Mon, 25 Jan 2021

Package stringb updated to version 0.1.17 with previous version 0.1.14 dated 2020-02-05

Title: Convenient Base R String Handling
Description: Base R already ships with string handling capabilities 'out- of-the-box' but lacks streamlined function names and workflow. The 'stringi' ('stringr') package on the other hand has well named functions, extensive Unicode support and allows for a streamlined workflow. On the other hand it adds dependencies and regular expression interpretation between base R functions and 'stringi' functions might differ. This packages aims at providing a solution to the use case of unwanted dependencies on the one hand but the need for streamlined text processing on the other. The packages' functions are solely based on wrapping base R functions into 'stringr'/'stringi' like function names. Along the way it adds one or two extra functions and last but not least provides all functions as generics, therefore allowing for adding methods for other text structures besides plain character vectors.
Author: Peter Meissner [aut, cre]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

Diff between stringb versions 0.1.14 dated 2020-02-05 and 0.1.17 dated 2021-01-25

 stringb-0.1.14/stringb/README.md                     |only
 stringb-0.1.17/stringb/DESCRIPTION                   |   13 ++---
 stringb-0.1.17/stringb/MD5                           |   45 +++++++++----------
 stringb-0.1.17/stringb/NEWS.md                       |    8 +++
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 24 files changed, 154 insertions(+), 92 deletions(-)

More information about stringb at CRAN
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Package stars updated to version 0.5-1 with previous version 0.5-0 dated 2021-01-19

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

Diff between stars versions 0.5-0 dated 2021-01-19 and 0.5-1 dated 2021-01-25

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More information about stars at CRAN
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New package BLCOP with initial version 0.3.3
Package: BLCOP
Type: Package
Title: Black-Litterman and Copula Opinion Pooling Frameworks
Version: 0.3.3
Authors@R: c(person(given = "Francisco", family = "Gochez", role = "aut"), person(given = "Richard", family = "Chandler-Mant", role = "aut"), person(given = "Suchen", family = "Jin", role = "aut"), person(given = "Jinjing", family = "Xie", role = "aut"), person(given = "Ava", family = "Yang", role = "ctb", email = "ayang@mango-solutions.com", comment = "Previous maintainer"), person(given = "Joe", family = "Russell", role = "cre", email = "jrussell@mango-solutions.com"))
Description: An implementation of the Black-Litterman Model and Attilio Meucci's copula opinion pooling framework as described in Meucci, Attilio (2005) <doi:10.2139/ssrn.848407>, Meucci, Attilio (2006) <doi:10.2139/ssrn.872577> and Meucci, Attilio (2008) <doi:10.2139/ssrn.1117574>.
License: MIT + file LICENSE
LazyData: true
NeedsCompilation: no
URL: https://github.com/mangothecat/BLCOP
BugReports: https://github.com/mangothecat/BLCOP/issues
Imports: methods, MASS, quadprog, RUnit (>= 0.4.22), timeSeries, fBasics, fMultivar, fPortfolio (>= 3011.81), rmarkdown, knitr
Suggests: sn, corpcor, mnormt
VignetteBuilder: knitr
Packaged: 2021-01-25 15:30:56 UTC; jrussell
Author: Francisco Gochez [aut], Richard Chandler-Mant [aut], Suchen Jin [aut], Jinjing Xie [aut], Ava Yang [ctb] (Previous maintainer), Joe Russell [cre]
Maintainer: Joe Russell <jrussell@mango-solutions.com>
Repository: CRAN
Date/Publication: 2021-01-25 23:00:02 UTC

More information about BLCOP at CRAN
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Package wrGraph updated to version 1.2.0 with previous version 1.1.1 dated 2020-12-03

Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here. This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots, automatic checking for optimal location of legends in plots, small histograms to insert as legends, histograms re-transforming axis labels to linear when plotting log2-transformed data, a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats, principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples, generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>, staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>

Diff between wrGraph versions 1.1.1 dated 2020-12-03 and 1.2.0 dated 2021-01-25

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More information about wrGraph at CRAN
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Package shinythemes updated to version 1.2.0 with previous version 1.1.2 dated 2018-11-06

Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes from <https://bootswatch.com/>, which are packaged for use with Shiny applications.
Author: Winston Chang [aut, cre], RStudio [cph], Thomas Park [ctb, cph] (Bootswatch themes), Lukasz Dziedzic [ctb, cph] (Lato font), Nathan Willis [ctb, cph] (News Cycle font), Google Corporation [ctb, cph] (Open Sans and Roboto fonts), Matt McInerney [ctb, cph] (Raleway font), Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font), Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between shinythemes versions 1.1.2 dated 2018-11-06 and 1.2.0 dated 2021-01-25

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More information about shinythemes at CRAN
Permanent link

Package shiny updated to version 1.6.0 with previous version 1.5.0 dated 2020-06-23

Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre], Joe Cheng [aut], JJ Allaire [aut], Carson Sievert [aut], Barret Schloerke [aut], Yihui Xie [aut], Jeff Allen [aut], Jonathan McPherson [aut], Alan Dipert [aut], Barbara Borges [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Dave Gandy [ctb, cph] (Font-Awesome font), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between shiny versions 1.5.0 dated 2020-06-23 and 1.6.0 dated 2021-01-25

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 shiny-1.6.0/shiny/R/map.R                                                                    |   15 
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Package rgnparser updated to version 0.2.0 with previous version 0.1.0 dated 2020-11-05

Title: Parse Scientific Names
Description: Parse scientific names using 'gnparser' (<https://github.com/gnames/gnparser>), written in Go. 'gnparser' parses scientific names into their component parts; it utilizes a Parsing Expression Grammar specifically for scientific names.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rgnparser versions 0.1.0 dated 2020-11-05 and 0.2.0 dated 2021-01-25

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Package microseq updated to version 2.1.4 with previous version 2.1.2 dated 2020-07-05

Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Author: Lars Snipen, Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>

Diff between microseq versions 2.1.2 dated 2020-07-05 and 2.1.4 dated 2021-01-25

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Package image.textlinedetector updated to version 0.1.3 with previous version 0.1.2 dated 2020-09-22

Title: Segment Images in Text Lines and Words
Description: Find text lines in scanned images and segment the lines into words. Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>, an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>, and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper), Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital Humanities [cph] (R wrapper), Jeroen Ooms [ctb, cph] (More details in LICENSE.note file), Arthur Flôr [ctb, cph] (More details in LICENSE.note file), Saverio Meucci [ctb, cph] (More details in LICENSE.note file), Yeara Kozlov [ctb, cph] (More details in LICENSE.note file), Tino Weinkauf [ctb, cph] (More details in LICENSE.note file)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>

Diff between image.textlinedetector versions 0.1.2 dated 2020-09-22 and 0.1.3 dated 2021-01-25

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Package gwaRs updated to version 0.2.0 with previous version 0.1.0 dated 2021-01-21

Title: Manhattan, Q-Q, and PCA Plots using 'ggplot2'
Description: Generate Manhattan, Q-Q, and PCA plots from GWAS and PCA results using 'ggplot2'.
Author: Lindokuhle Nkambule [aut, cre] (<https://orcid.org/0000-0002-5682-2834>)
Maintainer: Lindokuhle Nkambule <lindonkambule116@gmail.com>

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Package gert updated to version 1.1.0 with previous version 1.0.2 dated 2020-11-12

Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent. On Linux, a somewhat recent version of 'libgit2' is required; we provide a 'PPA' for older Ubuntu 'LTS' versions.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Jennifer Bryan [ctb] (<https://orcid.org/0000-0002-6983-2759>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package CruzPlot updated to version 1.4.4 with previous version 1.4.3 dated 2021-01-11

Title: Plot Shipboard DAS Data
Description: A utility program oriented to create maps, plot data, and do basic data summaries of 'DAS' data <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> produced by 'WinCruz' from the Southwest Fisheries Science Center. <https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>), Tim Gerrodette [aut]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

Diff between CruzPlot versions 1.4.3 dated 2021-01-11 and 1.4.4 dated 2021-01-25

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Package weibull4 updated to version 1.0.0 with previous version 0.1.0 dated 2020-09-17

Title: Fits Data into 4-Parameters Weibull Distribution
Description: Performs a curve fit to 4-parameters Weibull distribution using Metropolis algorithm - Markov chain-Monte Carlo method. Special usage for fitting COVID-19 epidemic data on daily new cases and deaths. Also, builds the 4-parameters Weibull distribution curve using given parameters (shape, scale, location and area).
Author: Vitor Hugo Moreau
Maintainer: Vitor Hugo Moreau <vitorhmc@ufba.br>

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Package fastmap updated to version 1.1.0 with previous version 1.0.1 dated 2019-10-08

Title: Fast Data Structures
Description: Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.
Author: Winston Chang [aut, cre], RStudio [cph, fnd], Tessil [cph] (hopscotch_map library)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between fastmap versions 1.0.1 dated 2019-10-08 and 1.1.0 dated 2021-01-25

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Package rmetalog updated to version 1.0.3 with previous version 1.0.2 dated 2020-03-10

Title: The Metalog Distribution
Description: Implementation of the metalog distribution in R. The metalog distribution is a modern, highly flexible, data-driven distribution. Metalogs are developed by Keelin (2016) <doi:10.1287/deca.2016.0338>. This package provides functions to build these distributions from raw data. Resulting metalog objects are then useful for exploratory and probabilistic analysis.
Author: Isaac Faber [aut, cre] (<https://orcid.org/0000-0002-4478-9598>), Jongbin Jung [aut]
Maintainer: Isaac Faber <isaacfab@gmail.com>

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Package mitml updated to version 0.4-0 with previous version 0.3-7 dated 2019-01-07

Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>

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Package sisireg updated to version 0.8.1 with previous version 0.8.0 dated 2021-01-22

Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 9798682394203, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 9798593470270, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>

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Package vcdExtra updated to version 0.7-5 with previous version 0.7-1 dated 2017-09-29

Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package simputation updated to version 0.2.6 with previous version 0.2.5 dated 2021-01-11

Title: Simple Imputation
Description: Easy to use interfaces to a number of imputation methods that fit in the not-a-pipe operator of the 'magrittr' package.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package memery updated to version 0.5.3 with previous version 0.5.2 dated 2019-04-19

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

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New package IPCAPS with initial version 1.1.8
Package: IPCAPS
Type: Package
Title: Iterative Pruning to Capture Population Structure
Version: 1.1.8
Authors@R: c(person(given = "Kridsadakorn", family = "Chaichoompu", email = "kridsadakorn@biostatgen.org", role = c("aut", "cre")), person(given = "Kristel", family = 'Van Steen', role = "aut"), person(given = "Fentaw", family = "Abegaz", role = "aut"), person(given = "Sissades", family = "Tongsima", role = "aut"), person(given = "Philip", family = "Shaw", role = "aut"), person(given = "Anavaj", family = "Sakuntabhai", role = "aut"), person(given = "Luisa", family = "Pereira", role = "aut"))
Description: An unsupervised clustering algorithm based on iterative pruning is for capturing population structure. This version supports ordinal data which can be applied directly to SNP data to identify fine-level population structure and it is built on the iterative pruning Principal Component Analysis ('ipPCA') algorithm as explained in Intarapanich et al. (2009) <doi:10.1186/1471-2105-10-382>. The 'IPCAPS' involves an iterative process using multiple splits based on multivariate Gaussian mixture modeling of principal components and 'Expectation-Maximization' clustering as explained in Lebret et al. (2015) <doi:10.18637/jss.v067.i06>. In each iteration, rough clusters and outliers are also identified using the function rubikclust() from the R package 'KRIS'.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: stats,utils,graphics,grDevices,MASS,Matrix,expm,KRIS,fpc,LPCM,apcluster,Rmixmod
Suggests: testthat
BugReports: https://gitlab.com/kris.ccp/ipcaps/-/issues
URL: https://gitlab.com/kris.ccp/ipcaps
Collate: 'parallelization.R' 'check.stopping.R' 'clustering.mode.R' 'clustering.R' 'data.R' 'export.groups.R' 'get.node.info.R' 'ipcaps-package.R' 'process.each.node.R' 'output.template.R' 'save.html.R' 'save.eigenplots.html.R' 'save.plots.label.html.R' 'save.plots.cluster.html.R' 'save.plots.R' 'postprocess.R' 'preprocess.R' 'ipcaps.R' 'top.discriminator.R'
NeedsCompilation: no
Packaged: 2021-01-25 11:25:50 UTC; kris
Author: Kridsadakorn Chaichoompu [aut, cre], Kristel Van Steen [aut], Fentaw Abegaz [aut], Sissades Tongsima [aut], Philip Shaw [aut], Anavaj Sakuntabhai [aut], Luisa Pereira [aut]
Maintainer: Kridsadakorn Chaichoompu <kridsadakorn@biostatgen.org>
Repository: CRAN
Date/Publication: 2021-01-25 17:00:15 UTC

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Package geneExpressionFromGEO updated to version 0.4 with previous version 0.3 dated 2020-11-17

Title: Retrieves Gene Expression Dataset and Gene Symbols from GEO Code
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optional) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, 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/>.
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>

Diff between geneExpressionFromGEO versions 0.3 dated 2020-11-17 and 0.4 dated 2021-01-25

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Package causact updated to version 0.4.0 with previous version 0.3.3 dated 2020-07-25

Title: Accelerated Bayesian Analytics with DAGs
Description: Accelerate Bayesian analytics workflows in 'R' through interactive modelling, visualization, and inference. Define probabilistic graphical models using directed acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians, and programmers. This package relies on the sleek and elegant 'greta' package for Bayesian inference. 'greta', in turn, is an interface into 'TensorFlow' from 'R'. Install 'greta' using instructions available here: <https://www.causact.com/install-tensorflow-greta-and-causact.html>. See <https://github.com/flyaflya/causact> or <https://www.causact.com/> for more documentation.
Author: Adam Fleischhacker [aut, cre, cph], Daniela Dapena [ctb], Rose Nguyen [ctb], Jared Sharpe [ctb]
Maintainer: Adam Fleischhacker <ajf@udel.edu>

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Package robomit updated to version 1.0.5 with previous version 1.0.3 dated 2020-09-15

Title: Robustness Checks for Omitted Variable Bias
Description: Robustness checks for omitted variable bias. The package includes robustness checks proposed by Oster (2019). robomit the estimate i) the bias-adjusted treatment correlation or effect and ii) the degree of selection on unobservables relative to observables (with respect to the treatment variable) that would be necessary to eliminate the result based on the framework by Oster (2019). Additionally, robomit offers a set of sensitivity analysis and visualization functions. See: Oster, E. 2019. <doi:10.1080/07350015.2016.1227711>.
Author: Sergei Schaub [aut, cre] (<https://orcid.org/0000-0001-8477-3737>), ETH Zurich [cph]
Maintainer: Sergei Schaub <seschaub@ethz.ch>

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Package paws.common updated to version 0.3.8 with previous version 0.3.7 dated 2021-01-18

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.common versions 0.3.7 dated 2021-01-18 and 0.3.8 dated 2021-01-25

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Package chronicle updated to version 0.2.1 with previous version 0.2.0 dated 2021-01-25

Title: Grammar for Creating R Markdown Reports
Description: A system for creating beautiful and interactive R Markdown reports by adding modules like plots and tables to an empty header.
Author: Philippe Heymans Smith [aut, cre]
Maintainer: Philippe Heymans Smith <pheymanss@gmail.com>

Diff between chronicle versions 0.2.0 dated 2021-01-25 and 0.2.1 dated 2021-01-25

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Package bamlss updated to version 1.1-3 with previous version 1.1-2 dated 2020-02-19

Title: Bayesian Additive Models for Location, Scale, and Shape (and Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019) <doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2019) <arXiv:1909.11784>.
Author: Nikolaus Umlauf [aut, cre] (<https://orcid.org/0000-0003-2160-9803>), Nadja Klein [aut] (<https://orcid.org/0000-0002-5072-5347>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Meike Koehler [ctb], Thorsten Simon [aut] (<https://orcid.org/0000-0002-3778-7738>), Stanislaus Stadlmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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New package rsqliteadmin with initial version 1.0.0
Package: rsqliteadmin
Title: A GUI to Manage SQLite Databases
Description: A comprehensive tool written in R Shiny to explore, manage and update SQLite Databases.
Version: 1.0.0
Date: 2021-01-20
Authors@R: c( person( "Vijay", "Barve", email = "vijay.barve@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0002-4852-2567')), person( "Thiloshon", "Nagarajah", email = "thiloshon@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0001-8607-7145')), person( "Narayani", "Barve", email = "narayani.ku@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0002-7893-8774')), person( "Marlon E.", "Cobos", email = "manubio13@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0002-2611-1767')), person( "Divyansh", "Chawla", email = "code.divyansh@gmail.com", role = c("cre", "aut")) )
Maintainer: Divyansh Chawla <code.divyansh@gmail.com>
Imports: config, golem, shiny, RSQLite, DT, shinyFiles, fs, shinyAce, shinyjqui, shinydashboard, disk.frame, data.table, magrittr
RoxygenNote: 7.1.1
URL: https://github.com/rsqliteadmin/rsqliteadmin
BugReports: https://github.com/rsqliteadmin/rsqliteadmin/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-01-22 20:27:39 UTC; divya
Author: Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Thiloshon Nagarajah [aut] (<https://orcid.org/0000-0001-8607-7145>), Narayani Barve [aut] (<https://orcid.org/0000-0002-7893-8774>), Marlon E. Cobos [aut] (<https://orcid.org/0000-0002-2611-1767>), Divyansh Chawla [cre, aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-01-25 14:10:02 UTC

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Package rrapply updated to version 1.2.2 with previous version 1.2.1 dated 2020-11-07

Title: Revisiting Base Rapply
Description: The minimal 'rrapply'-package contains a single function rrapply(), providing an extended implementation of 'R'-base rapply() by allowing to recursively apply a function to elements of a nested list based on a general condition function and including the possibility to prune or aggregate nested list elements from the result. In addition, special arguments can be supplied to access the name, location, parents and siblings in the nested list of the element under evaluation. The rrapply() function builds upon rapply()'s native 'C' implementation and requires no other package dependencies.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

Diff between rrapply versions 1.2.1 dated 2020-11-07 and 1.2.2 dated 2021-01-25

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Package island updated to version 0.2.7 with previous version 0.2.6 dated 2020-12-07

Title: Stochastic Island Biogeography Theory Made Easy
Description: Tools to develop stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <DOI:10.1023/A:1016393430551> and extensions. The package implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulate community assembly, and perform model selection.
Author: Vicente Jimenez [aut, cre], David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>

Diff between island versions 0.2.6 dated 2020-12-07 and 0.2.7 dated 2021-01-25

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New package wilcoxmed with initial version 0.0.1
Package: wilcoxmed
Title: Computes Values for the 1-Sample Wilcoxon Sign Rank Test for Medians
Version: 0.0.1
Date: 2021-01-20
Authors@R: c(person(given = "Dion", family = "Kwan", role = c("aut","cre"), email = "dkzk96@yahoo.com.sg"))
Author: Dion Kwan [aut, cre]
Maintainer: Dion Kwan <dkzk96@yahoo.com.sg>
Description: An implementation of the 1-Sample Wilcoxon Sign rank test for medians. It includes 2 functions, W_stat(), which computes the exact probabilities of the Wilcoxon Sign Rank Test Statistic, W. The second function, Wilcox.m.test() allows the user to conduct the 1-Sample Wilcoxon Sign Rank hypothesis test for medians, this also allows the user to conduct the hypothesis test for the normal approximation, based on the techniques of Bickel and Doksum (1973, ISBN:013850363X).
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-22 12:53:38 UTC; Dion
Repository: CRAN
Date/Publication: 2021-01-25 13:10:02 UTC

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New package rliger with initial version 0.5.0
Package: rliger
Version: 0.5.0
Date: 2021-01-18
Type: Package
Title: Linked Inference of Genomic Experimental Relationships
Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Authors@R: c( person(given = 'Joshua', family = 'Welch', email = 'welchjd@umich.edu', role = c('aut', 'ctb')), person(given = 'Chao', family = 'Gao', email = 'gchao@umich.edu', role = c('aut', 'ctb', 'cre')), person(given = 'Jialin', family = 'Liu', email = 'alanliu@umich.edu', role = c('aut', 'ctb')), person(given = 'Joshua', family = 'Sodicoff', email = 'sodicoff@umich.edu', role = c('aut', 'ctb')), person(given = 'Velina', family = 'Kozareva', role = c('aut', 'ctb')), person(given = 'Evan', family = 'Macosko', role = c('aut', 'ctb')), person(given = 'Paul', family = 'Hoffman', role = 'ctb'), person(given = 'Ilya', family = 'Korsunsky', role = 'ctb'), person(given = 'Robert', family = 'Lee', role = 'ctb') )
Author: Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]
Maintainer: Chao Gao <gchao@umich.edu>
BugReports: https://github.com/welch-lab/liger/issues
URL: https://github.com/welch-lab/liger
License: GPL-3
SystemRequirements: Java (>= 6)
Imports: Rcpp (>= 0.12.10), plyr, FNN, dplyr, grid, ggrepel, irlba, ica, Rtsne, ggplot2, riverplot, Hmisc, foreach, parallel, doParallel, mclust, stats, psych, RANN, uwot, rlang, utils, hdf5r
biocViews:
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Depends: cowplot, Matrix, methods, patchwork
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests: Seurat, knitr, reticulate, rmarkdown, testthat, GenomicRanges, S4Vectors, IRanges, org.Hs.eg.db, reactome.db, fgsea, AnnotationDbi
NeedsCompilation: yes
Packaged: 2021-01-22 15:47:03 UTC; gchao
Repository: CRAN
Date/Publication: 2021-01-25 13:30:02 UTC

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New package RcmdrPlugin.DCE with initial version 0.1-2
Package: RcmdrPlugin.DCE
Type: Package
Title: R Commander Plug-in for Discrete Choice Experiments
Version: 0.1-2
Date: 2021-01-10
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Depends: support.CEs, survival
Imports: Rcmdr
Description: Adds menu items for discrete choice experiments (DCEs) to the R Commander. DCE is a question-based survey method that designs various combinations (profiles) of attribute levels using the experimental designs, asks respondents to select the most preferred profile in each choice set, and then measures preferences for the attribute levels by analyzing the responses. For details on DCEs, refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831>.
License: GPL (>= 2)
RcmdrModels: clogit
NeedsCompilation: no
Packaged: 2021-01-10 09:47:23 UTC; user
Repository: CRAN
Date/Publication: 2021-01-25 13:30:09 UTC

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Package rasciidoc updated to version 3.0.1 with previous version 3.0.0 dated 2020-11-30

Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr' with 'asciidoc' (<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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New package ghcm with initial version 1.0.0
Package: ghcm
Type: Package
Title: Functional Conditional Independence Testing with the GHCM
Version: 1.0.0
Authors@R: c(person("Anton Rask", "Lundborg", email = "a.lundborg@statslab.cam.ac.uk", role = c("aut", "cre")), person("Rajen D.", "Shah", role = c("aut")), person("Jonas", "Peters", role = c("aut")))
Description: A statistical hypothesis test for conditional independence. Given residuals from a sufficiently powerful regression, it tests whether the covariance of the residuals is vanishing. It can be applied to both discretely-observed functional data and multivariate data. Details of the method can be found in Anton Rask Lundborg, Rajen D. Shah and Jonas Peters (2020) <arXiv:2101.07108>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: graphics, MASS, refund, stats, utils
Depends: R (>= 4.0.0)
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown, bookdown, GeneralisedCovarianceMeasure, ggplot2, reshape2
URL: https://github.com/arlundborg/ghcm
BugReports: https://github.com/arlundborg/ghcm/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-01-22 11:09:06 UTC; lundborg
Author: Anton Rask Lundborg [aut, cre], Rajen D. Shah [aut], Jonas Peters [aut]
Maintainer: Anton Rask Lundborg <a.lundborg@statslab.cam.ac.uk>
Repository: CRAN
Date/Publication: 2021-01-25 13:10:05 UTC

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Package flextable updated to version 0.6.2 with previous version 0.6.1 dated 2020-12-08

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word' and 'Microsoft PowerPoint' documents from 'R Markdown'. Functions are provided to let users create tables, modify and format their content. It also extends package 'officer' that does not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] (rmarkdown for docx output), Titouan Robert [ctb], Michael Barrowman [ctb] (inline footnotes), Atsushi Yasumoto [ctb] (support for bookdown cross reference), Paul Julian [ctb] (support for gam objects)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package eatTools updated to version 0.4.0 with previous version 0.3.8 dated 2020-10-19

Title: Miscellaneous Functions for the Analysis of Educational Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep', 'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN'). The function for defining (weighted) contrasts in weighted effect coding refers to te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>. Functions for weighted statistics refer to Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre], Martin Hecht [aut], Karoline Sachse [aut], Benjamin Becker [aut], Nicole Mahler [aut]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>

Diff between eatTools versions 0.3.8 dated 2020-10-19 and 0.4.0 dated 2021-01-25

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Package dbmss updated to version 2.7-4 with previous version 2.7-3 dated 2020-11-17

Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>. Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>), Gabriel Lang [aut] (<https://orcid.org/0000-0002-4325-6044>), Stephane Traissac [aut] (<https://orcid.org/0000-0001-9255-1616>), Florence Puech [aut] (<https://orcid.org/0000-0002-5279-6878>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

Diff between dbmss versions 2.7-3 dated 2020-11-17 and 2.7-4 dated 2021-01-25

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New package CohortPlat with initial version 1.0.0
Package: CohortPlat
Type: Package
Title: Simulation of Cohort Platform Trials for Combination Treatments
Version: 1.0.0
Author: Elias Laurin Meyer [aut, cre]
Maintainer: Elias Laurin Meyer <elias.meyer@meduniwien.ac.at>
Description: A collection of functions dedicated to simulating staggered entry platform trials whereby the treatment under investigation is a combination of two active compounds. In order to obtain approval for this combination therapy, superiority of the combination over the two active compounds and superiority of the two active compounds over placebo need to be demonstrated. A more detailed description of the design can be found in Meyer et al. (2021).
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
LazyData: true
RoxygenNote: 7.1.1
Imports: dplyr, purrr, ggplot2, plotly, tidyr, parallel, doParallel, foreach, openxlsx, forcats, epitools, zoo
Suggests: knitr, rmarkdown, DT, gtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-01-22 11:25:47 UTC; Elias
Repository: CRAN
Date/Publication: 2021-01-25 13:10:16 UTC

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New package ccboost with initial version 0.1-1.3
Package: ccboost
Type: Package
Title: Robust Boosting
Version: 0.1-1.3
Date: 2021-01-19
Authors@R: c(person("Zhu", "Wang", role = c("aut", "cre"), email = "zhuwang@gmail.com", comment = c(ORCID = "0000-0002-0773-0052")))
Author: Zhu Wang [aut, cre] (<https://orcid.org/0000-0002-0773-0052>)
Maintainer: Zhu Wang <zhuwang@gmail.com>
Description: Robust functional descent algorithm for concave-convex family through composite optimization by conjugation operator. Wang (2021) <arXiv:2101.07718>.
Depends: R (>= 3.5.0)
Imports: mpath, xgboost
Suggests: R.rsp, DiagrammeR
VignetteBuilder: R.rsp
License: GPL (>= 2)
Encoding: UTF-8
LazyLoad: yes
Packaged: 2021-01-22 17:50:23 UTC; zhu
RoxygenNote: 7.1.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2021-01-25 13:30:06 UTC

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Package spacetime updated to version 1.2-4 with previous version 1.2-3 dated 2020-01-21

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package rEDM updated to version 1.7.5 with previous version 1.7.4 dated 2021-01-11

Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] (<https://orcid.org/0000-0001-5411-1409>), Cameron Smith [aut], George Sugihara [aut, ccp] (<https://orcid.org/0000-0002-2863-6946>), Ethan Deyle [aut] (<https://orcid.org/0000-0001-8704-8434>), Erik Saberski [ctb] (<https://orcid.org/0000-0002-6475-6187>), Hao Ye [ctb] (<https://orcid.org/0000-0002-8630-1458>), The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>

Diff between rEDM versions 1.7.4 dated 2021-01-11 and 1.7.5 dated 2021-01-25

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New package INQC with initial version 2.0.4
Package: INQC
Title: Quality Control of Climatological Daily Time Series
Version: 2.0.4
Date: 2020-12-24
Authors@R: c( person(given = "Enric", family = "Aguilar", role = c("aut", "cre"), email = "enric.aguilar@urv.cat", comment = c(ORCID = "0000-0002-8384-377X")), person(given = "Oleg", family = "Skrynyk", role = "aut", email = "oleg.y.skrynyk@gmail.com", comment = c(ORCID = "0000-0001-8827-0280")))
Description: Collection of functions for quality control (QC) of climatological daily time series (e.g. the ECA&D station data).
License: GPL (>= 3)
URL: https://github.com/INDECIS-Project/INQC
BugReports: https://github.com/INDECIS-Project/INQC/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: evd, gdata, suncalc, stats, utils
Suggests: readr
NeedsCompilation: no
Packaged: 2021-01-22 08:31:42 UTC; Typhoon
Author: Enric Aguilar [aut, cre] (<https://orcid.org/0000-0002-8384-377X>), Oleg Skrynyk [aut] (<https://orcid.org/0000-0001-8827-0280>)
Maintainer: Enric Aguilar <enric.aguilar@urv.cat>
Repository: CRAN
Date/Publication: 2021-01-25 12:10:02 UTC

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New package FILEST with initial version 1.1.2
Package: FILEST
Type: Package
Title: Fine-Level Structure Simulator
Version: 1.1.2
Authors@R: c(person(given = "Kridsadakorn", family = "Chaichoompu", email = "kridsadakorn@biostatgen.org", role = c("aut", "cre")),person(given = "Kristel", family = 'Van Steen', role = "aut"),person(given = "Fentaw", family = "Abegaz", role = "aut"))
Description: A population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst) as explained in Balding and Nichols (1995) <doi:10.1007/BF01441146>. This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.
Depends: R (>= 3.2.4)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: KRIS (>= 1.1.1),rARPACK,grDevices,stats,utils
Suggests: testthat
BugReports: https://gitlab.com/kris.ccp/filest/-/issues
URL: https://gitlab.com/kris.ccp/filest
NeedsCompilation: no
Packaged: 2021-01-25 11:07:57 UTC; kris
Author: Kridsadakorn Chaichoompu [aut, cre], Kristel Van Steen [aut], Fentaw Abegaz [aut]
Maintainer: Kridsadakorn Chaichoompu <kridsadakorn@biostatgen.org>
Repository: CRAN
Date/Publication: 2021-01-25 12:50:06 UTC

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Package DoubleML updated to version 0.1.2 with previous version 0.1.1 dated 2020-12-16

Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear regression models, partially linear instrumental variable regression models, interactive regression models and interactive instrumental variable regression models. 'DoubleML' allows estimation of the nuisance parts in these models by machine learning methods and computation of the Neyman orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the 'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on the 'R6' package is very flexible.
Author: Philipp Bach [aut], Victor Chernozhukov [aut], Malte S. Kurz [aut, cre], Martin Spindler [aut]
Maintainer: Malte S. Kurz <malte.simon.kurz@uni-hamburg.de>

Diff between DoubleML versions 0.1.1 dated 2020-12-16 and 0.1.2 dated 2021-01-25

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Package creditmodel updated to version 1.3.0 with previous version 1.2.7 dated 2020-11-09

Title: Toolkit for Credit Modeling, Analysis and Visualization
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization.Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster. The references including: 1 Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS; 2 Bezdek, James C.FCM: The fuzzy c-means clustering algorithm. Computers & Geosciences (0098-3004),<DOI:10.1016/0098-3004(84)90020-7>.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>

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Package chronicle updated to version 0.2.0 with previous version 0.1.0 dated 2021-01-21

Title: Grammar for Creating R Markdown Reports
Description: A system for creating beautiful and interactive R Markdown reports by adding modules like plots and tables to an empty header.
Author: Philippe Heymans Smith [aut, cre]
Maintainer: Philippe Heymans Smith <pheymanss@gmail.com>

Diff between chronicle versions 0.1.0 dated 2021-01-21 and 0.2.0 dated 2021-01-25

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Package BoutrosLab.plotting.general updated to version 6.0.3 with previous version 6.0.2 dated 2021-01-11

Title: Functions to Create Publication-Quality Plots
Description: Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi: 10.1186/s12859-019-2610-2>.
Author: Paul Boutros [aut, cre], Christine P'ng [ctb], Jeff Green [ctb], Stephenie Prokopec [ctb], Ontario Institute for Cancer Research [cph], The R Core Team [cph], The R Foundation [cph], Robert Gentleman [ctb], Ross Ihaka [ctb], Caden Bugh [ctb]
Maintainer: Paul Boutros <PBoutros@mednet.ucla.edu>

Diff between BoutrosLab.plotting.general versions 6.0.2 dated 2021-01-11 and 6.0.3 dated 2021-01-25

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Package walker updated to version 1.0.1 with previous version 0.5.0 dated 2020-10-19

Title: Bayesian Generalized Linear Models with Time-Varying Coefficients
Description: Bayesian generalized linear models with time-varying coefficients as in Helske (2020, <arXiv:2009.07063>). Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, the package uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between walker versions 0.5.0 dated 2020-10-19 and 1.0.1 dated 2021-01-25

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New package swimplot with initial version 1.1
Package: swimplot
Title: Tools for Creating Swimmers Plots using 'ggplot2'
Description: Used for creating swimmers plots with functions to customize the bars, add points, add lines, and add arrows.
Version: 1.1
License: GPL-3
Author: Jessica Weiss <jessica.weiss@uhnresearch.ca>, Wei Xu<Wei.Xu@uhnresearch.ca>
Maintainer: Jessica Weiss <jessica.weiss@uhnresearch.ca>
Imports: tidyr, dplyr, ggplot2, data.table, magrittr, utils
LazyData: true
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-01-21 15:31:56 UTC; jweiss
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-01-25 08:20:02 UTC

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New package speakr with initial version 3.0.0
Package: speakr
Type: Package
Title: A Wrapper for the Phonetic Software Praat
Version: 3.0.0
Date: 2021-01-20
Authors@R: person("Stefano", "Coretta", email = "stefano.coretta@gmail.com", role = c("aut", "cre"))
Description: It allows running Praat scripts from R and it provides some wrappers for basic plotting. It also adds support for literate markdown tangling. The package is designed to bring reproducible phonetic research into R.
License: MIT + file LICENSE
URL: https://github.com/stefanocoretta/speakr
BugReports: https://github.com/stefanocoretta/speakr/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: tidyverse, readr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Language: en_GB
NeedsCompilation: no
Packaged: 2021-01-21 16:39:46 UTC; stefano
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Repository: CRAN
Date/Publication: 2021-01-25 08:30:03 UTC

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New package SOMEnv with initial version 0.1.1
Package: SOMEnv
Type: Package
Title: SOM Algorithm for the Analysis of Multivariate Environmental Data
Version: 0.1.1
Authors@R: c( person("Sabina", "Licen", role=c("aut", "cre"), email= "slicen@units.it"), person("Marco", "Franzon", role=c("aut"), email = "franzonmarco94@gmail.com"), person("Tommaso", "Rodani", role=c("aut"), email = "tommaso.rodani@gmail.com"), person("Pierluigi", "Barbieri", role=c("aut"), email = "barbierip@units.it") )
Maintainer: Sabina Licen <slicen@units.it>
Description: Analysis of multivariate environmental high frequency data by Self-Organizing Map and k-means clustering algorithms. By means of the graphical user interface it provides a comfortable way to elaborate by self-organizing map algorithm rather big datasets (txt files up to 100 MB ) obtained by environmental high-frequency monitoring by sensors/instruments. The functions present in the package are based on 'kohonen' and 'openair' packages implemented by functions embedding Vesanto et al. (2001) <http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf> heuristic rules for map initialization parameters, k-means clustering algorithm and map features visualization. Cluster profiles visualization as well as graphs dedicated to the visualization of time-dependent variables Licen et al. (2020) <doi:10.4209/aaqr.2019.08.0414> are provided.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: rlist, kohonen, shiny, dplyr, plyr, openair, colourpicker, shinycssloaders, shinycustomloader
URL: https://github.com/SomEnv/somenv
BugReports: https://github.com/SomEnv/somenv/issues
NeedsCompilation: no
Packaged: 2021-01-21 17:20:57 UTC; brobr
Author: Sabina Licen [aut, cre], Marco Franzon [aut], Tommaso Rodani [aut], Pierluigi Barbieri [aut]
Repository: CRAN
Date/Publication: 2021-01-25 08:30:09 UTC

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New package pgTools with initial version 0.1.0
Package: pgTools
Type: Package
Title: Functions for Generating PostgreSQL Statements/Scripts
Version: 0.1.0
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Description: Create PostgreSQL statements/scripts from R, optionally executing the SQL statements. Common SQL operations are included, although not every configurable option is available at this time. SQL output is intended to be compliant with PostgreSQL syntax specifications. PostgreSQL documentation is available here <https://www.postgresql.org/docs/current/index.html>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: DBI, data.table
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-21 15:10:03 UTC; tim
Repository: CRAN
Date/Publication: 2021-01-25 08:20:05 UTC

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New package pacviz with initial version 1.0.0.5
Package: pacviz
Title: Pac-Man Visualization Package
Version: 1.0.0.5
Authors@R: person(given = "Spencer", family = "Riley", role = c("aut", "cre"), email = "spencer.riley@student.nmt.edu")
Description: Provides a broad-view perspective on data via linear mapping of data onto a radial coordinate system. The package contains functions to visualize the residual values of linear regression and Cartesian data in the defined radial scheme. See the 'pacviz' documentation page for more information: <https://spencerriley.me/pacviz/book/>.
License: MIT + file LICENSE
Depends: R (>= 4.0.0)
Imports: circlize, e1071, graphics, plotrix, stats, utils
Suggests: knitr, markdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-21 15:51:54 UTC; root
Author: Spencer Riley [aut, cre]
Maintainer: Spencer Riley <spencer.riley@student.nmt.edu>
Repository: CRAN
Date/Publication: 2021-01-25 08:20:07 UTC

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New package NHSDataDictionaRy with initial version 0.1.2
Package: NHSDataDictionaRy
Type: Package
Title: NHS Data Dictionary Toolset for NHS Lookups
Version: 0.1.2
Author: Gary Hutson
Maintainer: Gary Hutson <g.hutson@nhs.net>
Description: Providing a common set of simplified web scraping tools for working with the NHS Data Dictionary <https://datadictionary.nhs.uk/data_elements_overview.html>. The intended usage is to access the data elements section of the NHS Data Dictionary to access key lookups. The benefits of having it in this package are that the lookups are the live lookups on the website and will not need to be maintained. This package was commissioned by the NHS-R community to provide this consistency of lookups.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: xml2, dplyr, magrittr, rvest, stringr, purrr
Collate: 'left_xl.R' 'len_xl.R' 'linkScrapeR.R' 'mid_xl.R' 'nhs_data_elements.R' 'right_xl.R' 'scrapeR.R' 'tableR.R' 'xpathTextR.R'
Suggests: knitr, rmarkdown, spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2021-01-21 15:18:37 UTC; garyh
Repository: CRAN
Date/Publication: 2021-01-25 08:20:16 UTC

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New package multibridge with initial version 1.0.0
Package: multibridge
Title: Evaluating Multinomial Order Restrictions with Bridge Sampling
Version: 1.0.0
Date: 2021-01-21
Authors@R: c( person(given = "Alexandra", family = "Sarafoglou", email = "alexandra.sarafoglou@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0031-685X")), person(given = "Frederik", family = "Aust", role = "aut", comment = c(ORCID = "0000-0003-4900-788X")), person(given = "Julia M.", family = "Haaf", role = "aut", comment = c(ORCID = "0000-0001-5122-706X")), person(given = "Joris", family = "Goosen", role = "aut"), person(given = "Quentin F.", family = "Gronau", role = "aut"), person(given = "Maarten", family = "Marsman", role = "aut", comment = c(ORCID = "0000-0001-5309-7502")) )
Description: Evaluate hypotheses concerning the distribution of multinomial proportions using bridge sampling. The bridge sampling routine is able to compute Bayes factors for hypotheses that entail inequality constraints, equality constraints, free parameters, and mixtures of all three. These hypotheses are tested against the encompassing hypothesis, that all parameters vary freely or against the null hypothesis that all category proportions are equal. For more information see Sarafoglou et al. (2020) <doi:10.31234/osf.io/bux7p>.
URL: https://github.com/asarafoglou/multibridge/
BugReports: https://github.com/asarafoglou/multibridge/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: Brobdingnag, coda, mvtnorm, purrr, Rcpp (>= 0.12.17), magrittr, progress, Rdpack, stringr
Suggests: knitr, rmarkdown, testthat
SystemRequirements: GNU make, mpfr (>= 3.0.0)
RoxygenNote: 7.1.1
LinkingTo: Rcpp
VignetteBuilder: knitr
RdMacros: Rdpack
Depends: R (>= 3.5.0)
NeedsCompilation: yes
Packaged: 2021-01-21 14:54:55 UTC; alexandra.sarafoglou
Author: Alexandra Sarafoglou [aut, cre] (<https://orcid.org/0000-0003-0031-685X>), Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>), Julia M. Haaf [aut] (<https://orcid.org/0000-0001-5122-706X>), Joris Goosen [aut], Quentin F. Gronau [aut], Maarten Marsman [aut] (<https://orcid.org/0000-0001-5309-7502>)
Maintainer: Alexandra Sarafoglou <alexandra.sarafoglou@gmail.com>
Repository: CRAN
Date/Publication: 2021-01-25 08:40:02 UTC

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New package leaflegend with initial version 0.1.0
Package: leaflegend
Type: Package
Title: Add Custom Legends to 'leaflet' Maps
Version: 0.1.0
Authors@R: person("Thomas", "Roh", email = "thomas@roh.engineering", role = c("aut", "cre"))
Description: Provides extensions to the 'leaflet' package to customize legends with images, text styling, orientation, sizing, and symbology.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: leaflet, htmltools, stats, base64enc
RoxygenNote: 7.1.0
URL: https://github.com/tomroh/leaflegend
BugReports: https://github.com/tomroh/leaflegend/issues
NeedsCompilation: no
Packaged: 2021-01-21 16:16:31 UTC; troh
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas@roh.engineering>
Repository: CRAN
Date/Publication: 2021-01-25 08:20:10 UTC

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New package iGraphMatch with initial version 1.0.0
Package: iGraphMatch
Type: Package
Title: Tools Graph Matching
Version: 1.0.0
Authors@R: c(person("Daniel", "Sussman", role = c("aut", "cre"), email = "sussman@bu.edu"), person("Zihuan", "Qiao", role = c("aut"), email = "zhqiao@bu.edu"), person("Joshua", "Agterberg", role = "ctb"), person("Lujia", "Wang", role = "ctb"), person("Vince", "Lyzinski", role = "ctb"))
Description: Graph matching methods and analysis. The package works for both 'igraph' objects and matrix objects. You provide the adjacency matrices of two graphs and some other information you might know, choose the graph matching method, and it returns the graph matching results. 'iGraphMatch' also provides a bunch of useful functions you might need related to graph matching.
Depends: R (>= 3.3.1)
Imports: clue (>= 0.3-54), Matrix (>= 1.2-11), igraph (>= 1.1.2), irlba, methods, Rcpp
Suggests: dplyr (>= 0.5.0), testthat (>= 2.0.0), knitr, rmarkdown
VignetteBuilder: knitr
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 7.1.1
Encoding: UTF-8
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-01-21 21:32:40 UTC; dsussman
Author: Daniel Sussman [aut, cre], Zihuan Qiao [aut], Joshua Agterberg [ctb], Lujia Wang [ctb], Vince Lyzinski [ctb]
Maintainer: Daniel Sussman <sussman@bu.edu>
Repository: CRAN
Date/Publication: 2021-01-25 08:40:07 UTC

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New package glme with initial version 0.1.0
Package: glme
Type: Package
Title: Generalized Linear Mixed Effects Models
Version: 0.1.0
Author: Sam Weerahandi [aut], Berna Yazici [aut], Ching-Ray Yu [aut], Mustafa Cavus [aut, cre]
Maintainer: Mustafa Cavus <mustafacavus@eskisehir.edu.tr>
Authors@R: c(person("Sam Weerahandi", role = "aut"), person("Berna Yazici", role = "aut"), person("Ching-Ray Yu", role = "aut"), person("Mustafa Cavus", role = c("aut", "cre"), email = "mustafacavus@eskisehir.edu.tr"))
Description: Provides Generalized Inferences based on exact distributions and exact probability statements for mixed effect models, provided by such papers as Weerahandi and Yu (2020) <doi:10.1186/s40488-020-00105-w> under the widely used Compound Symmetric Covariance structure. The package returns the estimation of the coefficients in random and fixed part of the mixed models by generalized inference.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: nlme, reshape, dplyr, stats
NeedsCompilation: no
Packaged: 2021-01-21 15:33:28 UTC; mustafacavus
Repository: CRAN
Date/Publication: 2021-01-25 08:20:13 UTC

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New package cropZoning with initial version 1.0.0
Package: cropZoning
Type: Package
Title: Climate Crop Zoning Based in Air Temperature for Brazil
Version: 1.0.0
Authors@R: c(person(given = "Roberto", family = "Filgueiras", role = c("aut","cre"), email = "betofilgueiras@gmail.com", comment = c(ORCID = "0000-0002-0186-8907")), person(given = "Luan P.", family = "Venancio", role = ("aut"), comment = c(ORCID = "0000-0002-5544-8588")), person(given = "Catariny C.", family = "Aleman", role = ("aut"), comment = c(ORCID = "0000-0002-3894-3077")), person(given = "Fernando F.", family = "da Cunha", role = ("aut"), comment = c(ORCID = "0000-0002-1671-1021")))
Description: Climate crop zoning based in minimum and maximum air temperature. The data used in the package are from 'TerraClimate' dataset (<http://www.climatologylab.org/terraclimate.html>), but, it have been calibrated with automatic weather stations of National Meteorological Institute of Brazil. The climate crop zoning of this package can be run for all the Brazilian territory.
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
License: CC BY 4.0
Depends: R (>= 2.10)
Imports: raster, tidyr, ggplot2, rgdal, ncdf4
BugReports: https://github.com/FilgueirasR/cropZoning/issues
NeedsCompilation: no
Packaged: 2021-01-21 16:22:35 UTC; betof
Author: Roberto Filgueiras [aut, cre] (<https://orcid.org/0000-0002-0186-8907>), Luan P. Venancio [aut] (<https://orcid.org/0000-0002-5544-8588>), Catariny C. Aleman [aut] (<https://orcid.org/0000-0002-3894-3077>), Fernando F. da Cunha [aut] (<https://orcid.org/0000-0002-1671-1021>)
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Repository: CRAN
Date/Publication: 2021-01-25 08:30:05 UTC

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New package acroname with initial version 0.1.0
Package: acroname
Type: Package
Title: Engine for Acronyms and Initialisms
Version: 0.1.0
Authors@R: c(person("VP", "Nagraj", role = c("aut", "cre"), email = "nagraj@nagraj.net"))
Maintainer: VP Nagraj <nagraj@nagraj.net>
Description: A tool for generating acronyms and initialisms from arbitrary text input.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: magrittr, R.utils, dplyr, purrr, readr, stringr, hunspell
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-01-21 23:58:43 UTC; vpnagraj
Author: VP Nagraj [aut, cre]
Repository: CRAN
Date/Publication: 2021-01-25 08:40:11 UTC

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New package bslib with initial version 0.2.4
Package: bslib
Title: Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Version: 0.2.4
Authors@R: c( person("Carson", "Sievert", role = c("aut", "cre"), email = "carson@rstudio.com"), person("Joe", "Cheng", role = "aut", email = "joe@rstudio.com"), person(family = "RStudio", role = "cph"), person(family = "Bootstrap contributors", role = "ctb", comment = "Bootstrap library"), person(family = "Twitter, Inc", role = "cph", comment = "Bootstrap library"), person("Javi", "Aguilar", role = c("ctb", "cph"), comment = "Bootstrap colorpicker library"), person("Thomas", "Park", role = c("ctb", "cph"), comment = "Bootswatch library"), person(family = "PayPal", role = c("ctb", "cph"), comment = "Bootstrap accessibility plugin") )
Description: Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports both 'Bootstrap' 3 and 4 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.
Depends: R (>= 2.10)
Imports: grDevices, htmltools (>= 0.5.1), jsonlite, sass (>= 0.3.0), digest (>= 0.6.25), jquerylib (>= 0.1.3), rlang, magrittr
Suggests: shiny, rmarkdown, knitr, testthat, withr, rappdirs, curl
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Collate: 'bootswatch.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'deprecated.R' 'files.R' 'fonts.R' 'imports.R' 'onLoad.R' 'precompiled.R' 'shiny-devmode.R' 'version-default.R' 'versions.R' 'web-font.R'
URL: https://rstudio.github.io/bslib/, https://github.com/rstudio/bslib
BugReports: https://github.com/rstudio/bslib/issues
NeedsCompilation: no
Packaged: 2021-01-20 15:08:19 UTC; cpsievert
Author: Carson Sievert [aut, cre], Joe Cheng [aut], RStudio [cph], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)
Maintainer: Carson Sievert <carson@rstudio.com>
Repository: CRAN
Date/Publication: 2021-01-25 08:00:02 UTC

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Package boot updated to version 1.3-26 with previous version 1.3-25 dated 2020-04-26

Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between boot versions 1.3-25 dated 2020-04-26 and 1.3-26 dated 2021-01-25

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Package petro.One (with last version 0.2.3) was removed from CRAN

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

2019-01-13 0.2.3

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Package rdacca.hp updated to version 0.3.0 with previous version 0.2.0 dated 2021-01-18

Title: Hierarchical Partitioning for Canonical Analysis
Description: This function calculates the independent contribution of each explanatory variable to explained variation (R-squared) on RDA,CCA and db-RDA, applying the hierarchy algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <DOI:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-neto
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>

Diff between rdacca.hp versions 0.2.0 dated 2021-01-18 and 0.3.0 dated 2021-01-25

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Package mixSPE updated to version 0.9.1 with previous version 0.1.1 dated 2019-06-19

Title: Mixtures of Power Exponential and Skew Power Exponential Distributions for Use in Model-Based Clustering and Classification
Description: Mixtures of skewed and elliptical distributions are implemented using mixtures of multivariate skew power exponential and power exponential distributions, respectively. A generalized expectation-maximization framework is used for parameter estimation. Methodology for mixtures of power exponential distributions is from Dang et al. (2015) <doi: 10.1111/biom.12351>.
Author: Ryan P. Browne[aut, cre], Utkarsh J. Dang[aut, cre], Michael P. B. Gallaugher[ctb], and Paul D. McNicholas[aut]
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>

Diff between mixSPE versions 0.1.1 dated 2019-06-19 and 0.9.1 dated 2021-01-25

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Package liger updated to version 2.0.1 with previous version 1.1.2 dated 2020-07-16

Title: Lightweight Iterative Geneset Enrichment
Description: Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian et al. with 'Java' implementations available through the Broad Institute (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>). The 'liger' package provides a lightweight R implementation of this enrichment test on a list of values (Fan et al., 2017 <doi:10.5281/zenodo.887386>). Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.
Author: Jean Fan [aut, cre] (<https://orcid.org/0000-0002-0212-5451>), Peter Kharchenko [aut]
Maintainer: Jean Fan <jeanfan@jhu.edu>

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Package ggpmisc updated to version 0.3.8 with previous version 0.3.7 dated 2020-11-09

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", "plot" and "grob" add insets to plots using native data coordinates, while "table_npc", "plot_npc" and "grob_npc" do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: locate and tag peaks and valleys; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package assertr updated to version 2.8 with previous version 2.7 dated 2020-02-05

Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>

Diff between assertr versions 2.7 dated 2020-02-05 and 2.8 dated 2021-01-25

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