Mon, 28 Sep 2020

Package FisherEM updated to version 1.6 with previous version 1.5.2 dated 2020-07-22

Title: The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data
Description: The FisherEM algorithm, proposed by Bouveyron & Brunet (2012) <doi:10.1007/s11222-011-9249-9>, is an efficient method for the clustering of high-dimensional data. FisherEM models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data. A sparse version of Fisher-EM algorithm is also provided.
Author: Charles Bouveyron, Camille Brunet & Nicolas Jouvin.
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

Diff between FisherEM versions 1.5.2 dated 2020-07-22 and 1.6 dated 2020-09-28

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Package av updated to version 0.5.1 with previous version 0.5.0 dated 2020-01-29

Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generates high quality video from images or R graphics with custom audio. Also offers high performance tools for reading raw audio, creating 'spectrograms', and converting between countless audio / video formats. This package interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between av versions 0.5.0 dated 2020-01-29 and 0.5.1 dated 2020-09-28

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Package ripserr (with last version 0.1.0) was removed from CRAN

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

2020-09-14 0.1.0

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Package torch updated to version 0.1.0 with previous version 0.0.3 dated 2020-09-18

Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <arXiv:1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph], Javier Luraschi [aut, cph], Dmitriy Selivanov [ctb], Athos Damiani [ctb], RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>

Diff between torch versions 0.0.3 dated 2020-09-18 and 0.1.0 dated 2020-09-28

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Package RcppBigIntAlgos updated to version 0.3.1 with previous version 0.2.4 dated 2020-06-22

Title: Factor Big Integers with the Quadratic Sieve
Description: Features the multiple polynomial quadratic sieve (MPQS) algorithm for factoring large integers and a vectorized factoring function that returns the complete factorization of an integer. The MPQS is based off of the seminal work of Carl Pomerance (1984) <doi:10.1007/3-540-39757-4_17> along with the modification of multiple polynomials introduced by Peter Montgomery and J. Davis as outlined by Robert D. Silverman (1987) <doi:10.1090/S0025-5718-1987-0866119-8>. Utilizes the C library GMP (GNU Multiple Precision Arithmetic). The Pollard's rho algorithm for factoring smaller numbers is the same algorithm used by the factorize function in the 'gmp' package.
Author: Joseph Wood [aut, cre], Free Software Foundation, Inc. [cph], Mike Tryczak [ctb]
Maintainer: Joseph Wood <jwood000@gmail.com>

Diff between RcppBigIntAlgos versions 0.2.4 dated 2020-06-22 and 0.3.1 dated 2020-09-28

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Package MAPITR updated to version 1.1.2 with previous version 1.1.1 dated 2020-09-23

Title: MArginal ePIstasis Test for Regions
Description: A genetic analysis tool and variance component model for identifying marginal epistasis between pathways and the rest of the genome. 'MAPITR' uses as input a matrix of genotypes, a vector of phenotypes, and a list of pathways. 'MAPITR' then iteratively tests each pathway for epistasis between any variants within the pathway versus any variants remaining in the rest of the genome. 'MAPITR' returns results in the form of p-values for every pathway indicating whether the null model of there being no epistatic interactions between a pathway and the rest of the genome can be rejected.
Author: Michael Turchin [aut, cre] (<https://orcid.org/0000-0003-3569-1529>), Gregory Darnell [aut, ctb] (<https://orcid.org/0000-0003-0425-940X>), Lorin Crawford [aut, ctb] (<https://orcid.org/0000-0003-0178-8242>), Sohini Ramachandran [aut] (<https://orcid.org/0000-0002-9588-7964>), Peter Carbonetto [ctb] (<https://orcid.org/0000-0003-1144-6780>)
Maintainer: Michael Turchin <michael_turchin@brown.edu>

Diff between MAPITR versions 1.1.1 dated 2020-09-23 and 1.1.2 dated 2020-09-28

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 6 files changed, 38 insertions(+), 29 deletions(-)

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Package highfrequency updated to version 0.7.0.1 with previous version 0.7.0 dated 2020-09-15

Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency trades and quotes data, calculate various liquidity measures, estimate and forecast volatility, detect price jumps and investigate microstructure noise and intraday periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>), Jonathan Cornelissen [aut], Scott Payseur [aut], Giang Nguyen [ctb], Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>), Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>

Diff between highfrequency versions 0.7.0 dated 2020-09-15 and 0.7.0.1 dated 2020-09-28

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 14 files changed, 85 insertions(+), 89 deletions(-)

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Package globalKinhom updated to version 0.1.2 with previous version 0.1.1 dated 2020-09-25

Title: Inhomogeneous K- And Pair Correlation Functions Using Global Estimators
Description: Second-order summary statistics K- and pair-correlation functions describe interactions in point pattern data. This package provides computations to estimate those statistics on inhomogeneous point processes, using the methods of in T Shaw, J Møller, R Waagepetersen, 2020 <arXiv:2004.00527>.
Author: Thomas Shaw [aut, cre], Ege Rubak [ctb], Adrian Baddeley [ctb], Rolf Turner [ctb]
Maintainer: Thomas Shaw <shawtr@umich.edu>

Diff between globalKinhom versions 0.1.1 dated 2020-09-25 and 0.1.2 dated 2020-09-28

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New package edgarWebR with initial version 1.0.3
Package: edgarWebR
Title: SEC Filings Access
Description: A set of methods to access and parse live filing information from the U.S. Securities and Exchange Commission (SEC - <https://www.sec.gov/>) including company and fund filings along with all associated metadata.
Version: 1.0.3
Authors@R: c( person(c("Micah", "J"), "Waldstein", email = "micah@waldste.in", role = c("aut", "cre")) )
Maintainer: Micah J Waldstein <micah@waldste.in>
Date: 2020-09-26
Depends: R (>= 3.4.0)
Imports: xml2 (>= 1.3.2), methods, httr
Suggests: covr, ggplot2, knitr, lintr, purrr, rmarkdown, httptest, tokenizers, devtools, dplyr, tidyr, roxygen2, pkgdown
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://mwaldstein.github.io/edgarWebR/, https://github.com/mwaldstein/edgarWebR
BugReports: https://github.com/mwaldstein/edgarWebR/issues
NeedsCompilation: no
Packaged: 2020-09-26 19:22:00 UTC; micah
Author: Micah J Waldstein [aut, cre]
Repository: CRAN
Date/Publication: 2020-09-28 13:20:06 UTC

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Package dtw updated to version 1.22-3 with previous version 1.21-3 dated 2019-09-01

Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc., as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.
Author: Toni Giorgino [aut, cre]
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>

Diff between dtw versions 1.21-3 dated 2019-09-01 and 1.22-3 dated 2020-09-28

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New package atakrig with initial version 0.9.7
Package: atakrig
Type: Package
Title: Area-to-Area Kriging
Version: 0.9.7
Authors@R: c( person("Maogui", "Hu", role = c("aut", "cre"), email = "humg@lreis.ac.cn"), person("Yanwei", "Huang", role = "ctb"), person("Roger", "Bivand", role = "ctb"))
Description: Point-scale variogram deconvolution from irregular/regular spatial support according to Goovaerts, P., (2008) <doi: 10.1007/s11004-007-9129-1>; ordinary area-to-area (co)Kriging and area-to-point (co)Kriging.
Imports: gstat, sp, rgeos, foreach, doSNOW, snow, FNN, methods, MASS, Rcpp
Suggests: raster, rgdal, rtop
License: GPL (>= 2.0)
NeedsCompilation: yes
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Packaged: 2020-09-23 05:13:20 UTC; humg
Author: Maogui Hu [aut, cre], Yanwei Huang [ctb], Roger Bivand [ctb]
Maintainer: Maogui Hu <humg@lreis.ac.cn>
Repository: CRAN
Date/Publication: 2020-09-28 13:20:09 UTC

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New package triangulr with initial version 1.0.0
Package: triangulr
Title: High-Performance Triangular Distribution Functions
Version: 1.0.0
Authors@R: person(given = "Alvin", family = "Nursalim", role = c("aut", "cre"), email = "alvin.nursalim@outlook.com")
Description: A collection of high-performance functions for the triangular distribution that consists of the probability density function, cumulative distribution function, quantile function, random variate generator, moment generating function, characteristic function, and expected shortfall function. References: Samuel Kotz, Johan Ren Van Dorp (2004) <doi:10.1142/5720> and Acerbi, Carlo & Tasche, Dirk. (2002) <doi:10.1111/1468-0300.00091>.
License: MIT + file LICENSE
URL: https://github.com/irkaal/triangulr/ https://irkaal.github.io/triangulr/
BugReports: https://github.com/irkaal/triangulr/issues
Depends: R (>= 3.1)
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 7.1.1
Collate: 'RcppExports.R' 'Triangular.R' 'ctri.R' 'dtri.R' 'error.R' 'estri.R' 'mgtri.R' 'ptri.R' 'qtri.R' 'rtri.R'
LinkingTo: Rcpp
Imports: Rcpp (>= 1.0.5), rlang (>= 0.4.7), vctrs (>= 0.3.4)
Suggests: testthat (>= 2.3.2)
NeedsCompilation: yes
Packaged: 2020-09-25 08:33:49 UTC; Alvin
Author: Alvin Nursalim [aut, cre]
Maintainer: Alvin Nursalim <alvin.nursalim@outlook.com>
Repository: CRAN
Date/Publication: 2020-09-28 12:30:02 UTC

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Package tidycensus updated to version 0.10.2 with previous version 0.10.1 dated 2020-09-27

Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census geographies.
Author: Kyle Walker [aut, cre], Matt Herman [aut], Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>

Diff between tidycensus versions 0.10.1 dated 2020-09-27 and 0.10.2 dated 2020-09-28

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 MD5                  |    8 ++++----
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 R/search_variables.R |    8 ++++++++
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 5 files changed, 36 insertions(+), 21 deletions(-)

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Package modeltime updated to version 0.2.0 with previous version 0.1.0 dated 2020-09-02

Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem. Models include ARIMA, Exponential Smoothing, and additional time series models from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition" (<https://otexts.com/fpp2/>). Refer to "Prophet: forecasting at scale" (<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre], Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between modeltime versions 0.1.0 dated 2020-09-02 and 0.2.0 dated 2020-09-28

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New package ConcordanceTest with initial version 0.1.0
Package: ConcordanceTest
Title: An Alternative to the Kruskal-Wallis Test Based on the Kendall Tau Ideas
Version: 0.1.0
Authors@R: c( person(given = "Javier", family = "Alcaraz", role = c("aut"), email = "jalcaraz@umh.es"), person(given = "Laura", family = "Anton-Sanchez", role = c("aut", "cre"), email = "l.anton@umh.es"), person(given = "Juan Francisco", family = "Monge", role = c("aut"), email = "monge@umh.es"))
Description: The Concordance Test is a non-parametric method for testing whether two o more samples originate from the same distribution. It extends the Kendall Tau correlation coefficient when there are only two groups. For details, see Monge (2019) <arXiv:1912.12880v1>.
Depends: R (>= 3.3.2)
Imports: Rglpk, stats, graphics
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-25 08:14:48 UTC; laura
Author: Javier Alcaraz [aut], Laura Anton-Sanchez [aut, cre], Juan Francisco Monge [aut]
Maintainer: Laura Anton-Sanchez <l.anton@umh.es>
Repository: CRAN
Date/Publication: 2020-09-28 12:30:05 UTC

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Package RPostgres updated to version 1.2.1 with previous version 1.2.0 dated 2019-12-18

Title: 'Rcpp' Interface to 'PostgreSQL'
Description: Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>, an open-source relational database.
Author: Hadley Wickham [aut], Jeroen Ooms [aut], Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph], R Consortium [fnd], Tomoaki Nishiyama [ctb] (Code for encoding vectors into strings derived from RPostgreSQL)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package outbreaks updated to version 1.9.0 with previous version 1.5.0 dated 2019-01-21

Title: A Collection of Disease Outbreak Data
Description: Empirical or simulated disease outbreak data, provided either as RData or as text files.
Author: Thibaut Jombart [aut], Simon Frost [aut], Pierre Nouvellet [aut], Finlay Campbell [aut, cre], Bertrand Sudre [aut], Sang Woo Park [ctb], Juliet R.C. Pulliam [ctb], Jakob Schumacher [ctb], Eric Brown [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>

Diff between outbreaks versions 1.5.0 dated 2019-01-21 and 1.9.0 dated 2020-09-28

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Package nonmem2R updated to version 0.2.2 with previous version 0.2.1 dated 2019-02-18

Title: Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>

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Package multiclassPairs updated to version 0.2.0 with previous version 0.1.6 dated 2020-09-10

Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>

Diff between multiclassPairs versions 0.1.6 dated 2020-09-10 and 0.2.0 dated 2020-09-28

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New package lazygreedy with initial version 1.0
Package: lazygreedy
Version: 1.0
Date: 2020-09-18
Title: Applying the Lazy-Greedy Spanning Algorithm
Type: Package
Author: Bokgyeong Kang, John Hughes, Quirijn W. Bouts, Alex P. ten Brink, and Kevin Buchin
Maintainer: Bokgyeong Kang <bxk487@psu.edu>
Depends: Rcpp
Description: Provides an R wrapper for an efficient C++ implementation of the Lazy-Greedy spanning algorithm of Bouts, ten Brink, and Buchin (2014) <DOI:10.1145/2582112.2582154>.
License: GPL (>= 2)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-09-24 20:05:24 UTC; bkang
Repository: CRAN
Date/Publication: 2020-09-28 11:50:02 UTC

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Package icesVocab updated to version 1.1.8 with previous version 1.1.7 dated 2020-09-18

Title: ICES Vocabularies Database Web Services
Description: R interface to access the RECO POX web services of the ICES (International Council for the Exploration of the Sea) Vocabularies database <https://vocab.ices.dk/services/POX.aspx>.
Author: Colin Millar [aut, cre], Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>

Diff between icesVocab versions 1.1.7 dated 2020-09-18 and 1.1.8 dated 2020-09-28

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Package fakemake updated to version 1.8.0 with previous version 1.7.2 dated 2020-09-24

Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package bibliometrix updated to version 3.0.3 with previous version 3.0.2 dated 2020-06-17

Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from 'SCOPUS' (<https://scopus.com>), 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>) and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

Diff between bibliometrix versions 3.0.2 dated 2020-06-17 and 3.0.3 dated 2020-09-28

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New package BayesSPsurv with initial version 0.1.0
Package: BayesSPsurv
Type: Package
Title: Bayesian Spatial Split Population Survival Model
Version: 0.1.0
Authors@R: c(person(given = "Brandon L.", family = "Bolte", role = c("aut")), person(given = "Nicolas", family = "Schmidt", role = c("aut", "cre"), email = "nschmidt@cienciassociales.edu.uy"), person(given = "Sergio", family = "Bejar", role = c("aut")), person(given = "Bumba", family = "Mukherjee", role = c("aut")), person(given = "Minnie M.", family = "Joo", role = c("ctb")), person(given = "Nguyen K.", family = "Huynh", role = c("ctb")) )
Description: Parametric spatial split-population (SP) survival models for clustered event processes. The models account for structural and spatial heterogeneity among “at risk” and “immune” populations, and incorporate time-varying covariates. This package currently implements Weibull, Exponential and Log-logistic forms for the duration component. It also includes functions for a series of diagnostic tests and plots to easily visualize convergence and spatial effects. Users can create their own spatial weights matrix based on their units and adjacencies of interest, making the use of these models flexible and broadly applicable to a variety of research areas. Joo et al. (2020) <https://github.com/Nicolas-Schmidt/BayesSPsurv/blob/master/man/figures/SPcure.pdf> describe the estimators included in this package.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
RoxygenNote: 7.1.0
LinkingTo: Rcpp, RcppArmadillo
Imports: MCMCpack, FastGP, stats, Rcpp (>= 1.0.3), coda, dplyr, reshape2
Suggests: spduration, countrycode
NeedsCompilation: yes
Packaged: 2020-09-24 20:36:37 UTC; Nicolás Schmidt
Author: Brandon L. Bolte [aut], Nicolas Schmidt [aut, cre], Sergio Bejar [aut], Bumba Mukherjee [aut], Minnie M. Joo [ctb], Nguyen K. Huynh [ctb]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>
Repository: CRAN
Date/Publication: 2020-09-28 11:50:09 UTC

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Package packager updated to version 1.5.0 with previous version 1.4.0 dated 2020-08-24

Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and maintenance. Designed to work with a build system such as 'GNU make' or package 'fakemake' to help you to conditionally work through the stages of package development (such as spell checking, linting, testing, before building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between packager versions 1.4.0 dated 2020-08-24 and 1.5.0 dated 2020-09-28

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More information about packager at CRAN
Permanent link

New package simfinapi with initial version 0.1.0
Type: Package
Package: simfinapi
Title: Accessing 'SimFin' Data
Version: 0.1.0
Authors@R: person(given = "Matthias", family = "Gomolka", role = c("aut", "cre"), email = "matthias.gomolka@posteo.de")
Description: Through simfinapi, you can intuitively access the 'SimFin' Web-API (<https://simfin.com/>) to make 'SimFin' data easily available in R. To obtain an 'SimFin' API key (and thus to use this package), you need to register at <https://simfin.com/login>.
License: GPL-3
URL: https://github.com/Plebejer/simfinapi
BugReports: https://github.com/Plebejer/simfinapi/issues
Depends: R (>= 3.2)
Imports: checkmate (>= 2.0.0), data.table (>= 1.12.8), future.apply (>= 1.4.0), httr, memoise (>= 1.1.0), RcppSimdJson (>= 0.1.1), utils
Suggests: covr (>= 3.5.0), secret, testthat, knitr, rmarkdown, fastmatch
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-24 09:46:21 UTC; gomolka
Author: Matthias Gomolka [aut, cre]
Maintainer: Matthias Gomolka <matthias.gomolka@posteo.de>
Repository: CRAN
Date/Publication: 2020-09-28 09:20:02 UTC

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New package medrxivr with initial version 0.0.3
Package: medrxivr
Title: Access and Search MedRxiv and BioRxiv Preprint Data
Version: 0.0.3
Authors@R: c( person("Luke", "McGuinness", role = c("aut", "cre"), email = "luke.mcguinness@bristol.ac.uk", comment = c(ORCID = "0000-0001-8730-9761")), person("Lena", "Schmidt", role = "aut", comment = c(ORCID = "0000-0003-0709-8226")), person("Tuija", "Sonkkila", role = "rev"), person("Najko", "Jahn", role = "rev"))
Description: An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv <https://www.medrxiv.org/> and bioRxiv <https://www.biorxiv.org/>, both of which are operated by the Cold Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the 'Cold Spring Harbour Laboratory (CSHL)' API <https://api.biorxiv.org/>, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. 'medrxivr' also provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Language: en-US
URL: https://github.com/ropensci/medrxivr
BugReports: https://github.com/ropensci/medrxivr/issues
Imports: methods, dplyr, curl, jsonlite, httr, stringr, rlang, vroom, bib2df, tibble, progress, lubridate
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, covr, kableExtra, spelling
VignetteBuilder: knitr, rmarkdown
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-24 14:28:06 UTC; lm16564
Author: Luke McGuinness [aut, cre] (<https://orcid.org/0000-0001-8730-9761>), Lena Schmidt [aut] (<https://orcid.org/0000-0003-0709-8226>), Tuija Sonkkila [rev], Najko Jahn [rev]
Maintainer: Luke McGuinness <luke.mcguinness@bristol.ac.uk>
Repository: CRAN
Date/Publication: 2020-09-28 09:40:02 UTC

More information about medrxivr at CRAN
Permanent link

Package experDesign updated to version 0.0.4 with previous version 0.0.2 dated 2020-09-08

Title: Design Experiments for Batches
Description: Distributes samples in batches while making batches homogeneous according to their description. Allows for an arbitrary number of variables, both numeric and categorical. For quality control it provides functions to subset a representative sample.
Author: Lluís Revilla Sancho [aut, cre] (<https://orcid.org/0000-0001-9747-2570>)
Maintainer: Lluís Revilla Sancho <lluis.revilla@gmail.com>

Diff between experDesign versions 0.0.2 dated 2020-09-08 and 0.0.4 dated 2020-09-28

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New package EDNE.EQ with initial version 1.0
Package: EDNE.EQ
Type: Package
Title: Implements the EDNE-Test for Equivalence
Version: 1.0
Date: 2020-09-24
Author: Thomas Hoffelder
Maintainer: Thomas Hoffelder <thomas.hoffelder@boehringer-ingelheim.com>
Description: Package implements the EDNE-test for equivalence according to Hoffelder et al. (2015) <DOI:10.1080/10543406.2014.920344>. "EDNE" abbreviates "Euclidean Distance between the Non-standardized Expected values". The EDNE-test for equivalence is a multivariate two-sample equivalence test. Distance measure of the test is the Euclidean distance. The test is an asymptotically valid test for the family of distributions fulfilling the assumptions of the multivariate central limit theorem (see Hoffelder et al.,2015). The function EDNE.EQ() implements the EDNE-test for equivalence according to Hoffelder et al. (2015). The function EDNE.EQ.dissolution.profiles() implements a variant of the EDNE-test for equivalence analyses of dissolution profiles (see Suarez-Sharp et al.,2020 <DOI:10.1208/s12248-020-00458-9>). EDNE.EQ.dissolution.profiles() checks whether the quadratic mean of the differences of the expected values of both dissolution profile populations is statistically significantly smaller than 10 [\% of label claim]. The current regulatory standard approach for equivalence analyses of dissolution profiles is the similarity factor f2. The statistical hypotheses underlying EDNE.EQ.dissolution.profiles() coincide with the hypotheses for f2 (see Hoffelder et al.,2015, Suarez-Sharp et al., 2020).
Imports: MASS
License: GPL-3
NeedsCompilation: no
Packaged: 2020-09-24 12:44:19 UTC; hoffelde
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2020-09-28 09:30:03 UTC

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New package ACEsearch with initial version 1.0.0
Package: ACEsearch
Type: Package
Title: 'ACE' Search Engine API
Version: 1.0.0
Author: Vladimir Polony
Date: 2020-09-09
Maintainer: Vladimir Polony <podalv@gmail.com>
Description: 'ACE' (Advanced Cohort Engine) is a powerful tool that allows constructing cohorts of patients extremely quickly and efficiently. This package is designed to interface directly with an instance of 'ACE' search engine and facilitates API queries and data dumps. Prerequisite is a good knowledge of the temporal language to be able to efficiently construct a query. More information available at <https://shahlab.stanford.edu/start>.
License: MIT + file LICENSE
URL: https://shahlab.stanford.edu/start
Imports: httr, testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2020-09-24 16:11:54 UTC; podalv
Repository: CRAN
Date/Publication: 2020-09-28 09:40:06 UTC

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Package ThresholdROC updated to version 2.8.3 with previous version 2.8.2 dated 2020-03-03

Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. The package also provides functions for sample size determination and estimation of diagnostic accuracy measures. It also includes graphical tools.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>

Diff between ThresholdROC versions 2.8.2 dated 2020-03-03 and 2.8.3 dated 2020-09-28

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Package survival updated to version 3.2-7 with previous version 3.2-3 dated 2020-06-13

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

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More information about survival at CRAN
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Package quantreg updated to version 5.70 with previous version 5.67 dated 2020-09-09

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

Diff between quantreg versions 5.67 dated 2020-09-09 and 5.70 dated 2020-09-28

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Package mlr3db updated to version 0.2.0 with previous version 0.1.5 dated 2020-02-19

Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to transparently work with data bases. Internally relies on the abstraction of package 'dbplyr' to interact with one of the many supported data base management systems (DBMS).
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3db versions 0.1.5 dated 2020-02-19 and 0.2.0 dated 2020-09-28

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Package coxphf updated to version 1.13.1 with previous version 1.13 dated 2018-03-03

Title: Cox Regression with Firth's Penalized Likelihood
Description: Implements Firth's penalized maximum likelihood bias reduction method for Cox regression which has been shown to provide a solution in case of monotone likelihood (nonconvergence of likelihood function), see Heinze and Schemper (2001) and Heinze and Dunkler (2008). The program fits profile penalized likelihood confidence intervals which were proved to outperform Wald confidence intervals.
Author: Georg Heinze [aut, cre], Meinhard Ploner [aut], Lena Jiricka [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>

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Package bomrang updated to version 0.7.1 with previous version 0.7.0 dated 2020-01-20

Title: Australian Government Bureau of Meteorology ('BOM') Data Client
Description: Provides functions to interface with Australian Government Bureau of Meteorology ('BOM') data, fetching data and returning a data frame of precis forecasts, historical and current weather data from stations, agriculture bulletin data, 'BOM' 0900 or 1500 weather bulletins and downloading and importing radar and satellite imagery files. Data (c) Australian Government Bureau of Meteorology Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See <http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>), James Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>), Dean Marchiori [aut], Paul Melloy [aut] (<https://orcid.org/0000-0003-4253-7167>), Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>), Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>), Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>), James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>), Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

Diff between bomrang versions 0.7.0 dated 2020-01-20 and 0.7.1 dated 2020-09-28

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Package sigminer updated to version 1.0.19 with previous version 1.0.16 dated 2020-09-12

Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>), Tao Wu [aut, ctb], Ziyu Tao [aut, ctb], Geoffrey Macintyre [ctb], Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between sigminer versions 1.0.16 dated 2020-09-12 and 1.0.19 dated 2020-09-28

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Package hypr updated to version 0.1.11 with previous version 0.1.10 dated 2020-09-08

Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038> and Rabe, Vasishth, Hohenstein, Kliegl, and Schad (2020) <doi:10.21105/joss.02134>.
Author: Maximilian M. Rabe [aut, cre] (<https://orcid.org/0000-0002-2556-5644>), Shravan Vasishth [aut] (<https://orcid.org/0000-0003-2027-1994>), Sven Hohenstein [aut] (<https://orcid.org/0000-0002-9708-1593>), Reinhold Kliegl [aut] (<https://orcid.org/0000-0002-0180-8488>), Daniel J. Schad [aut] (<https://orcid.org/0000-0003-2586-6823>)
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>

Diff between hypr versions 0.1.10 dated 2020-09-08 and 0.1.11 dated 2020-09-28

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Package graph4lg updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-22

Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://igraph.org/>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>

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New package covid19.analytics with initial version 2.0
Package: covid19.analytics
Type: Package
Title: Load and Analyze Live Data from the CoViD-19 Pandemic
Version: 2.0
Date: 2020-09-22
Author: Marcelo Ponce [aut, cre], Amit Sandhel [ctb]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
Description: Load and analyze updated time series worldwide data of reported cases for the Novel CoronaVirus Disease (CoViD-19) from the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) data repository <https://github.com/CSSEGISandData/COVID-19>. The datasets are available in two main modalities, as a time series sequences and aggregated for the last day with greater spatial resolution. Several analysis, visualization and modelling functions are available in the package that will allow the user to compute and visualize total number of cases, total number of changes and growth rate globally or for an specific geographical location, while at the same time generating models using these trends; generate interactive visualizations and generate Susceptible-Infected-Recovered (SIR) model for the disease spread.
Imports: readxl, ape, rentrez, plotly, htmlwidgets, deSolve, gplots, pheatmap, shiny, shinydashboard, shinycssloaders, DT, dplyr, collapsibleTree
Suggests: knitr, devtools, roxygen2, markdown, rmarkdown, testthat
License: GPL (>= 2)
URL: https://mponce0.github.io/covid19.analytics/
BugReports: https://github.com/mponce0/covid19.analytics/issues
RoxygenNote: 7.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-24 19:58:02 UTC; marcelo
Repository: CRAN
Date/Publication: 2020-09-28 07:22:17 UTC

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Package SimSurvNMarker (with last version 0.1.0) was removed from CRAN

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

2020-09-11 0.1.0

Permanent link
Package fingertipsR (with last version 1.0.5) was removed from CRAN

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

2020-09-16 1.0.5

Permanent link

Sun, 27 Sep 2020

Package distr6 updated to version 1.4.4 with previous version 1.4.3 dated 2020-08-26

Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut], Peter Ruckdeschel [ctb] (Author of distr), Matthias Kohl [ctb] (Author of distr), Shen Chen [ctb], Jordan Deenichin [ctb], Chengyang Gao [ctb], Chloe Zhaoyuan Gu [ctb], Yunjie He [ctb], Xiaowen Huang [ctb], Shuhan Liu [ctb], Runlong Yu [ctb], Chijing Zeng [ctb], Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>

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Package tensorsparse updated to version 3.0 with previous version 2.0 dated 2020-03-22

Title: Multiway Clustering via Tensor Block Models
Description: Implements the multiway sparse clustering approach of M. Wang and Y. Zeng, "Multiway clustering via tensor block models". Advances in Neural Information Processing System 32 (NeurIPS), 715-725, 2019.
Author: Miaoyan Wang, Yuchen Zeng
Maintainer: Yuchen Zeng <yzeng58@wisc.edu>

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Package WLinfer updated to version 1.1.0 with previous version 1.0.0 dated 2020-09-09

Title: Statistical Inference in Weighted Lindley Distribution
Description: Estimate the parameters of weighted Lindley distribution, and provide some useful results like goodness of fit or confidence interval etc. Ghitany, M., Alqallaf, F., Al-Mutairi, D., Husain, H. (2011) <doi:10.1016/j.matcom.2010.11.005>. Hyoung-Moon Kim. and Yu-Hyeong Jang. (2020) submitted. Wang, M., Wang, W. (2017) <doi:10.1080/03610918.2014.970696>.
Author: Yu-Hyeong Jang, SungBum Kim, Hyun-Ju Jung and Hyoung-Moon Kim
Maintainer: SungBum Kim <kimsb0707@hanmail.net>

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Package shinybusy updated to version 0.2.2 with previous version 0.2.1 dated 2020-09-10

Title: Busy Indicator for 'Shiny' Applications
Description: Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Silex Technologies [fnd] (https://www.silex-ip.com)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package rbibutils updated to version 1.1.0 with previous version 1.0.3 dated 2020-07-20

Title: Convert Between Bibliography Formats
Description: Converts between a number of bibliography formats, including 'BibTeX', 'BibLaTeX' and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, modifications to bibutils' C code), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package qdap updated to version 2.4.3 with previous version 2.4.1 dated 2020-04-20

Title: Bridging the Gap Between Qualitative Data and Quantitative Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.
Author: Tyler Rinker [aut, cre], Bryan Goodrich [ctb], Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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Package PMCMRplus updated to version 1.5.1 with previous version 1.5.0 dated 2020-09-12

Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Description: For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra test, Spearman test) are included. In addition, a Friedman-test for one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack test for unbalanced CRBD is provided with consequent all-pairs tests (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be tested with Pages's test. Durbin's test for a two-way balanced incomplete block design (BIBD) is given in this package as well as Gore's test for CRBD with multiple observations per cell is given. Outlier tests, Mandel's k- and h statistic as well as functions for Type I error and Power analysis as well as generic summary, print and plot methods are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

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Package esquisse updated to version 0.3.1 with previous version 0.3.0 dated 2020-01-27

Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables. You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint', and retrieve the code to reproduce the chart.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Ian Carroll [ctb] (Faceting support), Xiangnan Dang [ctb] (Facets rows and cols, X/Y limits)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package powerLATE updated to version 0.1.1 with previous version 0.1.0 dated 2020-08-14

Title: Generalized Power Analysis for LATE
Description: An implementation of the generalized power analysis for the local average treatment effect (LATE), proposed by Bansak (2020) <doi:10.1214/19-STS732>. Power analysis is in the context of estimating the LATE (also known as the complier average causal effect, or CACE), with calculations based on a test of the null hypothesis that the LATE equals 0 with a two-sided alternative. The method uses standardized effect sizes to place a conservative bound on the power under minimal assumptions. Package allows users to recover power, sample size requirements, or minimum detectable effect sizes. Package also allows users to work with absolute effects rather than effect sizes, to specify an additional assumption to narrow the bounds, and to incorporate covariate adjustment.
Author: Kirk Bansak [aut], Eddie Yang [aut, cre]
Maintainer: Eddie Yang <z5yang@ucsd.edu>

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Package numform updated to version 0.6.4 with previous version 0.6.0 dated 2020-04-16

Title: Tools to Format Numbers for Publication
Description: Format numbers and plots for publication; includes the removal of leading zeros, standardization of number of digits, addition of affixes, and a p-value formatter. These tools combine the functionality of several 'base' functions such as 'paste()', 'format()', and 'sprintf()' into specific use case functions that are named in a way that is consistent with usage, making their names easy to remember and easy to deploy.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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Package pkgKitten updated to version 0.2.0 with previous version 0.1.5 dated 2019-10-22

Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little packages which pass R package checks. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative. Unit test support is added if the 'tinytest' package is present.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package tidycensus updated to version 0.10.1 with previous version 0.9.9.5 dated 2020-06-10

Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census geographies.
Author: Kyle Walker [aut, cre], Matt Herman [aut], Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>

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Package orloca updated to version 4.10 with previous version 4.9 dated 2020-03-04

Title: Operations Research LOCational Analysis Models
Description: Objects and methods to handle and solve the min-sum location problem, also known as Fermat-Weber problem. The min-sum location problem search for a point such that the weighted sum of the distances to the demand points are minimized. See "The Fermat-Weber location problem revisited" by Brimberg, Mathematical Programming, 1, pg. 71-76, 1995. <DOI:10.1007/BF01592245>. General global optimization algorithms are used to solve the problem, along with the adhoc Weiszfeld method, see "Sur le point pour lequel la Somme des distances de n points donnes est minimum", by Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pg. 355-386, 1937 or "On the point for which the sum of the distances to n given points is minimum", by E. Weiszfeld and F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z>.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>

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Package emld updated to version 0.5.1 with previous version 0.5.0 dated 2020-07-08

Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Matthew B. Jones [aut, cph] (<https://orcid.org/0000-0003-0077-4738>), Bryce Mecum [aut, cph] (<https://orcid.org/0000-0002-0381-3766>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package correlation updated to version 0.4.0 with previous version 0.3.0 dated 2020-06-19

Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Relies on the easystats ecosystem (Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>), Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package epuR (with last version 0.1) was removed from CRAN

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

2020-04-10 0.1

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Package h2o (with last version 3.30.1.2) was removed from CRAN

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

2020-09-12 3.30.1.2
2020-04-09 3.30.0.1
2020-02-26 3.28.0.4
2020-01-22 3.28.0.2
2019-08-01 3.26.0.2
2019-06-21 3.24.0.5
2019-01-10 3.22.1.1
2018-09-25 3.20.0.8
2018-06-17 3.20.0.2
2018-05-24 3.18.0.11
2018-05-02 3.18.0.8
2017-12-01 3.16.0.2
2017-11-27 3.16.0.1
2017-09-27 3.14.0.3
2017-07-01 3.10.5.3
2017-06-23 3.10.5.2
2017-05-02 3.10.4.6
2017-04-17 3.10.4.4
2017-02-22 3.10.3.6
2017-02-03 3.10.3.3
2017-01-17 3.10.2.2
2016-10-14 3.10.0.8
2016-09-03 3.10.0.6
2016-07-13 3.8.3.3
2016-06-02 3.8.2.6
2016-03-15 3.8.1.3
2015-11-24 3.6.0.8
2015-09-22 3.2.0.3
2015-09-14 3.2.0.1
2015-07-22 3.0.0.30
2015-06-14 3.0.0.22
2015-02-07 2.8.4.4
2014-10-27 2.8.1.1

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Package totalcensus updated to version 0.6.4 with previous version 0.6.3 dated 2020-01-08

Title: Extract Decennial Census and American Community Survey Data
Description: Download summary files from Census Bureau <https://www2.census.gov/> and extract data, in particular high resolution data at block, block group, and tract level, from decennial census and American Community Survey 1-year and 5-year estimates.
Author: Guanglai Li
Maintainer: Guanglai Li <liguanglai@gmail.com>

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Package mcmcr updated to version 0.4.0 with previous version 0.3.0 dated 2020-07-13

Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and summarise Monte Carlo Markov Chain (MCMC) samples. For more information see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package BVAR updated to version 1.0.1 with previous version 1.0.0 dated 2020-05-05

Title: Hierarchical Bayesian Vector Autoregression
Description: Estimation of hierarchical Bayesian vector autoregressive models. Implements hierarchical prior selection for conjugate priors in the fashion of Giannone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Functions to compute and identify impulse responses, calculate forecasts, forecast error variance decompositions and scenarios are available. Several methods to print, plot and summarise results facilitate analysis.
Author: Nikolas Kuschnig [aut, cre] (<https://orcid.org/0000-0002-6642-2543>), Lukas Vashold [aut] (<https://orcid.org/0000-0002-3562-3414>), Michael McCracken [dtc], Serena Ng [dtc]
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>

Diff between BVAR versions 1.0.0 dated 2020-05-05 and 1.0.1 dated 2020-09-27

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More information about BVAR at CRAN
Permanent link

Package BE updated to version 0.1.2 with previous version 0.1.1 dated 2018-07-19

Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design. Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Sat, 26 Sep 2020

Package zcurve updated to version 1.0.6 with previous version 1.0.0 dated 2020-03-31

Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery and replicability rates on the bases of test-statistics of published studies. The package provides functions for fitting the new density and EM version (Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density z-curve (Brunner & Schimmack, 2017, <doi:10.31219/osf.io/wr93f>). Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects. See the aforementioned articles for more information about the z-curves, expected discovery and replicability rates, validation studies, and limitations.
Author: František Bartoš [aut, cre], Ulrich Schimmack [aut]
Maintainer: František Bartoš <f.bartos96@gmail.com>

Diff between zcurve versions 1.0.0 dated 2020-03-31 and 1.0.6 dated 2020-09-26

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Package tidygate updated to version 0.2.8 with previous version 0.2.7 dated 2020-07-06

Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions. The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid. The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots; (ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre], Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>

Diff between tidygate versions 0.2.7 dated 2020-07-06 and 0.2.8 dated 2020-09-26

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Package RAthena updated to version 1.10.1 with previous version 1.10.0 dated 2020-08-06

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package packagefinder updated to version 0.3.1 with previous version 0.3.0 dated 2020-09-14

Title: Comfortable Search for R Packages on CRAN, Either Directly from the R Console or with an R Studio Add-in
Description: Search for R packages on CRAN directly from the R console, based on the packages' titles, short and long descriptions, or other fields. Combine multiple keywords with logical operators ('and', 'or'), view detailed information on any package and keep track of the latest package contributions to CRAN. If you don't want to search from the R console, use the comfortable R Studio add-in.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>

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Package modelbased updated to version 0.3.0 with previous version 0.1.2 dated 2020-03-12

Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package carat updated to version 1.4 with previous version 1.3 dated 2020-09-08

Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut], Xiaoqing Ye [aut, cre], Wei Ma [aut, ths], Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>

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Package spaero updated to version 0.6.0 with previous version 0.5.0 dated 2019-05-24

Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication of infectious diseases from surveillance time series. Also provides support for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>

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Package SemNeT updated to version 1.4.0 with previous version 1.3.0 dated 2020-06-09

Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre] (<https://orcid.org/0000-0002-9798-7037>), Yoed N. Kenett [aut, ctb] (<https://orcid.org/0000-0003-3872-7689>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>

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Package PortalHacienda (with last version 0.1.4) was removed from CRAN

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

2020-07-20 0.1.4

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Package pwrFDR updated to version 2.8.4 with previous version 1.95 dated 2018-08-22

Title: FDR Power
Description: This is a package for calculating two differing notions of power, or deriving sample sizes for specified requisite power in multiple testing experiments under a variety of methods for control of the distribution of the False Discovery Proportion (FDP). More specifically, one can choose to control the FDP distribution according to control of its (i) mean, e.g. the usual BH-FDR procedure, or via the probability that it exceeds a given value, delta, via (ii) the Romano procedure, or via (iii) my procedure based upon asymptotic approximation. Likewise, we can think of the power in multiple testing experiments in terms of a summary of the distribution of the True Positive Proportion (TPP). The package will compute power, sample size or any other missing parameter required for power based upon (i) the mean of the TPP which is the average power (ii) the probability that the TPP exceeds a given value, lambda, via my asymptotic approximation procedure. The theoretical results are described in Izmirlian, G. (2020) Stat. and Prob. letters, <doi:10.1016/j.spl.2020.108713>, and an applied paper describing the methodology with a simulation study is in preparation.
Author: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian Jr <izmirlig@mail.nih.gov>

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Package Seurat updated to version 3.2.2 with previous version 3.2.1 dated 2020-09-07

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>

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Package SemNetDictionaries updated to version 0.1.7 with previous version 0.1.6 dated 2020-06-08

Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre] (<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>

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Package lava updated to version 1.6.8 with previous version 1.6.7 dated 2020-03-05

Title: Latent Variable Models
Description: A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2019) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Author: Klaus K. Holst [aut, cre], Brice Ozenne [ctb], Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>

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Package farrell updated to version 0.2.1 with previous version 0.2.0 dated 2020-06-03

Title: Interactive Interface to Data Envelopment Analysis Modeling
Description: Allows the user to execute interactively radial data envelopment analysis models. The user has the ability to upload a data frame, select the input/output variables, choose the technology assumption to adopt and decide whether to run an input or an output oriented model. When the model is executed a set of results are displayed which include efficiency scores, peers' determination, scale efficiencies' evaluation and slacks' calculation. Fore more information about the theoretical background of the package, please refer to Bogetoft & Otto (2011) <doi:10.1007/978-1-4419-7961-2>.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>

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Package extras updated to version 0.1.0 with previous version 0.0.1 dated 2020-06-16

Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric objects) and summarise 'MCMC' (Monte Carlo Markov Chain) samples as well as 'R' translations of 'BUGS' (Bayesian Using Gibbs Sampling) and 'JAGS' (Just Another Gibbs Sampler) functions.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package cyclestreets updated to version 0.3.0 with previous version 0.1.5 dated 2018-05-06

Title: Cycle Routing and Data for Cycling Advocacy
Description: An interface to the cycle routing/data services provided by 'CycleStreets', a not-for-profit social enterprise and advocacy organisation. The application programming interfaces (APIs) provided by 'CycleStreets' are documented at (<https://www.cyclestreets.net/api/>). The focus of this package is the journey planning API, which aims to emulate the routes taken by a knowledgeable cyclist. An innovative feature of the routing service of its provision of fastest, quietest and balanced profiles. These represent routes taken to minimise time, avoid traffic and compromise between the two, respectively.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Martin Lucas-Smith [aut], Eric Krueger [ctb], Joey Talbot [aut] (<https://orcid.org/0000-0002-6520-4560>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package Claddis updated to version 0.6.3 with previous version 0.6.1 dated 2020-08-26

Title: Measuring Morphological Diversity and Evolutionary Tempo
Description: Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and MatrixDistances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.
Author: Graeme T. Lloyd [aut, cre, cph], Thomas Guillerme [aut, cph], Emma Sherratt [aut, cph], Steve C. Wang [aut, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>

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Fri, 25 Sep 2020

Package starschemar updated to version 1.2.0 with previous version 1.1.0 dated 2020-09-13

Title: Obtaining Star Schemas from Flat Tables
Description: Data in multidimensional systems is obtained from operational systems and is transformed to adapt it to the new structure. Frequently, the operations to be performed aim to transform a flat table into a star schema. Transformations can be carried out using professional ETL (extract, transform and load) tools or tools intended for data transformation for end users. With the tools mentioned, this transformation can be carried out, but it requires a lot of work. The main objective this package is to define transformations that allow obtaining star schemas from flat tables easily. In addition, it includes basic data cleaning, dimension enrichment, incremental data refresh and query operations, adapted to this context.
Author: Jose Samos [aut, cre, cph] (<https://orcid.org/0000-0002-4457-3439>)
Maintainer: Jose Samos <jsamos@ugr.es>

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Package nimbleEcology updated to version 0.3.1 with previous version 0.3.0 dated 2020-05-29

Title: Distributions for Ecological Models in 'nimble'
Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models. (Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
Author: Benjamin R. Goldstein [aut, cre], Daniel Turek [aut], Lauren Ponisio [aut], Perry de Valpine [aut]
Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu>

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Package matrixStats updated to version 0.57.0 with previous version 0.56.0 dated 2020-03-13

Title: Functions that Apply to Rows and Columns of Matrices (and to Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb], Peter Hickey [ctb], Brian Montgomery [ctb], Constantin Ahlmann-Eltze [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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 tests/rowAllAnys.R                |   49 ++++++++--------
 tests/rowAvgsPerColSet.R          |   96 ++++++++++++++++----------------
 tests/rowCollapse_subset.R        |   31 +++++-----
 tests/rowCumprods.R               |   17 +++--
 26 files changed, 290 insertions(+), 506 deletions(-)

More information about matrixStats at CRAN
Permanent link

Package jrc updated to version 0.4.0 with previous version 0.3.1 dated 2020-02-07

Title: Exchange Commands Between R and 'JavaScript'
Description: An 'httpuv' based bridge between R and 'JavaScript'. Provides an easy way to exchange commands and data between a web page and a currently running R session.
Author: Svetlana Ovchinnikova [aut, cre], Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>

Diff between jrc versions 0.3.1 dated 2020-02-07 and 0.4.0 dated 2020-09-25

 DESCRIPTION               |   12 +-
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More information about jrc at CRAN
Permanent link

Package discourseGT updated to version 1.1.0 with previous version 1.0.0 dated 2020-02-17

Title: Analyze Group Patterns using Graph Theory in Educational Settings
Description: Analyzes group patterns using discourse analysis data with graph theory mathematics. Takes the order of which individuals talk and converts it to a network edge and weight list. Returns the density, centrality, centralization, and subgroup information for each group. Based on the analytical framework laid out in Chai et al. (2019) <doi:10.1187/cbe.18-11-0222>.
Author: Albert Chai [aut], Andrew Lee [aut], Joshua Le [aut, cre], Katherine Ly [ctb], Kevin Banh [ctb], Priya Pahal [ctb], Stanley Lo [aut]
Maintainer: Joshua Le <jpl038@ucsd.edu>

Diff between discourseGT versions 1.0.0 dated 2020-02-17 and 1.1.0 dated 2020-09-25

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 discourseGT-1.1.0/discourseGT/NAMESPACE                   |    1 
 discourseGT-1.1.0/discourseGT/R/coreNetAnalysis.R         |   32 +---
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 discourseGT-1.1.0/discourseGT/R/plotNGTData.R             |   98 +++++++++++---
 discourseGT-1.1.0/discourseGT/R/prepareGraphs.R           |   26 +--
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 discourseGT-1.1.0/discourseGT/R/summaryNet.R              |   13 -
 discourseGT-1.1.0/discourseGT/R/tabulate_edges.R          |   26 ++-
 discourseGT-1.1.0/discourseGT/R/writeData.R               |   13 -
 discourseGT-1.1.0/discourseGT/README.md                   |    6 
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 discourseGT-1.1.0/discourseGT/man/subgroupsNetAnalysis.Rd |    5 
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 27 files changed, 241 insertions(+), 198 deletions(-)

More information about discourseGT at CRAN
Permanent link

Package redland updated to version 1.0.17-12 with previous version 1.0.17-11 dated 2019-10-13

Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Jeroen Ooms [aut], Carl Boettiger [aut], Scott Chamberlain [aut], David Beckett [cph], University of Bristol [cph], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>

Diff between redland versions 1.0.17-11 dated 2019-10-13 and 1.0.17-12 dated 2020-09-25

 DESCRIPTION                                           |   12 
 MD5                                                   |  526 +++++++++---------
 NEWS                                                  |   11 
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 R/redland-package.R                                   |    2 
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 build/vignette.rds                                    |binary
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 inst/doc/redland_overview.Rmd                         |    4 
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 tests/testthat/test.Storage.R                         |    2 
 tests/testthat/test.World.R                           |    1 
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 vignettes/redland_overview.Rmd                        |    4 
 264 files changed, 642 insertions(+), 629 deletions(-)

More information about redland at CRAN
Permanent link

Package nlist updated to version 0.3.0 with previous version 0.2.0 dated 2020-06-25

Title: Lists of Numeric Atomic Objects
Description: Create and manipulate numeric list ('nlist') objects. An 'nlist' is an S3 list of uniquely named numeric objects. An numeric object is an integer or double vector, matrix or array. An 'nlists' object is a S3 class list of 'nlist' objects with the same names, dimensionalities and typeofs. Numeric list objects are of interest because they are the raw data inputs for analytic engines such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for storing multiple realizations of of simulated data sets, can be converted to coda::mcmc and coda::mcmc.list objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between nlist versions 0.2.0 dated 2020-06-25 and 0.3.0 dated 2020-09-25

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Package sparklyr.flint updated to version 0.2.0 with previous version 0.1.1 dated 2020-08-24

Title: Sparklyr Extension for 'Flint'
Description: This sparklyr extension makes 'Flint' time series library functionalities (<https://github.com/twosigma/flint>) easily accessible through R.
Author: Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>)
Maintainer: Yitao Li <yitao@rstudio.com>

Diff between sparklyr.flint versions 0.1.1 dated 2020-08-24 and 0.2.0 dated 2020-09-25

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Package dispRity updated to version 1.5.0 with previous version 1.4.2 dated 2020-09-04

Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph], Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>

Diff between dispRity versions 1.4.2 dated 2020-09-04 and 1.5.0 dated 2020-09-25

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Package term updated to version 0.3.0 with previous version 0.2.0 dated 2020-06-20

Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors of parameter terms. Parameter terms are the labels used to reference values in vectors, matrices and arrays. They represent the names in coefficient tables and the column names in 'mcmc' and 'mcmc.list' objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package mlegp updated to version 3.1.8 with previous version 3.1.7 dated 2018-04-14

Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots following Santner et al (2003) <doi:10.1007/978-1-4757-3799-8>. Contact the maintainer for a package version that includes sensitivity analysis.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>

Diff between mlegp versions 3.1.7 dated 2018-04-14 and 3.1.8 dated 2020-09-25

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Package liver updated to version 1.2 with previous version 1.1 dated 2020-09-10

Title: "Eating the Liver of Data Science"
Description: Provides a collection of helper functions that make various techniques from data science more user-friendly for non-experts. In this way, our aim is to allow non-experts to become familiar with the techniques with only a minimal level of coding knowledge. Indeed, following an ancient Persian idiom, we refer to this as "eating the liver of data science" which could be interpreted as "getting intimately close with data science". Examples of procedures we include are: data partitioning for out-of-sample testing, computing Mean Squared Error (MSE) for quantifying prediction accuracy, and data transformation (z-score and min-max). Besides such helper functions, the package also includes several interesting datasets that are useful for multivariate analysis.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>), Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

Diff between liver versions 1.1 dated 2020-09-10 and 1.2 dated 2020-09-25

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Package RRphylo updated to version 2.4.11 with previous version 2.4.7 dated 2020-07-13

Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>

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Package rpact updated to version 3.0.1 with previous version 3.0.0 dated 2020-09-07

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

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Package r5r updated to version 0.1-1 with previous version 0.1.0 dated 2020-09-18

Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks (walk, bike, public transport and car) using 'R5', the Rapid Realistic Routing on Real-world and Reimagined networks <https://github.com/conveyal/r5>. The package allows users to generate detailed routing analysis or calculate travel time matrices using seamless parallel computing on top of the R5 Java machine.
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>), Rafael H. M. Pereira [aut, cre] (<https://orcid.org/0000-0003-2125-7465>), Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>), Carlos Kaue Vieira Braga [aut] (<https://orcid.org/0000-0002-6104-7297>), Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>

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Package corTest updated to version 1.0.7 with previous version 1.0.4 dated 2020-07-19

Title: Robust Tests for Equal Correlation
Description: There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. The score statistic U is proportion to difference of two correlations based on different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the article titled ''New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs'' published in Scientific Reports. Please see the reference: Yu et al. (2019) <doi:10.1038/s41598-019-40167-8>.
Author: Danyang Yu, Weiliang Qiu, Zeyu Zhang, Kimberly Glass, Jessica Su, Dawn L. DeMeo, Kelan Tantisira, Scott T. Weiss
Maintainer: Danyang Yu <dyu33@jhu.edu>

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Package noctua updated to version 1.8.1 with previous version 1.8.0 dated 2020-08-10

Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package mlr3learners updated to version 0.4.0 with previous version 0.3.0 dated 2020-08-29

Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' and 'mlr3proba' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Quay Au [aut] (<https://orcid.org/0000-0002-5252-8902>), Stefan Coors [aut] (<https://orcid.org/0000-0002-7465-2146>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>

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New package txshift with initial version 0.3.4
Package: txshift
Title: Efficient Estimation of the Causal Effects of Stochastic Interventions
Version: 0.3.4
Authors@R: c( person("Nima", "Hejazi", email = "nh@nimahejazi.org", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-7127-2789")), person("David", "Benkeser", email = "benkeser@emory.edu", role = "aut", comment = c(ORCID = "0000-0002-1019-8343")), person("Iván", "Díaz", email = "ild2005@med.cornell.edu", role = "ctb", comment = c(ORCID = "0000-0001-9056-2047")), person("Jeremy", "Coyle", email = "jeremy.coyle@gmail.com", role = "ctb", comment = c(ORCID = "0000-0002-9874-6649")), person("Mark", "van der Laan", email = "laan@berkeley.edu", role = c("ctb", "ths"), comment = c(ORCID = "0000-0003-1432-5511")) )
Maintainer: Nima Hejazi <nh@nimahejazi.org>
Description: Efficient estimation of the population-level causal effects of stochastic interventions on a continuous-valued exposure. Both one-step and targeted minimum loss estimators are implemented for a causal parameter defined as the counterfactual mean of an outcome of interest under a stochastic intervention that may depend on the natural value of the exposure (i.e., a modified treatment policy). To accommodate settings in which two-phase sampling is employed, procedures for making use of inverse probability of censoring weights are provided to facilitate construction of inefficient and efficient one-step and targeted minimum loss estimators. The causal parameter and estimation methodology were first described by Díaz and van der Laan (2013) <doi:10.1111/j.1541-0420.2011.01685.x>). Estimation of nuisance parameters may be enhanced through the Super Learner ensemble model in 'sl3', available for download from GitHub using 'remotes::install_github("tlverse/sl3")'.
Depends: R (>= 3.2.0)
Imports: stats, stringr, data.table, assertthat, mvtnorm, hal9001 (>= 0.2.6), haldensify (>= 0.0.6), lspline, ggplot2, tibble, latex2exp, Rdpack
Suggests: testthat, knitr, rmarkdown, covr, future, future.apply, origami (>= 1.0.3), ranger, Rsolnp, nnls, rlang
Enhances: sl3 (>= 1.3.7)
License: MIT + file LICENSE
URL: https://github.com/nhejazi/txshift
BugReports: https://github.com/nhejazi/txshift/issues
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2020-09-23 22:29:09 UTC; nsh
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>), David Benkeser [aut] (<https://orcid.org/0000-0002-1019-8343>), Iván Díaz [ctb] (<https://orcid.org/0000-0001-9056-2047>), Jeremy Coyle [ctb] (<https://orcid.org/0000-0002-9874-6649>), Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>)
Repository: CRAN
Date/Publication: 2020-09-25 13:50:02 UTC

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Package tufte updated to version 0.7 with previous version 0.6 dated 2020-05-08

Title: Tufte's Styles for R Markdown Documents
Description: Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [aut], Andrzej Oles [ctb], Dave Liepmann [ctb] (Tufte CSS in inst/rmarkdown/templates/tufte_html/resources), RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between tufte versions 0.6 dated 2020-05-08 and 0.7 dated 2020-09-25

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Package survPen updated to version 1.5.1 with previous version 1.5.0 dated 2020-05-25

Title: Multidimensional Penalized Splines for Survival and Net Survival Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics. See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>

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New package SC2API with initial version 1.0.0
Package: SC2API
Title: Blizzard SC2 API Wrapper
Version: 1.0.0
Authors@R: person('Samuel', 'Morrissette', email = 'samuel.morrissette01@gmail.com', role = c('cre', 'aut'))
Description: A wrapper for Blizzard's Starcraft II (a 2010 real-time strategy game) Application Programming Interface (API). All documented API calls are implemented in an easy-to-use and consistent manner.
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
Imports: data.table, httr, jsonlite
Suggests: rmarkdown, knitr, httptest, ggplot2, testthat
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-23 14:31:27 UTC; Sam
Author: Samuel Morrissette [cre, aut]
Maintainer: Samuel Morrissette <samuel.morrissette01@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-25 13:20:06 UTC

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New package rct3 with initial version 1.0.4
Package: rct3
Version: 1.0.4
Date: 2020-09-17
Title: Predict Fish Year-Class Strength from Survey Data
Authors@R: c( person("Colin", "Millar", role = c("aut", "cre"), email="colin.millar@ices.dk"), person("Marc", "Taylor", role = "aut") )
LazyData: yes
Description: Predict fish year-class strength by calibration regression analysis of multiple recruitment index series.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-23 14:02:32 UTC; colin
Author: Colin Millar [aut, cre], Marc Taylor [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Repository: CRAN
Date/Publication: 2020-09-25 13:10:02 UTC

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New package o2geosocial with initial version 1.0.1
Package: o2geosocial
Type: Package
Title: Reconstruction of Transmission Chains from Surveillance Data
Version: 1.0.1
URL: https://github.com/alxsrobert/o2geosocial
Encoding: UTF-8
Authors@R: c(person("Alexis", "Robert", email = "alexis.robert@lshtm.ac.uk", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-4516-2965")), person("Sebastian", "Funk", email = "sebastian.funk@lshtm.ac.uk", role = c("aut"), comment = c(ORCID = "0000-0002-2842-3406")), person("Adam J", "Kucharski", email = "adam.kucharski@lshtm.ac.uk", role = c("aut"), comment = c(ORCID = "0000-0001-8814-9421")), person("Thibaut", "Jombart", role = c("ctb")))
Maintainer: Alexis Robert <alexis.robert@lshtm.ac.uk>
Description: Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. 2020 <doi:10.1098/rsif.2020.0084>).
License: MIT + file LICENSE
Imports: Rcpp, methods, stats, grDevices, geosphere, ggplot2, visNetwork, data.table, outbreaker2
LazyData: true
Depends: R(>= 3.5.0)
LinkingTo: Rcpp
RoxygenNote: 7.1.1
Suggests: testthat, tigris, sf, knitr, socialmixr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/alxsrobert/o2geosocial/issues
NeedsCompilation: yes
Packaged: 2020-09-23 21:20:59 UTC; Alexis Robert
Author: Alexis Robert [aut, cre, cph] (<https://orcid.org/0000-0002-4516-2965>), Sebastian Funk [aut] (<https://orcid.org/0000-0002-2842-3406>), Adam J Kucharski [aut] (<https://orcid.org/0000-0001-8814-9421>), Thibaut Jombart [ctb]
Repository: CRAN
Date/Publication: 2020-09-25 13:40:02 UTC

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Package mlr3viz updated to version 0.3.0 with previous version 0.2.0 dated 2020-08-07

Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks, predictions, resample results or benchmark results via the autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are intended to provide sensible defaults, yet can easily be customized to create camera-ready figures. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>), Raphael Sonabend [aut] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3viz versions 0.2.0 dated 2020-08-07 and 0.3.0 dated 2020-09-25

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New package metabolic with initial version 0.1.0
Package: metabolic
Title: Datasets and Functions for Reproducing Meta-Analyses
Version: 0.1.0
Authors@R: person(given = "Felipe", family = "Mattioni Maturana", role = c("aut", "cre", "cph"), email = "felipe.mattioni@med.uni-tuebingen.de", comment = c(ORCID = "0000-0002-4221-6104"))
Description: Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise. It contains all the data and functions to reproduce the analysis. "Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis". Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieß (2020) <doi:10.1249/MSS.0000000000002506>.
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/fmmattioni/metabolic
BugReports: https://github.com/fmmattioni/metabolic/issues
Imports: tibble, magrittr, usethis, dplyr (>= 1.0.0), ggplot2 (>= 3.2.1), ggfittext, cli (>= 2.0.1), forcats, ggimage, patchwork (>= 1.0.0), scales, stringr, tidyr (>= 1.0.2), purrr, meta (>= 4.11-0), glue, rmarkdown
Depends: R (>= 3.2)
Suggests: knitr, here, Rd2roxygen, kableExtra, fansi, downloadthis (>= 0.2.0), spelling
Language: en-US
NeedsCompilation: no
Packaged: 2020-09-23 21:07:25 UTC; fmattioni
Author: Felipe Mattioni Maturana [aut, cre, cph] (<https://orcid.org/0000-0002-4221-6104>)
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Repository: CRAN
Date/Publication: 2020-09-25 13:40:09 UTC

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Package influential updated to version 2.0.0 with previous version 1.1.2 dated 2020-06-26

Title: Identification and Classification of the Most Influential Nodes
Description: Contains functions for the classification and ranking of top candidate features, reconstruction of networks from adjacency matrices and data frames, analysis of the topology of the network and calculation of centrality measures, and identification of the most influential nodes. Also, a function is provided for running SIRIR model, which is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment of dependence and correlation of two network centrality measures as well as the conditional probability of deviation from their corresponding means in opposite direction. Fred Viole and David Nawrocki (2013, ISBN:1490523995). Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695. Adopted algorithms and sources are referenced in function document.
Author: Adrian (Abbas) Salavaty [aut, cre], Mirana Ramialison [ths], Peter D. Currie [ths]
Maintainer: Adrian Salavaty <abbas.salavaty@gmail.com>

Diff between influential versions 1.1.2 dated 2020-06-26 and 2.0.0 dated 2020-09-25

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Package ImpactEffectsize updated to version 0.6.1 with previous version 0.6.0 dated 2020-07-18

Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>

Diff between ImpactEffectsize versions 0.6.0 dated 2020-07-18 and 0.6.1 dated 2020-09-25

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Package ftsa updated to version 5.9 with previous version 5.8 dated 2020-06-15

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] (<https://orcid.org/0000-0002-2140-5352>), Han Lin Shang [aut, cre, cph] (<https://orcid.org/0000-0003-1769-6430>)
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>

Diff between ftsa versions 5.8 dated 2020-06-15 and 5.9 dated 2020-09-25

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New package befproj with initial version 0.1.1
Package: befproj
Type: Package
Title: Makes a Local Population Projection
Version: 0.1.1
Author: Peter Thuresson <jpeter.thuresson@gmail.com>
Maintainer: Peter Thuresson <jpeter.thuresson@gmail.com>
Description: This is a sub national population projection model for calculating population development. The model uses a cohort component method. Further reading: Stanley K. Smith: A Practitioner's Guide to State and Local Population Projections. 2013. <doi:10.1007/978-94-007-7551-0>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: dplyr (>= 0.8.5)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-09-23 15:34:40 UTC; prota
Repository: CRAN
Date/Publication: 2020-09-25 13:40:12 UTC

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New package albatross with initial version 0.1-1
Package: albatross
Type: Package
Title: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Version: 0.1-1
Date: 2020-09-16
Authors@R: c(person('Timur', 'Labutin', role = 'aut'), person('Ivan', 'Krylov', role = 'cre', email = 'ikrylov@laser.chem.msu.ru'))
Depends: R (>= 2.10)
Imports: multiway (>= 1.0-4), pracma, lattice
Description: Perform parallel factor analysis (PARAFAC: Harshman, 2005) <doi:10.1121/1.1977523>) on fluorescence excitation-emission matrices (FEEMs): handle scattering signal (Bahram, 2007) <doi:10.1002/cem.978> and inner filter effect (Kothawala, 2013) <doi:10.4319/lom.2013.11.616>, scale the dataset, fit the model; perform split-half validation (DeSarbo, 1984) <https://papers.ssrn.com/abstract=2783446> or jack-knifing (Riu, 2003) <doi:10.1016/S0169-7439(02)00090-4>. The package has a low dependency footprint (only two direct dependencies not in core or recommended; four total non-core/recommended dependencies) and has been tested on a wide range of R versions (including R as old as 3.3.3 from Debian Stretch).
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2020-09-23 14:22:54 UTC; nobody
Author: Timur Labutin [aut], Ivan Krylov [cre]
Maintainer: Ivan Krylov <ikrylov@laser.chem.msu.ru>
Repository: CRAN
Date/Publication: 2020-09-25 14:00:14 UTC

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New package miRecSurv with initial version 0.0.1
Package: miRecSurv
Type: Package
Title: Left-Censored Recurrent Events Survival Models
Version: 0.0.1
Authors@R: c(person(given = "David", family = "Moriña", role = c("aut", "cre"), email = "dmorina@ub.edu", comment = c(ORCID = "0000-0001-5949-7443")), person(given = "Gilma", family = "Hernández-Herrera", role = c("aut"), email = "gilmah@yahoo.com"), person(given = "Albert", family = "Navarro", role = c("aut"), email = "albert.navarro@uab.cat"))
Maintainer: David Moriña <dmorina@ub.edu>
Description: Fitting recurrent events survival models for left-censored data with multiple imputation of the number of previous episodes. See Hernández-Herrera G, Moriña D, Navarro A. (2020) <arXiv:2007.15031>.
Depends: R (>= 3.5.0), COMPoissonReg, matrixStats, survival, stringi
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-09-23 09:01:13 UTC; dmorina
Author: David Moriña [aut, cre] (<https://orcid.org/0000-0001-5949-7443>), Gilma Hernández-Herrera [aut], Albert Navarro [aut]
Repository: CRAN
Date/Publication: 2020-09-25 12:50:02 UTC

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New package r2mlm with initial version 0.1.0
Package: r2mlm
Type: Package
Title: R-Squared Measures for Multilevel Models
Version: 0.1.0
Authors@R: c( person("Mairead", "Shaw", email = "mairead.shaw@mail.mcgill.ca", role = c("aut", "cre")), person("Jason", "Rights", email = "jrights@psych.ubc.ca", role = "aut"), person("Sonya", "Sterba", email = "sonya.sterba@vanderbilt.edu", role = "aut"), person("Jessica", "Flake", email = "jessica.flake@mcgill.ca", role = "aut"))
Maintainer: Mairead Shaw <mairead.shaw@mail.mcgill.ca>
Description: Generates both total- and level-specific R-squared measures from Rights and Sterba’s (2019) <doi:10.1037/met0000184> framework of R-squared measures for multilevel models with random intercepts and/or slopes, which is based on a completely full decomposition of variance. Additionally generates graphical representations of these R-squared measures to allow visualizing and interpreting all measures in the framework together as an integrated set. This framework subsumes 10 previously-developed R-squared measures for multilevel models as special cases of 5 measures from the framework, and it also includes several newly-developed measures. Measures in the framework can be used to compute R-squared differences when comparing multilevel models (following procedures in Rights & Sterba (2020) <doi:10.1080/00273171.2019.1660605>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr (>= 0.8.5), magrittr (>= 1.5), rlang (>= 0.4.6), stringr (>= 1.4.0), tidyselect (>= 1.0.0)
Depends: lme4 (>= 1.1.23), nlme (>= 3.1.14), R (>= 3.2.0)
RoxygenNote: 7.1.0
Suggests: testthat, Matrix
URL: https://github.com/mkshaw/r2mlm
BugReports: https://github.com/mkshaw/r2mlm/issues
NeedsCompilation: no
Packaged: 2020-09-23 05:22:34 UTC; maireadshaw
Author: Mairead Shaw [aut, cre], Jason Rights [aut], Sonya Sterba [aut], Jessica Flake [aut]
Repository: CRAN
Date/Publication: 2020-09-25 12:00:03 UTC

More information about r2mlm at CRAN
Permanent link

Package httk updated to version 2.0.3 with previous version 2.0.2 dated 2020-07-19

Title: High-Throughput Toxicokinetics
Description: Generic models and chemical-specific data for simulation and statistical analysis of chemical toxicokinetics ("TK") as described by Pearce et al. (2017) <doi:10.18637/jss.v079.i04>. Chemical-specific in vitro data have been obtained from relatively high throughput experiments. Both physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models can be parameterized with the data provided for thousands of chemicals, multiple exposure routes, and various species. The models consist of systems of ordinary differential equations which are solved using compiled (C-based) code for speed. A Monte Carlo sampler is included, which allows for simulating human biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and propagating parameter uncertainty. Calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre] (<https://orcid.org/0000-0002-4024-534X>), Robert Pearce [aut] (<https://orcid.org/0000-0003-3168-4049>), Caroline Ring [aut] (<https://orcid.org/0000-0002-0463-1251>), Greg Honda [aut] (<https://orcid.org/0000-0001-7713-9850>), Mark Sfeir [aut], Matt Linakis [aut] (<https://orcid.org/0000-0003-0526-2395>), Jimena Davis [ctb], James Sluka [ctb] (<https://orcid.org/0000-0002-5901-1404>), Nisha Sipes [ctb] (<https://orcid.org/0000-0003-4203-6426>), Barbara Wetmore [ctb] (<https://orcid.org/0000-0002-6878-5348>), Woodrow Setzer [ctb] (<https://orcid.org/0000-0002-6709-9186>)
Maintainer: John Wambaugh <wambaugh.john@epa.gov>

Diff between httk versions 2.0.2 dated 2020-07-19 and 2.0.3 dated 2020-09-25

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More information about httk at CRAN
Permanent link

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

Title: The 'Monaco' Editor in 'Shiny'
Description: A 'Shiny' app including the 'Monaco' editor. The 'Monaco' editor is the code editor which powers 'VS Code'. It is particularly well developed for 'JavaScript'. In addition to the 'Monaco' editor features, the app provides prettifiers and minifiers for multiple languages, 'SCSS' and 'TypeScript' compilers, code checking for 'C' and 'C++' (requires 'cppcheck').
Author: Stéphane Laurent [aut, cre], Microsoft Corporation [ctb, cph] (Monaco Editor), Brijesh Brittu [ctb, cph] (monaco-ace-tokenizer), James Long and contributors [ctb, cph] (Prettier), Leandro Vital [ctb, cph] (Bootstrap Flash Alert), Daniel Eden [ctb, cph] (animate.css), Adam Schwartz [ctb, cph] (chrome-tabs), David DeSandro [ctb, cph] (Draggabilly), JakubPawlowicz.com [ctb, cph] (clean-css), Mihai Bazon [ctb, cph] (terser), Juriy "kangax" Zaytsev [ctb, cph] (HTMLMinifier), Rodney Rehm [ctb, cph] (Sass.js), Rich Harris [ctb, cph] (svg-parser), Lionel Tzatzkin [ctb, cph] (scale-that-svg), Andrei Kashcha [ctb, cph] (panzoom), Vitaly Puzrin [ctb, cph] (markdown-it), Alex Kocharin [ctb, cph] (markdown-it), John Schlinkert [ctb, cph] (word-wrap), Terence Eden [ctb, cph] (SuperTinyIcons), www.jeasyui.com [ctb, cph] (EasyUI)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between shinyMonacoEditor versions 0.1.0 dated 2020-09-09 and 1.0.0 dated 2020-09-25

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Permanent link

New package shattering with initial version 1.0
Package: shattering
Title: Estimate the Shattering Coefficient for a Particular Dataset
Version: 1.0
Authors@R: person(given = "Rodrigo", family = "F. de Mello", role = c("aut", "cre"), email = "mello@icmc.usp.br", comment = c(ORCID = "0000-0002-0435-3992"))
Description: The Statistical Learning Theory (SLT) provides the theoretical background to ensure that a supervised algorithm generalizes the mapping f:X -> Y given f is selected from its search space bias F. This formal result depends on the Shattering coefficient function N(F,2n) to upper bound the empirical risk minimization principle, from which one can estimate the necessary training sample size to ensure the probabilistic learning convergence and, most importantly, the characterization of the capacity of F, including its under and overfitting abilities while addressing specific target problems. In this context, we propose a new approach to estimate the maximal number of hyperplanes required to shatter a given sample, i.e., to separate every pair of points from one another, based on the recent contributions by Har-Peled and Jones in the dataset partitioning scenario, and use such foundation to analytically compute the Shattering coefficient function for both binary and multi-class problems. As main contributions, one can use our approach to study the complexity of the search space bias F, estimate training sample sizes, and parametrize the number of hyperplanes a learning algorithm needs to address some supervised task, what is specially appealing to deep neural networks. Reference: de Mello, R.F. (2019) "On the Shattering Coefficient of Supervised Learning Algorithms" <arXiv:1911.05461>; de Mello, R.F., Ponti, M.A. (2018, ISBN: 978-3319949888) "Machine Learning: A Practical Approach on the Statistical Learning Theory".
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
Imports: FNN, pdist, Matrix
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-09-21 13:46:39 UTC; mello
Author: Rodrigo F. de Mello [aut, cre] (<https://orcid.org/0000-0002-0435-3992>)
Maintainer: Rodrigo F. de Mello <mello@icmc.usp.br>
Repository: CRAN
Date/Publication: 2020-09-25 09:10:03 UTC

More information about shattering at CRAN
Permanent link

New package rjqpd with initial version 0.2.3
Package: rjqpd
Type: Package
Title: The Johnson Quantile-Parameterised Distribution
Version: 0.2.3
Authors@R: person("Bobby", "Ingram", email = "ingram.bob@gmail.com", role = c("aut", "cre"))
Maintainer: Bobby Ingram <ingram.bob@gmail.com>
Description: Implementation of the Johnson Quantile-Parameterised Distribution in R. The Johnson Quantile-Parameterised Distribution (J-QPD) is a flexible distribution system that is parameterised by a symmetric percentile triplet of quantile values (typically the 10th-50th-90th) along with known support bounds for the distribution. The J-QPD system was developed by Hadlock and Bickel (2017) <doi:10.1287/deca.2016.0343>. This package implements the density, quantile, CDF and random number generator functions.
Suggests: devtools, knitr, rmarkdown, testthat
URL: https://github.com/bobbyingram/rjqpd
BugReports: https://github.com/bobbyingram/rjqpd/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-21 19:22:20 UTC; BobbyIngram
Author: Bobby Ingram [aut, cre]
Repository: CRAN
Date/Publication: 2020-09-25 09:20:06 UTC

More information about rjqpd at CRAN
Permanent link

Package qtlcharts updated to version 0.12-10 with previous version 0.11-6 dated 2019-02-05

Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. Broman (2015) <doi:10.1534/genetics.114.172742>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib, https://d3js.org), jQuery Foundation [cph] (jQuery library in htmlwidgets/lib, https://jquery.com), jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see https://github.com/jquery/jquery/blob/master/AUTHORS.txt), jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see https://jqueryui.com/about/)
Maintainer: Karl W Broman <broman@wisc.edu>

Diff between qtlcharts versions 0.11-6 dated 2019-02-05 and 0.12-10 dated 2020-09-25

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 qtlcharts-0.12-10/qtlcharts/DESCRIPTION                                                                            |   38 -
 qtlcharts-0.12-10/qtlcharts/LICENSE                                                                                |   78 --
 qtlcharts-0.12-10/qtlcharts/MD5                                                                                    |  311 ++++------
 qtlcharts-0.12-10/qtlcharts/NEWS.md                                                                                |   50 +
 qtlcharts-0.12-10/qtlcharts/R/convert4crosstab.R                                                                   |   24 
 qtlcharts-0.12-10/qtlcharts/R/convert_pxg.R                                                                        |   20 
 qtlcharts-0.12-10/qtlcharts/R/estQTLeffects.R                                                                      |   32 -
 qtlcharts-0.12-10/qtlcharts/R/geneExpr-data.R                                                                      |    4 
 qtlcharts-0.12-10/qtlcharts/R/grav-data.R                                                                          |    6 
 qtlcharts-0.12-10/qtlcharts/R/iboxplot.R                                                                           |    6 
 qtlcharts-0.12-10/qtlcharts/R/idotplot.R                                                                           |    4 
 qtlcharts-0.12-10/qtlcharts/R/iheatmap.R                                                                           |   10 
 qtlcharts-0.12-10/qtlcharts/R/ipleiotropy.R                                                                        |   30 
 qtlcharts-0.12-10/qtlcharts/R/iplot.R                                                                              |    6 
 qtlcharts-0.12-10/qtlcharts/R/iplotCorr.R                                                                          |   26 
 qtlcharts-0.12-10/qtlcharts/R/iplotCurves.R                                                                        |    4 
 qtlcharts-0.12-10/qtlcharts/R/iplotMScanone.R                                                                      |   31 
 qtlcharts-0.12-10/qtlcharts/R/iplotMap.R                                                                           |   12 
 qtlcharts-0.12-10/qtlcharts/R/iplotPXG.R                                                                           |   22 
 qtlcharts-0.12-10/qtlcharts/R/iplotRF.R                                                                            |   24 
 qtlcharts-0.12-10/qtlcharts/R/iplotScanone.R                                                                       |   36 -
 qtlcharts-0.12-10/qtlcharts/R/iplotScantwo.R                                                                       |   46 -
 qtlcharts-0.12-10/qtlcharts/R/itriplot.R                                                                           |    8 
 qtlcharts-0.12-10/qtlcharts/R/qtlcharts.R                                                                          |   30 
 qtlcharts-0.12-10/qtlcharts/R/scat2scat.R                                                                          |   10 
 qtlcharts-0.12-10/qtlcharts/R/setScreenSize.R                                                                      |    4 
 qtlcharts-0.12-10/qtlcharts/R/util.R                                                                               |   20 
 qtlcharts-0.12-10/qtlcharts/README.md                                                                              |   26 
 qtlcharts-0.12-10/qtlcharts/data/geneExpr.rda                                                                      |binary
 qtlcharts-0.12-10/qtlcharts/data/grav.rda                                                                          |binary
 qtlcharts-0.12-10/qtlcharts/inst/CITATION                                                                          |    6 
 qtlcharts-0.12-10/qtlcharts/inst/LICENSE                                                                           |   78 --
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iboxplot.coffee                                                       |    2 
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 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iboxplot.yaml                                                         |   11 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/idotplot.coffee                                                       |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/idotplot.js                                                           |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/idotplot.yaml                                                         |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iheatmap.coffee                                                       |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iheatmap.js                                                           |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iheatmap.yaml                                                         |   11 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/ipleiotropy.coffee                                                    |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/ipleiotropy.js                                                        |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/ipleiotropy.yaml                                                      |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplot.coffee                                                          |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplot.js                                                              |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplot.yaml                                                            |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCorr.coffee                                                      |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCorr.js                                                          |   14 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCorr.yaml                                                        |   11 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCurves.coffee                                                    |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCurves.js                                                        |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotCurves.yaml                                                      |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMScanone.coffee                                                  |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMScanone.js                                                      |    9 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMScanone.yaml                                                    |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMap.coffee                                                       |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMap.js                                                           |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMap.yaml                                                         |   13 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.coffee                                                        |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.js                                                            |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.yaml                                                          |   11 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.coffee                                                   |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.js                                                       |    9 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.yaml                                                     |   11 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.coffee                                                   |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.js                                                       |   10 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.yaml                                                     |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.coffee                                                       |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.js                                                           |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.yaml                                                         |   17 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/d3/d3.min.js                                                      |    4 
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 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMap.js                                             |   99 +--
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotRF.coffee                                          |    3 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotRF.js                                              |  140 +++-
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 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/qtlcharts/itriplot.js                                             |   45 +
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/package.json                                                          |    6 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/scat2scat.coffee                                                      |    2 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/scat2scat.js                                                          |    8 
 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/scat2scat.yaml                                                        |   17 
 qtlcharts-0.12-10/qtlcharts/man/cbindQTLeffects.Rd                                                                 |    4 
 qtlcharts-0.12-10/qtlcharts/man/estQTLeffects.Rd                                                                   |   12 
 qtlcharts-0.12-10/qtlcharts/man/geneExpr.Rd                                                                        |    6 
 qtlcharts-0.12-10/qtlcharts/man/grav.Rd                                                                            |    8 
 qtlcharts-0.12-10/qtlcharts/man/iboxplot.Rd                                                                        |   16 
 qtlcharts-0.12-10/qtlcharts/man/idotplot.Rd                                                                        |    7 
 qtlcharts-0.12-10/qtlcharts/man/iheatmap.Rd                                                                        |   10 
 qtlcharts-0.12-10/qtlcharts/man/ipleiotropy.Rd                                                                     |   40 -
 qtlcharts-0.12-10/qtlcharts/man/iplot.Rd                                                                           |    9 
 qtlcharts-0.12-10/qtlcharts/man/iplotCorr.Rd                                                                       |   40 -
 qtlcharts-0.12-10/qtlcharts/man/iplotCurves.Rd                                                                     |   15 
 qtlcharts-0.12-10/qtlcharts/man/iplotMScanone.Rd                                                                   |   37 -
 qtlcharts-0.12-10/qtlcharts/man/iplotMap.Rd                                                                        |   13 
 qtlcharts-0.12-10/qtlcharts/man/iplotPXG.Rd                                                                        |   30 
 qtlcharts-0.12-10/qtlcharts/man/iplotRF.Rd                                                                         |   24 
 qtlcharts-0.12-10/qtlcharts/man/iplotScanone.Rd                                                                    |   46 -
 qtlcharts-0.12-10/qtlcharts/man/iplotScantwo.Rd                                                                    |   33 -
 qtlcharts-0.12-10/qtlcharts/man/itriplot.Rd                                                                        |    7 
 qtlcharts-0.12-10/qtlcharts/man/qtlcharts-package.Rd                                                               |   20 
 qtlcharts-0.12-10/qtlcharts/man/qtlcharts-shiny.Rd                                                                 |   10 
 qtlcharts-0.12-10/qtlcharts/man/scat2scat.Rd                                                                       |   13 
 qtlcharts-0.12-10/qtlcharts/man/setScreenSize.Rd                                                                   |    4 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/Rmdtest.Rmd                                                              |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iboxplot.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/idotplot.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iheatmap.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/ipleiotropy.Rmd                                                          |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplot.Rmd                                                                |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotCorr.Rmd                                                            |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotCurves.Rmd                                                          |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotCurves_justcurves.Rmd                                               |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotMScanone.Rmd                                                        |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotMap.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotPXG.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotRF.Rmd                                                              |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotScanone.Rmd                                                         |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/iplotScantwo.Rmd                                                         |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/itriplot.Rmd                                                             |    2 
 qtlcharts-0.12-10/qtlcharts/tests/Rmdtest/scat2scat.Rmd                                                            |    2 
 160 files changed, 2068 insertions(+), 1601 deletions(-)

More information about qtlcharts at CRAN
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Package mrbin updated to version 1.4.3 with previous version 1.4.2 dated 2020-06-01

Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science research. The package (<http://www.kleinomicslab.com/software>) converts 1D or 2D data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, are replaced by positive values. All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>

Diff between mrbin versions 1.4.2 dated 2020-06-01 and 1.4.3 dated 2020-09-25

 DESCRIPTION         |    6 +++---
 MD5                 |   12 ++++++------
 NEWS.md             |    5 +++++
 R/mrbin.R           |   26 ++++++++++++++------------
 inst/doc/mrbin.Rnw  |    2 +-
 inst/doc/mrbin.pdf  |binary
 vignettes/mrbin.Rnw |    2 +-
 7 files changed, 30 insertions(+), 23 deletions(-)

More information about mrbin at CRAN
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New package IntCal with initial version 0.1.3
Package: IntCal
Type: Package
Title: Radiocarbon Calibration Curves
Version: 0.1.3
Date: 2020-09-04
Authors@R: c( person("Maarten", "Blaauw", email = "maarten.blaauw@qub.ac.uk", role = c("aut", "cre")))
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves.
License: GPL (>= 2)
RoxygenNote: 7.1.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-09-21 18:35:52 UTC; maarten
Language: en-GB
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Repository: CRAN
Date/Publication: 2020-09-25 09:20:12 UTC

More information about IntCal at CRAN
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New package htmldf with initial version 0.1.0
Package: htmldf
Title: Simple Scraping and Tidy Webpage Summaries
Version: 0.1.0
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Description: Simple tools for scraping webpages, extracting common html tags and parsing contents to a tidy, tabular format. Tools help with extraction of page titles, links, images, rss feeds, social media handles and page metadata.
License: GPL-2
Imports: cld3, dplyr, httr, lubridate, magrittr, progress, R.utils, ranger, rvest, stringr, tibble, tidyr, tools, urltools, xml2
Depends: R (>= 3.5.0)
Encoding: UTF-8
Language: en_GB
LazyData: true
URL: https://github.com/alastairrushworth/htmldf/
BugReports: https://github.com/alastairrushworth/htmldf/issues
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-09-22 05:28:26 UTC; alastairrushworth
Repository: CRAN
Date/Publication: 2020-09-25 09:50:02 UTC

More information about htmldf at CRAN
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New package globalKinhom with initial version 0.1.1
Package: globalKinhom
Type: Package
Title: Inhomogeneous K- And Pair Correlation Functions Using Global Estimators
Version: 0.1.1
Date: 2020-09-11
Encoding: UTF-8
Authors@R: c(person("Thomas", "Shaw", role=c("aut", "cre"), email="shawtr@umich.edu"), person("Ege", "Rubak", role="ctb"), person("Adrian", "Baddeley", role="ctb"), person("Rolf", "Turner", role="ctb"))
Author: Thomas Shaw [aut, cre], Ege Rubak [ctb], Adrian Baddeley [ctb], Rolf Turner [ctb]
Maintainer: Thomas Shaw <shawtr@umich.edu>
Depends: R (>= 3.5.0), spatstat
Imports: stats, utils, grDevices
Description: Second-order summary statistics K- and pair-correlation functions describe interactions in point pattern data. This package provides computations to estimate those statistics on inhomogeneous point processes, using the methods of in T Shaw, J Møller, R Waagepetersen, 2020 <arXiv:2004.00527>.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2020-09-21 15:50:45 UTC; tshaw
Repository: CRAN
Date/Publication: 2020-09-25 09:10:05 UTC

More information about globalKinhom at CRAN
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Package ezcox updated to version 0.8.0 with previous version 0.7.0 dated 2020-07-01

Title: Easily Process a Batch of Cox Models
Description: A tool to operate a batch of univariate or multivariate Cox models and return tidy result.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>)
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between ezcox versions 0.7.0 dated 2020-07-01 and 0.8.0 dated 2020-09-25

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Package condvis2 updated to version 0.1.1 with previous version 0.1.0 dated 2019-06-28

Title: Interactive Conditional Visualization for Supervised and Unsupervised Models in Shiny
Description: Constructs a shiny app function with interactive displays for conditional visualization of models, data and density functions. An extended version of package 'condvis'. Mark O'Connell, Catherine B. Hurley, Katarina Domijan (2017) <doi:10.18637/jss.v081.i05>.
Author: Catherine Hurley [aut, cre], Mark OConnell [aut], Katarina Domijan [aut]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>

Diff between condvis2 versions 0.1.0 dated 2019-06-28 and 0.1.1 dated 2020-09-25

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Package CLA updated to version 0.96-1 with previous version 0.96-0 dated 2020-09-07

Title: Critical Line Algorithm in Pure R
Description: Implements 'Markowitz' Critical Line Algorithm ('CLA') for classical mean-variance portfolio optimization, see Markowitz (1952) <doi:10.2307/2975974>. Care has been taken for correctness in light of previous buggy implementations.
Author: Yanhao Shi <syhelena@163.com>, Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

Diff between CLA versions 0.96-0 dated 2020-09-07 and 0.96-1 dated 2020-09-25

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 build/partial.rdb |binary
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 4 files changed, 15 insertions(+), 13 deletions(-)

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Package anticlust updated to version 0.5.3 with previous version 0.5.0 dated 2020-06-29

Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) in such a way that the between-group similarity is maximized and -- at the same time -- the within-group heterogeneity is maximized. This reverses the logic of cluster analysis that strives for high within-group homogeneity and low similarity of the different groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The function anticlustering() implements exact and heuristic anticlustering algorithms as described in Papenberg and Klau (2020; <doi:10.1037/met0000301>). The exact approach requires that the GNU linear programming kit (<https://www.gnu.org/software/glpk/glpk.html>) is available and the R package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is installed. Some other functions are available to solve classical clustering problems. The function balanced_clustering() applies a cluster analysis under size constraints, i.e., creates equal-sized clusters. The function matching() can be used for (unrestricted, bipartite, or K-partite) matching. The function wce() can be used optimally solve the (weighted) cluster editing problem, also known as correlation clustering, clique partitioning problem or transitivity clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>), Meik Michalke [ctb] (centroid based clustering algorithm), Gunnar W. Klau [ths], Juliane V. Tkotz [ctb] (package logo)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>

Diff between anticlust versions 0.5.0 dated 2020-06-29 and 0.5.3 dated 2020-09-25

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New package shiny.pwa with initial version 0.2.0
Package: shiny.pwa
Type: Package
Title: Progressive Web App Support for Shiny
Version: 0.2.0
Authors@R: person("Pedro", "Silva", email = "pedrocoutinhosilva@gmail.com", role = c("aut", "cre"))
Description: Adds Progressive Web App support for Shiny apps, including desktop and mobile installations.
License: MIT + file LICENSE
URL: https://github.com/pedrocoutinhosilva/shiny.pwa
Encoding: UTF-8
LazyData: true
Imports: shiny, htmltools, readr, utils, urltools
Suggests: testthat
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-20 14:53:46 UTC; pedro
Author: Pedro Silva [aut, cre]
Maintainer: Pedro Silva <pedrocoutinhosilva@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-25 08:20:02 UTC

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New package RVIpkg with initial version 0.1.1
Package: RVIpkg
Title: Regional Vulnerability Index
Version: 0.1.1
Authors@R: c( person(given = "Peter", family = "Kochunov", role = c("aut"), email = "pkochunov@gmail.com"), person(given = "Si", family = "Gao", role = c("aut", "cre"), email = "sgao@som.umaryland.edu"), person(given = "Fatima", family = "Talib", role = c("aut"), email = "fatal1@umbc.edu") )
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual’s similarity to the expected pattern of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
Imports: stats
NeedsCompilation: no
Packaged: 2020-09-20 18:38:48 UTC; AbestSG
Author: Peter Kochunov [aut], Si Gao [aut, cre], Fatima Talib [aut]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Repository: CRAN
Date/Publication: 2020-09-25 08:30:02 UTC

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New package rle with initial version 0.9.2
Package: rle
Version: 0.9.2
Date: 2020-09-21
Title: Common Functions for Run-Length Encoded Vectors
Authors@R: person("Pavel N.", "Krivitsky", role=c("aut","cre"), email="pavel@statnet.org", comment=c(ORCID="0000-0002-9101-3362"))
Description: Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors.
Depends: R (>= 3.5)
Imports: methods
Copyright: file inst/COPYRIGHT
BugReports: https://github.com/statnet/rle/issues
License: GPL-3
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests: covr
NeedsCompilation: yes
Packaged: 2020-09-21 03:24:29 UTC; pavel
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>)
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Repository: CRAN
Date/Publication: 2020-09-25 08:40:02 UTC

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New package ggip with initial version 0.1.0
Package: ggip
Title: Data Visualization for IP Addresses and Networks
Version: 0.1.0
Authors@R: person(given = "David", family = "Hall", role = c("aut", "cre"), email = "david.hall.physics@gmail.com", comment = c(ORCID = "0000-0002-2193-0480"))
Description: A 'ggplot2' extension that enables visualization of IP (Internet Protocol) addresses and networks. The address space is mapped onto the Cartesian coordinate system using a space-filling curve. Offers full support for both IPv4 and IPv6 (Internet Protocol versions 4 and 6) address spaces.
License: MIT + file LICENSE
URL: https://davidchall.github.io/ggip/, https://github.com/davidchall/ggip
BugReports: https://github.com/davidchall/ggip/issues
Depends: ggplot2 (>= 3.3.0), ipaddress (>= 0.5.1), R (>= 3.3.0)
Imports: glue, Rcpp, rlang (>= 0.4.2), tidyr, vctrs (>= 0.3.0)
Suggests: dplyr (>= 1.0.0), knitr, rmarkdown, testthat
LinkingTo: ipaddress, Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2020-09-20 18:03:14 UTC; david
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-25 08:20:05 UTC

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Package palm updated to version 1.1.4 with previous version 1.1.3 dated 2018-12-08

Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit the void processes proposed by Jones-Todd et al. (2019) <DOI:10.1002/sim.8046>. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process (Stevenson, Borchers, and Fewster, 2019 <DOI:10.1111/biom.12983>). As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Maintainer: Ben Stevenson <ben.stevenson@auckland.ac.nz>

Diff between palm versions 1.1.3 dated 2018-12-08 and 1.1.4 dated 2020-09-25

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New package dPCP with initial version 1.0.3
Package: dPCP
Title: Automated Analysis of Multiplex Digital PCR Data
Version: 1.0.3
Authors@R: c(person(given = "Alfonso", family = "De Falco", role = c("aut", "cre"), email = "alfonso.defalco@lns.etat.lu", comment = c(ORCID = "0000-0001-9985-9920")), person(given = "Michel", family = "Mittelbronn", role = c("ctb")), person(given = "Christophe", family = "Olinger", role = c("ctb")), person(given = "Daniel", family = "Stieber", role = c("ctb")), person(given = "Laboratoire national de santé", role = c("cph")))
Description: The automated clustering and quantification of the digital PCR data is based on the combination of 'DBSCAN' (Hahsler et al. (2019) <doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et l. (1981) <doi:10.1007/978-1-4757-0450-1>) algorithms. The analysis is independent of multiplexing geometry, dPCR system, and input amount. The details about input data and parameters are available in the vignette.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
Imports: dbscan, e1071, exactci, ggplot2, ggpubr, graphics, raster, rlist, scales, shiny, shinyjs, stats, stringr, utils
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-19 13:59:13 UTC; gen_adef
Author: Alfonso De Falco [aut, cre] (<https://orcid.org/0000-0001-9985-9920>), Michel Mittelbronn [ctb], Christophe Olinger [ctb], Daniel Stieber [ctb], Laboratoire national de santé [cph]
Maintainer: Alfonso De Falco <alfonso.defalco@lns.etat.lu>
Repository: CRAN
Date/Publication: 2020-09-25 07:50:02 UTC

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Package RiemBaseExt (with last version 0.1.2) was removed from CRAN

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

2020-03-21 0.1.2
2019-12-02 0.1.1
2019-11-25 0.1.0

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Package RiemGrassmann (with last version 0.1.0) was removed from CRAN

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

2020-03-25 0.1.0

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Package RiemStiefel (with last version 0.1.1) was removed from CRAN

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

2020-03-25 0.1.1
2020-03-15 0.1.0

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Package dynOmics (with last version 1.2) was removed from CRAN

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

2018-06-28 1.2

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Package MixSIAR (with last version 3.1.11) was removed from CRAN

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

2020-05-13 3.1.11
2018-04-12 3.1.10
2018-03-30 3.1.9
2016-08-23 3.1.7
2016-06-25 3.1.6

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Package NAPPA (with last version 2.0.1) was removed from CRAN

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

2015-03-03 2.0.1
2014-07-16 2.0
2013-10-29 1.0

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Package tidyseurat (with last version 0.1.8) was removed from CRAN

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

2020-09-15 0.1.8
2020-09-11 0.1.6

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Package miic (with last version 1.5.2) was removed from CRAN

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

2020-09-23 1.5.2
2020-09-18 1.5.1
2020-09-11 1.5.0

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Package testit updated to version 0.12 with previous version 0.11 dated 2019-11-12

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

Diff between testit versions 0.11 dated 2019-11-12 and 0.12 dated 2020-09-25

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Package strex updated to version 1.3.0 with previous version 1.2.0 dated 2019-09-13

Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged: it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between strex versions 1.2.0 dated 2019-09-13 and 1.3.0 dated 2020-09-25

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Package neonUtilities updated to version 1.3.7 with previous version 1.3.6 dated 2020-07-26

Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://data.neonscience.org/home> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb], Christine Laney [aut, ctb], Nathan Mietkiewicz [aut, ctb], Eric Sokol [aut, ctb], Kaelin Cawley [aut, ctb], NEON (National Ecological Observatory Network) [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>

Diff between neonUtilities versions 1.3.6 dated 2020-07-26 and 1.3.7 dated 2020-09-25

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Package downlit updated to version 0.2.0 with previous version 0.1.0 dated 2020-09-01

Title: Syntax Highlighting and Automatic Linking
Description: Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between downlit versions 0.1.0 dated 2020-09-01 and 0.2.0 dated 2020-09-25

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Package contentid updated to version 0.0.8 with previous version 0.0.7 dated 2020-09-08

Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based identifiers for data management. Content-based identifiers rely on the 'cryptographic' hashes to refer to the files they identify, thus, anyone possessing the file can compute the identifier using a well-known standard algorithm, such as 'SHA256'. By registering a URL at which the content is accessible to a public archive, such as <https://hash-archive.org>, the content identifier can serve many functions typically associated with A Digital Object Identifier ('DOI'). Unlike location-based identifiers like 'DOIs', content-based identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>), Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>), NSF OAC 1839201 [fnd] (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1839201)
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between contentid versions 0.0.7 dated 2020-09-08 and 0.0.8 dated 2020-09-25

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Thu, 24 Sep 2020

Package opencv updated to version 0.2.0 with previous version 0.1 dated 2019-04-01

Title: Bindings to 'OpenCV' Computer Vision Library
Description: Experimenting with computer vision and machine learning in R. This package exposes some of the available 'OpenCV' <https://opencv.org/> algorithms, such as edge, body or face detection. These can either be applied to analyze static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package sjlabelled updated to version 1.1.7 with previous version 1.1.6 dated 2020-06-25

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), David Ranzolin [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package PRIMME updated to version 3.1-2 with previous version 3.1-1 dated 2020-05-26

Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software/>, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute singular values and vectors of a square or rectangular matrix. 'PRIMME' finds largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence. General description of the methods are provided in the papers Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>). See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], Lingfei Wu [aut], College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>

Diff between PRIMME versions 3.1-1 dated 2020-05-26 and 3.1-2 dated 2020-09-24

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Package nflfastR updated to version 3.0.0 with previous version 2.2.1 dated 2020-09-01

Title: Functions to Efficiently Access NFL Play by Play Data
Description: A set of functions to access National Football League play-by-play data from <https://www.nfl.com/>.
Author: Sebastian Carl [aut], Ben Baldwin [cre, aut], Lee Sharpe [ctb], Maksim Horowitz [ctb], Ron Yurko [ctb], Samuel Ventura [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>

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Package MAINT.Data updated to version 2.5.0 with previous version 2.4.0 dated 2020-06-25

Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal and Skew-Normal distributions, considering appropriate parameterizations of the variance-covariance matrix that takes into account the intrinsic nature of interval data, and lead to four different possible configuration structures. The Skew-Normal parameters can be estimated by maximum likelihood, while Normal parameters may be estimated by maximum likelihood or robust trimmed maximum likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>

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Package APfun updated to version 0.1.6 with previous version 0.1.4 dated 2019-08-19

Title: Geo-Processing Helper Functions
Description: Helper tools for facilitating basic geo-processing tasks, such as reading/writing Shapefiles, merging polygons or generating terrain contours.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

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Package scam updated to version 1.2-7 with previous version 1.2-6 dated 2020-06-10

Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape constraints on the component functions of the linear predictor (Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>. Models can contain multiple shape constrained (univariate and/or bivariate) and unconstrained terms. The routines of gam() in package 'mgcv' are used for setting up the model matrix, printing and plotting the results. Penalized likelihood maximization based on Newton-Raphson method is used to fit a model with multiple smoothing parameter selection by GCV or UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>

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Package SemNetCleaner updated to version 1.3.0 with previous version 1.2.0 dated 2020-06-09

Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Description: Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.
Author: Alexander P. Christensen [aut, cre] (<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>

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Package ChemometricsWithR (with last version 0.1.13) was removed from CRAN

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

2019-01-07 0.1.13
2017-09-01 0.1.11
2017-08-21 0.1.10
2015-09-04 0.1.9
2014-08-04 0.1.8
2012-10-12 0.1.7
2012-01-04 0.1.5
2011-02-17 0.1.3

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Package semantic.dashboard (with last version 0.1.5) was removed from CRAN

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

2020-04-07 0.1.5
2018-04-23 0.1.1

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Package elaborator (with last version 1.0) was removed from CRAN

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

2020-03-16 1.0

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Package sjPlot updated to version 2.8.5 with previous version 2.8.4 dated 2020-05-24

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>), Carsten Schwemmer [ctb], Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>), Amir Djalovski [ctb], Johannes Titz [ctb] (<https://orcid.org/0000-0002-1102-5719>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package psfmi updated to version 0.5.0 with previous version 0.2.0 dated 2020-02-03

Title: Prediction Model Selection and Performance Evaluation in Multiple Imputed Datasets
Description: Pooling, backward and forward selection of logistic and Cox regression models in multiply imputed datasets. Backward and forward selection can be done from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and the median p-values method. This is also possible for Mixed models. The models can contain continuous, dichotomous, categorical and restricted cubic spline predictors and interaction terms between all these type of predictors. The stability of the models can be evaluated using bootstrapping and cluster bootstrapping. The package further contains functions to pool the model performance as ROC/AUC, R-squares, scaled Brier score and calibration plots for logistic regression models. Internal validation can be done with cross-validation or bootstrapping. The adjusted intercept after shrinkage of pooled regression coefficients can be obtained. Backward and forward selection as part of internal validation is possible. Also a function to externally validate logistic prediction models in multiple imputed datasets is available. Eekhout (2017) <doi:10.1186/s12874-017-0404-7>. Wiel (2009) <doi:10.1093/biostatistics/kxp011>. Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut] (<https://orcid.org/0000-0002-3889-0921>), Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>

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Package import updated to version 1.2.0 with previous version 1.1.0 dated 2015-06-21

Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages and R modules. The syntax allows for importing multiple objects with a single command in an expressive way. The import package bridges some of the gap between using library (or require) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut], Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>

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Package iml updated to version 0.10.1 with previous version 0.10.0 dated 2020-03-26

Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and predictions of any machine learning model. Implemented methods are: Feature importance described by Fisher et al. (2018) <arXiv:1801.01489>, accumulated local effects plots described by Apley (2018) <arXiv:1612.08468>, partial dependence plots described by Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional expectation ('ice') plots described by Goldstein et al. (2013) <doi:10.1080/10618600.2014.907095>, local models (variant of 'lime') described by Ribeiro et. al (2016) <arXiv:1602.04938>, the Shapley Value described by Strumbelj et. al (2014) <doi:10.1007/s10115-013-0679-x>, feature interactions described by Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Christoph Molnar [aut, cre], Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>

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Package gaston updated to version 1.5.7 with previous version 1.5.6 dated 2020-02-26

Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Author: Hervé Perdry [cre, aut, cph], Claire Dandine-Roulland [aut, cph], Deepak Bandyopadhyay [cph] (C++ gzstream class), Lutz Kettner [cph] (C++ gzstream class)
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>

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Package norris (with last version 0.1.1) was removed from CRAN

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

2019-01-18 0.1.1
2018-06-12 0.1.0

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Package prioritylasso (with last version 0.2.4) was removed from CRAN

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

2020-09-07 0.2.4
2019-12-17 0.2.3
2019-06-05 0.2.2
2017-09-25 0.2.1
2017-07-17 0.2.0
2017-03-16 0.1.0

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Package st updated to version 1.2.6 with previous version 1.2.5 dated 2015-07-08

Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Description: Implements the "shrinkage t" statistic introduced in Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-6115.1252> and a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described in Zuber and Strimmer (2009) <DOI:10.1093/bioinformatics/btp460>. It also offers a convenient interface to a number of other regularized t-statistics commonly employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>

Diff between st versions 1.2.5 dated 2015-07-08 and 1.2.6 dated 2020-09-24

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Package rprime updated to version 0.1.2 with previous version 0.1.0 dated 2015-05-29

Title: Functions for Working with 'Eprime' Text Files
Description: 'Eprime' is a set of programs for administering psychological experiments by computer. This package provides functions for loading, parsing, filtering and exporting data in the text files produced by 'Eprime' experiments.
Author: Tristan Mahr [aut, cre] (<https://orcid.org/0000-0002-8890-5116>)
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>

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Package orders updated to version 0.1.4 with previous version 0.1.3 dated 2019-05-16

Title: Sampling from Order Statistics of New Families of Distributions
Description: Set of tools to generate samples of order statistics and others quantities of interest from new families of distributions. The main references for this package are: Gentle, J. (2009), Computational Statistics, Springer-Verlag; Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>. The families of distributions are: Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, and exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distribution, Skew normal type 1 distributions, Skew student t distribution, Sinh-Arcsinh distribution, Sichel distribution and Zero inflated Poisson.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>

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Package SubtypeDrug updated to version 0.1.2 with previous version 0.1.1 dated 2020-06-26

Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <DOI:10.1126/science.1132939>).
Author: Xudong Han, Junwei Han, Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>

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New package uwo4419 with initial version 0.3.0
Package: uwo4419
Type: Package
Title: UWO POLSCI 4419/9715
Version: 0.3.0
Authors@R: c(person("Dave", "Armstrong", role=c("aut", "cre"), email="dave@quantoid.net"))
Description: Supports the course Introduction to Methodology (POLSCI 4419/9715) at the University of Western Ontario.
Depends: R (>= 3.5.0)
Imports: DescTools, RColorBrewer, gmodels, haven, psych, stats, ggplot2, tibble, tidyr, dplyr, magrittr, rio
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-09-18 17:33:49 UTC; parallels
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <dave@quantoid.net>
Repository: CRAN
Date/Publication: 2020-09-24 09:10:02 UTC

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Package ScriptMapR updated to version 0.0.3 with previous version 0.0.2 dated 2020-09-21

Title: R Script Visualization in Cytoscape
Description: Displays the content of a R script into the 'Cytoscape' network-visualization app <https://cytoscape.org/>.
Author: Raphael Bonnet [aut, cre], Marion Guernoté [ctb], Terry Gouin [ctb], Maxime Laurens [ctb], Thibault Meekel [ctb], Jean-François Peyron[aut,ths]
Maintainer: Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>

Diff between ScriptMapR versions 0.0.2 dated 2020-09-21 and 0.0.3 dated 2020-09-24

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Package roundhouse updated to version 0.0.2 with previous version 0.0.1 dated 2018-09-16

Title: Random Chuck Norris Facts
Description: R functions for generating and/or displaying random Chuck Norris facts. Based on data from the 'Internet Chuck Norris database' ('ICNDb').
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>

Diff between roundhouse versions 0.0.1 dated 2018-09-16 and 0.0.2 dated 2020-09-24

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New package panelr with initial version 0.7.4
Package: panelr
Title: Regression Models and Utilities for Repeated Measures and Panel Data
Version: 0.7.4
Authors@R: person("Jacob A.", "Long", email = "jacob.long@sc.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1582-6214"))
Description: Provides an object type and associated tools for storing and wrangling panel data. Implements several methods for creating regression models that take advantage of the unique aspects of panel data. Among other capabilities, automates the "within-between" (also known as "between-within" and "hybrid") panel regression specification that combines the desirable aspects of both fixed effects and random effects econometric models and fits them as multilevel models (Allison, 2009 <doi:10.4135/9781412993869.d33>; Bell & Jones, 2015 <doi:10.1017/psrm.2014.7>). These models can also be estimated via generalized estimating equations (GEE; McNeish, 2019 <doi:10.1080/00273171.2019.1602504>) and Bayesian estimation is (optionally) supported via 'Stan'. Supports estimation of asymmetric effects models via first differences (Allison, 2019 <doi:10.1177/2378023119826441>) as well as a generalized linear model extension thereof using GEE.
URL: https://panelr.jacob-long.com
BugReports: https://github.com/jacob-long/panelr
Depends: R (>= 3.4.0), lme4
Imports: crayon, dplyr, Formula, ggplot2, jtools (>= 2.0.1), lmerTest, magrittr, methods, purrr, rlang (>= 0.3.0), stringr, tibble (>= 2.0.0)
Suggests: brms, broom.mixed, car, clubSandwich, geepack, generics, nlme, plm, sandwich, skimr, tidyr (>= 0.8.3), testthat, covr, knitr, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-24 00:19:39 UTC; jlong
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <jacob.long@sc.edu>
Repository: CRAN
Date/Publication: 2020-09-24 09:10:08 UTC

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New package metamisc with initial version 0.2.3
Package: metamisc
Type: Package
Title: Meta-Analysis of Diagnosis and Prognosis Research Studies
Version: 0.2.3
Date: 2020-09-23
Authors@R: c(person(given = "Thomas", family = "Debray", role = c("aut", "cre"), email = "thomas.debray@gmail.com", comment="https://orcid.org/0000-0002-1790-2719"), person(given = "Valentijn", family = "de Jong", role = "aut", email="Valentijn.M.T.de.Jong@gmail.com", comment="https://orcid.org/0000-0001-9921-3468"))
Description: Facilitate meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance, as described by Debray et al. (2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry, as described by Debray et al. (2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering.
Imports: metafor (>= 2.0.0), mvtnorm, lme4, plyr, methods, pROC, ggplot2
Depends: R (>= 3.5.0), stats, graphics
Suggests: runjags, rjags, logistf (>= 1.23), testthat (>= 1.0.2)
License: GPL-3
URL: https://r-forge.r-project.org/projects/metamisc/
RoxygenNote: 7.1.1
Author: Thomas Debray [aut, cre] (<https://orcid.org/0000-0002-1790-2719>), Valentijn de Jong [aut] (<https://orcid.org/0000-0001-9921-3468>)
Maintainer: Thomas Debray <thomas.debray@gmail.com>
Repository: CRAN
Repository/R-Forge/Project: metamisc
Repository/R-Forge/Revision: 567
Repository/R-Forge/DateTimeStamp: 2020-09-23 08:55:00
Date/Publication: 2020-09-24 09:20:02 UTC
NeedsCompilation: no
Packaged: 2020-09-23 09:08:09 UTC; rforge

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Package lorentz updated to version 1.0-5 with previous version 1.0-2 dated 2019-03-21

Title: The Lorentz Transform in Relativistic Physics
Description: The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Includes active and passive transforms and the ability to use units in which the speed of light is not one. For general relativity, see the 'schwarzschild' package.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between lorentz versions 1.0-2 dated 2019-03-21 and 1.0-5 dated 2020-09-24

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Package interval updated to version 1.1-0.7 with previous version 1.1-0.1 dated 2014-01-22

Title: Weighted Logrank Tests and NPMLE for Interval Censored Data
Description: Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>

Diff between interval versions 1.1-0.1 dated 2014-01-22 and 1.1-0.7 dated 2020-09-24

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Package gSeg updated to version 1.0 with previous version 0.7 dated 2020-04-12

Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen, Nancy R. Zhang, Lynna Chu, and Hoseung Song
Maintainer: Hao Chen <hxchen@ucdavis.edu>

Diff between gSeg versions 0.7 dated 2020-04-12 and 1.0 dated 2020-09-24

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New package akmbiclust with initial version 0.1.0
Package: akmbiclust
Title: Alternating K-Means Biclustering
Version: 0.1.0
Authors@R: c( person("Zichao", "Li", role = c("aut", "cre"), email = "lizichao@live.unc.edu"), person("Nicolas", "Fraiman", role = "aut", email = "fraiman@email.unc.edu"))
Description: Implements the alternating k-means biclustering algorithm in Fraiman and Li (2020) <arXiv:2009.04550>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-09-18 17:38:42 UTC; lizichao
Author: Zichao Li [aut, cre], Nicolas Fraiman [aut]
Maintainer: Zichao Li <lizichao@live.unc.edu>
Repository: CRAN
Date/Publication: 2020-09-24 09:10:15 UTC

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Package universals updated to version 0.0.4 with previous version 0.0.3 dated 2020-07-08

Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples. The purpose of 'universals' is to reduce package dependencies and conflicts. The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between universals versions 0.0.3 dated 2020-07-08 and 0.0.4 dated 2020-09-24

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Package tsapp updated to version 1.0.2 with previous version 1.0.1 dated 2020-09-21

Title: Time Series, Analysis and Application
Description: Accompanies the book Rainer Schlittgen and Cristina Sattarhoff (2020) <https://www.degruyter.com/view/title/575978> "Angewandte Zeitreihenanalyse mit R, 4. Auflage" . The package contains the time series and functions used therein. It was developed over many years teaching courses about time series analysis.
Author: Rainer Schlittgen
Maintainer: Rainer Schlittgen <R.Schlittgen@t-online.de>

Diff between tsapp versions 1.0.1 dated 2020-09-21 and 1.0.2 dated 2020-09-24

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New package topsa with initial version 0.1.0
Package: topsa
Type: Package
Title: Topological Sensitivity Analysis
Version: 0.1.0
Authors@R: c( person(given = "Maikol", family = "Solís", email = "maikol.solis@ucr.ac.cr", role = c("aut", "cre")), person(given = "Alberto", family = "Hernández", email = "albertojose.hernandez@ucr.ac.cr", role = c("ctb")), person(given = "Ronald A.", family = "Zuñiga-Rojas", email = "ronald.zunigarojas@ucr.ac.cr", role = c("ctb")), person(given = "Carlos", family = "Pasquier", email = "carlos.pasquier@ucr.ac.cr", role = c("ctb")) )
Maintainer: Maikol Solís <maikol.solis@ucr.ac.cr>
Description: Estimate geometric sensitivity indices reconstructing the embedding manifold of the data. The reconstruction is done via a Vietoris Rips with a fixed radius. With the homology of order 2 we estimate symmetric reflections of the those manifold to determine a sensitivity index on of the input model. Detailed information of the methods can be found in <https://www.dropbox.com/s/0kcrjhhkl7899n1/article-symmetric-reflection.pdf> (WIP preprint).
License: MIT + file LICENSE
URL: https://github.com/maikol-solis/topsa
BugReports: https://github.com/maikol-solis/topsa/issues
Encoding: UTF-8
LazyData: true
Imports: ggplot2, scales, sf, TDA, parallel, methods
RoxygenNote: 7.1.0
Depends: R (>= 3.6.0)
Suggests: testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2020-09-18 12:45:23 UTC; maikol
Author: Maikol Solís [aut, cre], Alberto Hernández [ctb], Ronald A. Zuñiga-Rojas [ctb], Carlos Pasquier [ctb]
Repository: CRAN
Date/Publication: 2020-09-24 09:00:02 UTC

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New package simcross with initial version 0.3-6
Package: simcross
Version: 0.3-6
Date: 2020-09-17
Title: Simulate Experimental Crosses
Description: Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl W Broman <broman@wisc.edu>
Authors@R: c(person("Karl W", "Broman", role=c("aut", "cre"), email="broman@wisc.edu", comment=c(ORCID = "0000-0002-4914-6671")))
Depends: R (>= 3.1.0)
Imports: graphics, stats, Rcpp (>= 0.12.17)
Suggests: qtl, knitr, rmarkdown, testthat, devtools, roxygen2
License: GPL-3
URL: https://kbroman.org/simcross/, https://github.com/kbroman/simcross
BugReports: https://github.com/kbroman/simcross/issues
VignetteBuilder: knitr
LinkingTo: Rcpp
LazyData: true
Encoding: UTF-8
ByteCompile: true
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-09-17 15:28:19 UTC; kbroman
Repository: CRAN
Date/Publication: 2020-09-24 08:50:02 UTC

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Package ProbReco updated to version 0.1.0.1 with previous version 0.1.0 dated 2020-08-18

Title: Score Optimal Probabilistic Forecast Reconciliation
Description: Training of reconciliation weights for probabilistic forecasts to optimise total energy (or variogram) score using Stochastic Gradient Descent with automatically differentiated gradients. See Panagiotelis, Gamakumara, Athanasopoulos and Hyndman, (2020) <https://www.monash.edu/business/ebs/research/publications/ebs/wp26-2020.pdf> for a description of the methods.
Author: Anastasios Panagiotelis [aut, cre] (<https://orcid.org/0000-0001-8678-7294>)
Maintainer: Anastasios Panagiotelis <anastasios.panagiotelis@sydney.edu.au>

Diff between ProbReco versions 0.1.0 dated 2020-08-18 and 0.1.0.1 dated 2020-09-24

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Package PHInfiniteEstimates updated to version 1.5 with previous version 1.3 dated 2020-03-29

Title: Tools for Inference in the Presence of a Monotone Likelihood
Description: Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist. These difficulties are related to those arising from logistic and multinomial regression. References for methods are given in the separate function documents.
Author: John E. Kolassa and Juan Zhang
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>

Diff between PHInfiniteEstimates versions 1.3 dated 2020-03-29 and 1.5 dated 2020-09-24

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New package KneeArrower with initial version 1.0.0
Package: KneeArrower
Type: Package
Title: Finds Cutoff Points on Knee Curves
Version: 1.0.0
Author: Alan Tseng
Maintainer: Alan Tseng <alan.tseng@alum.utoronto.ca>
Description: Given a set of points around a knee curve, analyzes first and second derivatives to find knee points.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: signal
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-18 01:07:10 UTC; aklt
Repository: CRAN
Date/Publication: 2020-09-24 08:30:02 UTC

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Package fakemake updated to version 1.7.2 with previous version 1.7.1 dated 2020-04-12

Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between fakemake versions 1.7.1 dated 2020-04-12 and 1.7.2 dated 2020-09-24

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Package AnnotationBustR updated to version 1.3.0 with previous version 1.2 dated 2018-04-09

Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Author: Samuel R. Borstein <sam@borstein.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Samuel R. Borstein <sam@borstein.com>

Diff between AnnotationBustR versions 1.2 dated 2018-04-09 and 1.3.0 dated 2020-09-24

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Package xaringan updated to version 0.17 with previous version 0.16 dated 2020-03-31

Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>), Benjie Gillam [ctb], Claus Thorn Ekstrøm [ctb], Daniel Anderson [ctb], Dawei Lang [ctb], Emi Tanaka [ctb], Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>), Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>), John Little [ctb], Joselyn Chávez [ctb] (<https://orcid.org/0000-0002-4974-4591>), Joseph Casillas [ctb], Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>), Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>), Matthew Mark Strasiotto [ctb] (mstr3336), Michael Wayne Kearney [ctb], Nan-Hung Hsieh [ctb], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/default.css), Patrick Schratz [ctb], Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>), Paul Lemmens [ctb], Sean Lopp [ctb], Yongfu Liao [ctb], Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between xaringan versions 0.16 dated 2020-03-31 and 0.17 dated 2020-09-24

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Package koRpus updated to version 0.13-2 with previous version 0.13-1 dated 2020-09-21

Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable frequency analyses (supports Celex and Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For full functionality a local installation of TreeTagger is recommended. It is also recommended to not load this package directly, but by loading one of the available language support packages from the 'l10n' repository <https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for its basic features. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard. To make full use of this feature, please install RKWard from <https://rkward.kde.org> (plugins are detected automatically). Due to some restrictions on CRAN, the full package sources are only available from the project homepage. To ask for help, report bugs, request features, or discuss the development of the package, please subscribe to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre], Earl Brown [ctb], Alberto Mirisola [ctb], Alexandre Brulet [ctb], Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>

Diff between koRpus versions 0.13-1 dated 2020-09-21 and 0.13-2 dated 2020-09-24

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Package doFuture updated to version 0.10.0 with previous version 0.9.0 dated 2020-01-11

Title: A Universal Foreach Parallel Adapter using the Future API of the 'future' Package
Description: Provides a '%dopar%' adapter such that any type of futures can be used as backends for the 'foreach' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between doFuture versions 0.9.0 dated 2020-01-11 and 0.10.0 dated 2020-09-24

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Package crossmap updated to version 0.2.0 with previous version 0.1.0 dated 2020-09-10

Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping functions to apply a function to each combination of elements in a list of inputs. Also includes functions for automatically detecting output type in mapping functions, finding every combination of elements of lists or rows of data frames, and applying multiple models to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph] (<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>

Diff between crossmap versions 0.1.0 dated 2020-09-10 and 0.2.0 dated 2020-09-24

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New package irt with initial version 0.1.1
Package: irt
Type: Package
Title: Item Response Theory and Computerized Adaptive Testing Functions
Version: 0.1.1
Authors@R: c(person("Emre", "Gonulates", email = "egonulates@gmail.com", role = c("aut", "cre"), comment = c(ORCID="0000-0002-3834-3266")))
Maintainer: Emre Gonulates <egonulates@gmail.com>
Description: A collection of Item Response Theory (IRT) and Computerized Adaptive Testing (CAT) functions that are used in psychometrics.
License: GPL-3
Depends: methods
LinkingTo: Rcpp
Imports: Rcpp (>= 1.0.4), ggplot2, parallel
NeedsCompilation: yes
RoxygenNote: 7.1.1
Encoding: UTF-8
LazyData: true
Collate: 'Item-class.R' 'Item-class-methods.R' 'Itempool-class.R' 'Itempool-class-methods.R' 'RcppExports.R' 'Testlet-class-methods.R' 'ability_estimation.R' 'cat_sim.R' 'cat_sim_helper_functions.R' 'dif.R' 'info.R' 'ipd.R' 'irt.R' 'item_analysis.R' 'item_fit.R' 'misc.R' 'person_fit.R' 'plot_IRT.R' 'prob.R' 'resp_lik.R' 'resp_loglik.R' 'rsss.R' 'sim_resp.R'
Packaged: 2020-09-15 18:42:13 UTC; gonul
Author: Emre Gonulates [aut, cre] (<https://orcid.org/0000-0002-3834-3266>)
Repository: CRAN
Date/Publication: 2020-09-24 06:40:03 UTC

More information about irt at CRAN
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Package DICOMread updated to version 0.0.0.2 with previous version 0.0.0.1 dated 2020-09-01

Title: Reading and Saving DICOM Image Files
Description: This function provides an interface between 'Matlab' and 'R' in facilitating fast processing for reading and saving DICOM images.
Author: Shu Jiang [aut, cre] (<https://orcid.org/0000-0003-1464-4838>)
Maintainer: Shu Jiang <jiang.shu@wustl.edu>

Diff between DICOMread versions 0.0.0.1 dated 2020-09-01 and 0.0.0.2 dated 2020-09-24

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Wed, 23 Sep 2020

Package SailoR updated to version 1.2 with previous version 1.1.2 dated 2020-07-16

Title: An Extension of the Taylor Diagram to Two-Dimensional Vector Data
Description: A new diagram for the verification of vector variables (wind, current, etc) generated by multiple models against a set of observations is presented in this package. It has been designed as a generalization of the Taylor diagram to two dimensional quantities. It is based on the analysis of the two-dimensional structure of the mean squared error matrix between model and observations. The matrix is divided into the part corresponding to the relative rotation and the bias of the empirical orthogonal functions of the data. The full set of diagnostics produced by the analysis of the errors between model and observational vector datasets comprises the errors in the means, the analysis of the total variance of both datasets, the rotation matrix corresponding to the principal components in observation and model, the angle of rotation of model-derived empirical orthogonal functions respect to the ones from observations, the standard deviation of model and observations, the root mean squared error between both datasets and the squared two-dimensional correlation coefficient. See the output of function UVError() in this package.
Author: Jon Sáenz [aut, cph] (<https://orcid.org/0000-0002-5920-7570>), Sheila Carreno-Madinabeitia [aut, cph] (<https://orcid.org/0000-0003-4625-6178>), Santos J. González-Rojí [aut, cre, cph] (<https://orcid.org/0000-0003-4737-0984>), Ganix Esnaola [ctb, cph] (<https://orcid.org/0000-0001-9058-043X>), Gabriel Ibarra-Berastegi [ctb, cph] (<https://orcid.org/0000-0001-8681-3755>), Alain Ulazia [ctb, cph] (<https://orcid.org/0000-0002-4124-2853>)
Maintainer: Santos J. González-Rojí <santosjose.gonzalez@ehu.eus>

Diff between SailoR versions 1.1.2 dated 2020-07-16 and 1.2 dated 2020-09-23

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Package ojsr updated to version 0.1.2 with previous version 0.1.1 dated 2020-07-01

Title: Crawler and Data Scraper for Open Journal System ('OJS')
Description: Crawler for 'OJS' pages and scraper for meta-data from articles. You can crawl 'OJS' archives, issues, articles, galleys, and search results. You can scrape articles metadata from their head tag in html, or from Open Archives Initiative ('OAI') records. Most of these functions rely on 'OJS' routing conventions (<https://docs.pkp.sfu.ca/dev/documentation/en/architecture-routes>).
Author: Gaston Becerra [aut, cre] (<https://orcid.org/0000-0001-9432-8848>)
Maintainer: Gaston Becerra <gaston.becerra@gmail.com>

Diff between ojsr versions 0.1.1 dated 2020-07-01 and 0.1.2 dated 2020-09-23

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Package miic updated to version 1.5.2 with previous version 1.5.1 dated 2020-09-18

Title: Learning Causal or Non-Causal Graphical Models Using Information Theory
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>, Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre], Honghao Li [aut], Marcel Ribeiro Dantas [aut], Nadir Sella [aut], Louis Verny [aut], Severine Affeldt [aut], Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>

Diff between miic versions 1.5.1 dated 2020-09-18 and 1.5.2 dated 2020-09-23

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Package asnipe updated to version 1.1.13 with previous version 1.1.12 dated 2019-08-19

Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@ab.mpg.de>
Maintainer: Damien R. Farine <dfarine@ab.mpg.de>

Diff between asnipe versions 1.1.12 dated 2019-08-19 and 1.1.13 dated 2020-09-23

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Package lessR updated to version 3.9.7 with previous version 3.9.6 dated 2020-06-11

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

Diff between lessR versions 3.9.6 dated 2020-06-11 and 3.9.7 dated 2020-09-23

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Package gimme updated to version 0.7-3 with previous version 0.7-2 dated 2020-09-03

Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and individual-level relations in time series data from within a structural equation modeling framework.
Author: Stephanie Lane [aut, trl], Kathleen Gates [aut, cre], Zachary Fisher [aut], Cara Arizmendi [aut], Peter Molenaar [aut], Michael Hallquist [ctb], Hallie Pike [ctb], Teague Henry [ctb], Kelly Duffy [ctb], Lan Luo [ctb], Adriene Beltz [csp]
Maintainer: KM Gates <gateskm@email.unc.edu>

Diff between gimme versions 0.7-2 dated 2020-09-03 and 0.7-3 dated 2020-09-23

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Package FHtest updated to version 1.5 with previous version 1.4 dated 2017-11-08

Title: Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class
Description: Functions to compare two or more survival curves with: a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes. b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>

Diff between FHtest versions 1.4 dated 2017-11-08 and 1.5 dated 2020-09-23

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More information about FHtest at CRAN
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Package rsample updated to version 0.0.8 with previous version 0.0.7 dated 2020-06-04

Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre], Fanny Chow [aut], Hadley Wickham [aut], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between rsample versions 0.0.7 dated 2020-06-04 and 0.0.8 dated 2020-09-23

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Package aziztest updated to version 0.2.0 with previous version 0.1.0 dated 2020-04-01

Title: Novel Statistical Test for Aberration Enrichment
Description: Testing for heterogeneous effects in a case-control setting. The aim here to discover an association that is beyond a mean difference between all cases and all controls. Instead, the signal of interest here is present in only a proportion of the cases. This test should be more powerful than a t-test or Wilcoxon test in this heterogeneous setting. Please cite the corresponding paper: Mezlini et al. (2020) <doi:10.1101/2020.03.23.002972>.
Author: Aziz M. Mezlini [aut,cre,cph]
Maintainer: Aziz M. Mezlini <mmezlini@mgh.harvard.edu>

Diff between aziztest versions 0.1.0 dated 2020-04-01 and 0.2.0 dated 2020-09-23

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