion, elastic net regressions, factorization machines. Also 'rsparse' enhances 'Matrix' package by providing methods for multithreaded <sparse, dense> matrix products and native slicing of the sparse matrices in Compressed Sparse Row (CSR) format. List of the algorithms for regression problems: 1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL) Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>) 2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>) List of algorithms for matrix factorization and matrix completion: 1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>) 2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro (2005, <doi:10.1145/1102351.1102441>) 3) Fast Truncated Singular Value Decomposition (SVD), Soft-Thresholded SVD, Soft-Impute matrix completion via ALS - paper by Hastie, Mazumder et al. (2014, <arXiv:1410.2596>) 4) Linear-Flow matrix factorization, from 'Practical linear models for large-scale one-class collaborative filtering' by Sedhain, Bui, Kawale et al (2016, ISBN:978-1-57735-770-4) 5) GlobalVectors (GloVe) matrix factorization via SGD, paper by Pennington, Socher, Manning (2014, <https://aclanthology.org/D14-1162/>) Package is reasonably fast and memory efficient - it allows to work with large datasets - millions of rows and millions of columns. This is particularly useful for practitioners working on recommender systems.
Author: Dmitriy Selivanov [aut, cre, cph] (<https://orcid.org/0000-0001-5413-1506>), David Cortes [ctb], Drew Schmidt [ctb] (configure script for BLAS, LAPACK detection), Wei-Chen Chen [ctb] (configure script and work on linking to float package)
Maintainer: Dmitriy Selivanov <ds@rexy.ai>

Diff between rsparse versions 0.4.0 dated 2020-04-01 and 0.5.0 dated 2021-11-30

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 rsparse-0.5.0/rsparse/DESCRIPTION                           |   18 
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 rsparse-0.5.0/rsparse/NAMESPACE                             |    4 
 rsparse-0.5.0/rsparse/NEWS.md                               |    4 
 rsparse-0.5.0/rsparse/R/MatrixFactorizationRecommender.R    |    7 
 rsparse-0.5.0/rsparse/R/RcppExports.R                       |   68 
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Package rflsgen updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-25

Title: R Interface to the 'Flsgen' Neutral Landscape Generator with Targets on Landscape Indices
Description: Interface to the 'flsgen' neutral landscape generator <https://github.com/dimitri-justeau/flsgen>. It allows to - Generate fractal terrain; - Generate landscape structures satisfying user targets over landscape indices; - Generate landscape raster from landscape structures.
Author: Dimitri Justeau-Allaire, Grégoire Blanchard, Thomas Ibanez, Xavier Lorca, Ghislain Vieilledent, Philippe Birnbaum
Maintainer: Dimitri Justeau-Allaire <dimitri.justeau@gmail.com>

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Package ows4R updated to version 0.2 with previous version 0.1-5 dated 2020-05-27

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. Partial support is provided for the Web Map Service (WMS) and Web Processing Service (WPS). The purpose is to add support for additional OGC service standards such as Web Coverage Service (WCS), Web Coverage Processing Service (WCPS) or OGC API.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>), Alexandre Bennici [ctb] (<https://orcid.org/0000-0003-2160-3487>), Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package gesso updated to version 1.0.2 with previous version 1.0.1 dated 2021-06-16

Title: Hierarchical GxE Interactions in a Regularized Regression Model
Description: The method focuses on a single environmental exposure and induces a main-effect-before-interaction hierarchical structure for the joint selection of interaction terms in a regularized regression model. For details see Zemlianskaia et al. (2021) <arxiv:2103.13510>.
Author: Natalia Zemlianskaia
Maintainer: Natalia Zemlianskaia <natasha.zemlianskaia@gmail.com>

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Package decor updated to version 1.0.1 with previous version 1.0.0 dated 2020-06-30

Title: Retrieve Code Decorations
Description: Retrieves code comment decorations for C++ languages of the form '\\ [[xyz]]', which are used for automated wrapping of C++ functions.
Author: Romain François [aut, cre], Jim Hester [aut], RStudio [cph, fnd]
Maintainer: Romain François <romain@rstudio.com>

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Package BiDAG updated to version 2.0.4 with previous version 2.0.3 dated 2021-07-28

Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data or categorical data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks. References: J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>, N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>, D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>, J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>, M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>

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Package bench updated to version 1.1.2 with previous version 1.1.1 dated 2020-01-13

Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for R expressions.
Author: Jim Hester [aut], Davis Vaughan [aut, cre], Drew Schmidt [ctb] (read_proc_file implementation)
Maintainer: Davis Vaughan <davis@rstudio.com>

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Package BayesSUR updated to version 2.0-1 with previous version 2.0-0 dated 2021-05-05

Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, and the software paper is in Zhao et al. (2021) <arXiv:2104.14008>.
Author: Marco Banterle [aut], Zhi Zhao [aut, cre], Leonardo Bottolo [ctb], Sylvia Richardson [ctb], Waldir Leoncio [ctb], Alex Lewin [aut], Manuela Zucknick [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>

Diff between BayesSUR versions 2.0-0 dated 2021-05-05 and 2.0-1 dated 2021-11-30

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Package animint2 (with last version 2020.9.18) was removed from CRAN

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

2020-10-20 2020.9.18

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Package Rpadrino (with last version 0.0.2) was removed from CRAN

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

2021-11-16 0.0.2
2021-11-15 0.0.1

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Package biblio (with last version 0.0.5) was removed from CRAN

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

2021-11-20 0.0.5
2021-11-09 0.0.4
2021-11-06 0.0.3

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Package clpAPI (with last version 1.3.1) was removed from CRAN

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

2021-10-28 1.3.1
2020-08-10 1.3.0
2020-02-13 1.2.13
2019-06-14 1.2.11
2018-09-24 1.2.9
2016-04-19 1.2.7
2016-04-12 1.2.6-1
2013-10-26 1.2.6
2013-09-08 1.2.5
2013-07-17 1.2.4
2013-05-23 1.2.3
2013-01-16 1.2.2
2012-04-21 1.2.1
2011-08-22 1.1.7
2011-07-29 1.1.6
2011-07-28 1.1.5

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Package zen4R updated to version 0.5-2 with previous version 0.5-1 dated 2021-10-29

Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload and download of files.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>), Julien Barde [ctb] (<https://orcid.org/0000-0002-3519-6141>), Stephen Eglen [ctb] (<https://orcid.org/0000-0001-8607-8025>), Hans Van Calster [ctb] (<https://orcid.org/0000-0001-8595-8426>), Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package ggdist updated to version 3.0.1 with previous version 3.0.0 dated 2021-07-19

Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include but are not limited to: points with multiple uncertainty intervals, eye plots (Spiegelhalter D., 1999) <doi:10.1111/1467-985X.00120>, density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>, quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>, complementary cumulative distribution function barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>, and fit curves with multiple uncertainty ribbons.
Author: Matthew Kay [aut, cre], Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>

Diff between ggdist versions 3.0.0 dated 2021-07-19 and 3.0.1 dated 2021-11-30

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 ggdist-3.0.1/ggdist/DESCRIPTION                                                                                  |   12 
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 ggdist-3.0.1/ggdist/R/draw_key_slabinterval.R                                                                    |    6 
 ggdist-3.0.1/ggdist/R/geom_slabinterval.R                                                                        |    3 
 ggdist-3.0.1/ggdist/R/point_interval.R                                                                           |   12 
 ggdist-3.0.1/ggdist/R/stat_lineribbon.R                                                                          |  380 +++++-----
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 ggdist-3.0.1/ggdist/R/student_t.R                                                                                |  162 ++--
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 ggdist-3.0.1/ggdist/inst/doc/lineribbon.html                                                                     |    8 
 ggdist-3.0.1/ggdist/inst/doc/slabinterval.Rmd                                                                    |    2 
 ggdist-3.0.1/ggdist/inst/doc/slabinterval.html                                                                   |   10 
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 ggdist-3.0.1/ggdist/man/marginalize_lkjcorr.Rd                                                                   |  156 ++--
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 ggdist-3.0.1/ggdist/tests/testthat/test.lkj_marginal.R                                                           |    5 
 ggdist-3.0.1/ggdist/tests/testthat/test.point_interval.R                                                         |    2 
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 ggdist-3.0.1/ggdist/tests/testthat/test.stat_sample_slabinterval.R                                               |   16 
 ggdist-3.0.1/ggdist/vignettes/slabinterval.Rmd                                                                   |    2 
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Package Eagle updated to version 2.5 with previous version 2.4.5 dated 2021-06-10

Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre], Joshua Bowden [ctb], Ryan Stephenson [ctb], Hyun Kang [ctb], Noah Zaitlen [ctb], Claire Wade [ctb], Andrew Kirby [ctb], David Heckerman [ctb], Mark Daly [ctb], Eleazar Eskin [ctb]
Maintainer: Andrew George <geo047@gmail.com>

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More information about Eagle at CRAN
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