Sun, 30 Mar 2025

Package crm12Comb updated to version 0.1.11 with previous version 0.1.10 dated 2025-03-18

Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut], Song Wu [aut], Jie Yang [aut]
Maintainer: Junying Wang <junying.wang@stonybrook.edu>

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Package quartabs updated to version 0.1.1 with previous version 0.1.0 dated 2025-03-14

Title: Dynamically Generate Tabset Panels in 'Quarto' HTML Documents
Description: Dynamically generate tabset panels <https://quarto.org/docs/output-formats/html-basics.html#tabsets> in 'Quarto' HTML documents using a data frame as input.
Author: Yusuke Sasaki [aut, cre]
Maintainer: Yusuke Sasaki <sayuks.dev@gmail.com>

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Package iForecast updated to version 1.1.1 with previous version 1.1.0 dated 2025-01-08

Title: Machine Learning Time Series Forecasting
Description: Compute onestep and multistep time series forecasts for machine learning models.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

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Package ncaavolleyballr updated to version 0.4.2 with previous version 0.4.1 dated 2025-01-23

Title: Extract Data from NCAA Women's and Men's Volleyball Website
Description: Extracts team records/schedules and player statistics for the 2020-2024 National Collegiate Athletic Association (NCAA) women's and men's divisions I, II, and III volleyball teams from <https://stats.ncaa.org>. Functions can aggregate statistics for teams, conferences, divisions, or custom groups of teams.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>

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Package DatastreamDSWS2R updated to version 1.9.12 with previous version 1.9.10 dated 2024-09-05

Title: Provides a Link Between the 'LSEG Datastream' System and R
Description: Provides a set of functions and a class to connect, extract and upload information from the 'LSEG Datastream' database. This package uses the 'DSWS' API and server used by the 'Datastream DFO addin'. Details of this API are available at <https://www.lseg.com/en/data-analytics>. Please report issues at <https://github.com/CharlesCara/DatastreamDSWS2R/issues>.
Author: Charles Cara [aut, cre]
Maintainer: Charles Cara <charles.cara@absolute-strategy.com>

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Package bayesboot updated to version 0.2.3 with previous version 0.2.2 dated 2018-06-29

Title: An Implementation of Rubin's (1981) Bayesian Bootstrap
Description: Functions for performing the Bayesian bootstrap as introduced by Rubin (1981) <doi:10.1214/aos/1176345338> and for summarizing the result. The implementation can handle both summary statistics that works on a weighted version of the data and summary statistics that works on a resampled data set.
Author: Rasmus Baath [aut, cre]
Maintainer: Rasmus Baath <rasmus.baath@gmail.com>

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Package ritalic updated to version 0.11.0 with previous version 0.10.1 dated 2025-01-07

Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>). ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys. More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>. The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] , Luana Francesconi [aut], Alice Musina [aut], Luca Di Nuzzo [aut], Gabriele Gheza [aut], Chiara Pistocchi [aut], Juri Nascimbene [aut], Pier Luigi Nimis [aut], Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>

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Package RPEGLMEN updated to version 1.1.3 with previous version 1.1.2 dated 2023-01-28

Title: Gamma and Exponential Generalized Linear Models with Elastic Net Penalty
Description: Implements the fast iterative shrinkage-thresholding algorithm (FISTA) algorithm to fit a Gamma distribution with an elastic net penalty as described in Chen, Arakvin and Martin (2018) <doi:10.48550/arXiv.1804.07780>. An implementation for the case of the exponential distribution is also available, with details available in Chen and Martin (2018) <doi:10.2139/ssrn.3085672>.
Author: Anthony Christidis [aut, cre], Xin Chen [aut], Daniel Hanson [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package accessr updated to version 1.1.3 with previous version 1.1.2 dated 2025-03-15

Title: Command Line Tools to Produce Accessible Documents using 'R Markdown'
Description: Provides functions to produce accessible 'HTML' slides, 'HTML', 'Word' and 'PDF' documents from input 'R markdown' files. Accessible 'PDF' files are produced only on a 'Windows' Operating System. One aspect of accessibility is providing a headings structure that is recognised by a screen reader, providing a navigational tool for a blind or partially-sighted person. A key aim is to produce documents of different formats easily from each of a collection of 'R markdown' source files. Input 'R markdown' files are rendered using the render() function from the 'rmarkdown' package <https://cran.r-project.org/package=rmarkdown>. A 'zip' file containing multiple output files can be produced from one function call. A user-supplied template 'Word' document can be used to determine the formatting of an output 'Word' document. Accessible 'PDF' files are produced from 'Word' documents using 'OfficeToPDF' <https://github.com/cognidox/OfficeToPDF>. A convenience function, install_otp() is [...truncated...]
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>

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Package SplitReg updated to version 1.0.3 with previous version 1.0.2 dated 2020-02-05

Title: Split Regularized Regression
Description: Functions for computing split regularized estimators defined in Christidis, Lakshmanan, Smucler and Zamar (2019) <doi:10.48550/arXiv.1712.03561>. The approach fits linear regression models that split the set of covariates into groups. The optimal split of the variables into groups and the regularized estimation of the regression coefficients are performed by minimizing an objective function that encourages sparsity within each group and diversity among them. The estimated coefficients are then pooled together to form the final fit.
Author: Anthony Christidis [aut, cre], Ezequiel Smucler [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package SplitGLM updated to version 1.0.6 with previous version 1.0.5 dated 2022-11-22

Title: Split Generalized Linear Models
Description: Functions to compute split generalized linear models. The approach fits generalized linear models that split the covariates into groups. The optimal split of the variables into groups and the regularized estimation of the coefficients are performed by minimizing an objective function that encourages sparsity within each group and diversity among them. Example applications can be found in Christidis et al. (2021) <doi:10.48550/arXiv.2102.08591>.
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package RcppSpdlog updated to version 0.0.21 with previous version 0.0.20 dated 2025-02-01

Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides many desirable features. This package bundles these header files for easy use by R packages from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] , Gabi Melman [aut] , Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package explore updated to version 1.3.4 with previous version 1.3.3 dated 2024-11-12

Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated reporting or use an easy to remember set of tidy functions for low code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>

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Package CPGLIB updated to version 1.1.2 with previous version 1.1.1 dated 2022-11-22

Title: Competing Proximal Gradients Library
Description: Functions to generate ensembles of generalized linear models using competing proximal gradients. The optimal sparsity and diversity tuning parameters are selected via an alternating grid search.
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package PSGD updated to version 1.0.6 with previous version 1.0.4 dated 2024-12-18

Title: Projected Subset Gradient Descent
Description: Functions to generate ensembles of generalized linear models using a greedy projected subset gradient descent algorithm. The sparsity and diversity tuning parameters are selected by cross-validation.
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

Diff between PSGD versions 1.0.4 dated 2024-12-18 and 1.0.6 dated 2025-03-30

 DESCRIPTION  |    8 ++++----
 MD5          |    8 ++++----
 NEWS         |    8 +++++++-
 configure    |    4 ++--
 configure.ac |    4 ++--
 5 files changed, 19 insertions(+), 13 deletions(-)

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Package LJexm updated to version 1.0.5 with previous version 1.0.4 dated 2025-03-24

Title: Extract, Convert, and Merge 'pdf' Files from 'zip' Files
Description: Extracts 'zip' files, converts 'Word', 'Excel', and 'html'/'htm' files to 'pdf' format. 'Word' and 'Excel' conversion uses 'VBScript', while 'html'/'htm' conversion uses 'webshot' and 'PhantomJS'. Additionally, the package merges 'pdf' files into a single document. This package is only supported on 'Windows' due to 'VBScript' dependencies.
Author: Lijin Arakkandathil Thekkathil [aut, cre]
Maintainer: Lijin Arakkandathil Thekkathil <lijin5673@gmail.com>

Diff between LJexm versions 1.0.4 dated 2025-03-24 and 1.0.5 dated 2025-03-30

 DESCRIPTION                   |   10 ++--
 MD5                           |   18 ++++----
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 11 files changed, 85 insertions(+), 58 deletions(-)

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Package CDsampling updated to version 0.1.5 with previous version 0.1.4 dated 2025-01-11

Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre], Liping Tong [aut], Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>

Diff between CDsampling versions 0.1.4 dated 2025-01-11 and 0.1.5 dated 2025-03-30

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 R/approxtoexact_constrained_func.R    |    5 
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Package admisc updated to version 0.38 with previous version 0.37 dated 2024-12-08

Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between admisc versions 0.37 dated 2024-12-08 and 0.38 dated 2025-03-30

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Package stepSplitReg updated to version 1.0.5 with previous version 1.0.4 dated 2024-12-18

Title: Stepwise Split Regularized Regression
Description: Functions to perform stepwise split regularized regression. The approach first uses a stepwise algorithm to split the variables into the models with a goodness of fit criterion, and then regularization is applied to each model. The weights of the models in the ensemble are determined based on a criterion selected by the user.
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

Diff between stepSplitReg versions 1.0.4 dated 2024-12-18 and 1.0.5 dated 2025-03-30

 DESCRIPTION  |    8 ++++----
 MD5          |    8 ++++----
 NEWS         |    8 +++++++-
 configure    |    4 ++--
 configure.ac |    4 ++--
 5 files changed, 19 insertions(+), 13 deletions(-)

More information about stepSplitReg at CRAN
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Package RcppCWB updated to version 0.6.6 with previous version 0.6.5 dated 2024-09-23

Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre], Bernard Desgraupes [aut], Sylvain Loiseau [aut], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stephanie Evert [ctb], Arne Fitschen [ctb], Jeroen Ooms [ctb], Marius Bertram [ctb], Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

Diff between RcppCWB versions 0.6.5 dated 2024-09-23 and 0.6.6 dated 2025-03-30

 DESCRIPTION                      |   12 ++--
 MD5                              |   98 +++++++++++++++++++--------------------
 README.md                        |    4 -
 inst/doc/vignette.html           |    6 +-
 man/RcppCWB-packge.Rd            |    8 +++
 src/cwb/CQi/auth.c               |    2 
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 src/cwb/utils/cwb-s-encode.c     |    6 +-
 src/cwb/utils/cwb-scan-corpus.c  |    2 
 50 files changed, 510 insertions(+), 195 deletions(-)

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New package minimapR with initial version 0.0.1.1
Package: minimapR
Title: Wrapper for 'minimap2'
Version: 0.0.1.1
Date: 2025-03-28
Maintainer: Jake Reed <hreed.ga@gmail.com>
Description: Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <me@liheng.org>. *SPECIAL NOTES 1. Examples can only be run from 'GitHub' installation. 2. 'conda' or 'mamba' must be used to install 'minimapR' on your system. Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".
License: MIT + file LICENSE
Depends: R (>= 4.4.0), Rsamtools, pafr
URL: https://github.com/jake-bioinfo/minimapR
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-30 03:55:29 UTC; jakereed
Author: Jake Reed [aut, cre] , Pradyun Pulipaka [ctb]
Repository: CRAN
Date/Publication: 2025-03-30 16:10:02 UTC

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Package inferCSN updated to version 1.1.7 with previous version 1.1.6 dated 2025-03-27

Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>

Diff between inferCSN versions 1.1.6 dated 2025-03-27 and 1.1.7 dated 2025-03-30

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Package dtComb updated to version 1.0.7 with previous version 1.0.6 dated 2025-03-27

Title: Statistical Combination of Diagnostic Tests
Description: A system for combining two diagnostic tests using various approaches that include statistical and machine-learning-based methodologies. These approaches are divided into four groups: linear combination methods, non-linear combination methods, mathematical operators, and machine learning algorithms. See the <https://biotools.erciyes.edu.tr/dtComb/> website for more information, documentation, and examples.
Author: Serra Ilayda Yerlitas [aut, ctb], Serra Bersan Gengec [aut, ctb], Necla Kochan [aut, ctb], Gozde Erturk Zararsiz [aut, ctb], Selcuk Korkmaz [aut, ctb], Gokmen Zararsiz [aut, ctb, cre]
Maintainer: Gokmen Zararsiz <gokmen.zararsiz@gmail.com>

Diff between dtComb versions 1.0.6 dated 2025-03-27 and 1.0.7 dated 2025-03-30

 DESCRIPTION                                   |    6 +--
 MD5                                           |   41 +++++++++++++-------------
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 R/mathComb.R                                  |   33 +++++++++-----------
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 vignettes/vignettedtComb.Rnw                  |   18 +++++------
 22 files changed, 170 insertions(+), 190 deletions(-)

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New package CytOpT with initial version 0.9.7
Package: CytOpT
Title: Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation
Version: 0.9.7
Date: 2025-03-27
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
SystemRequirements: Python (>= 3.7)
Description: Supervised learning from a source distribution (with known segmentation into cell sub-populations) to fit a target distribution with unknown segmentation. It relies regularized optimal transport to directly estimate the different cell population proportions from a biological sample characterized with flow cytometry measurements. It is based on the regularized Wasserstein metric to compare cytometry measurements from different samples, thus accounting for possible mis-alignment of a given cell population across sample (due to technical variability from the technology of measurements). Supervised learning technique based on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a mixture model Details are presented in Freulon P, Bigot J and Hejblum BP (2023) <doi:10.1214/22-AOAS1660>.
License: GPL (>= 2)
Repository: CRAN
URL: https://sistm.github.io/CytOpT-R/, https://github.com/sistm/CytOpT-R/
Depends: R (>= 3.6)
LazyData: true
Encoding: UTF-8
Imports: ggplot2 (>= 3.0.0), MetBrewer, patchwork, reshape2, reticulate, stats, testthat (>= 3.0.0)
Suggests: rmarkdown, knitr, covr
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-28 14:46:08 UTC; boris
Author: Boris Hejblum [aut, cre], Paul Freulon [aut], Kalidou Ba [aut, trl]
Date/Publication: 2025-03-30 17:00:10 UTC

More information about CytOpT at CRAN
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Package simDAG updated to version 0.3.0 with previous version 0.2.2 dated 2025-02-23

Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node. Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to one of many implemented regressions, such as logistic regression, linear regression, poisson regression and more. Also includes a comprehensive framework for discrete-time simulation, which can generate even more complex longitudinal data.
Author: Robin Denz [aut, cre], Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>

Diff between simDAG versions 0.2.2 dated 2025-02-23 and 0.3.0 dated 2025-03-30

 DESCRIPTION                                         |    9 
 MD5                                                 |  148 +++++++-----
 NAMESPACE                                           |    8 
 NEWS.md                                             |   26 ++
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 inst/doc/v_using_formulas.R                         |   81 ++++++
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 man/as.igraph.DAG.Rd                                |    9 
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Package innsight updated to version 0.3.2 with previous version 0.3.1 dated 2024-11-26

Title: Get the Insights of Your Neural Network
Description: Interpretation methods for analyzing the behavior and individual predictions of modern neural networks in a three-step procedure: Converting the model, running the interpretation method, and visualizing the results. Implemented methods are, e.g., 'Connection Weights' described by Olden et al. (2004) <doi:10.1016/j.ecolmodel.2004.03.013>, layer-wise relevance propagation ('LRP') described by Bach et al. (2015) <doi:10.1371/journal.pone.0130140>, deep learning important features ('DeepLIFT') described by Shrikumar et al. (2017) <doi:10.48550/arXiv.1704.02685> and gradient-based methods like 'SmoothGrad' described by Smilkov et al. (2017) <doi:10.48550/arXiv.1706.03825>, 'Gradient x Input' or 'Vanilla Gradient'. Details can be found in the accompanying scientific paper: Koenen & Wright (2024, Journal of Statistical Software, <doi:10.18637/jss.v111.i08>).
Author: Niklas Koenen [aut, cre] , Raphael Baudeu [ctb]
Maintainer: Niklas Koenen <niklas.koenen@gmail.com>

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Package GET updated to version 1.0-5 with previous version 1.0-4 dated 2024-12-02

Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T in various applications. A 100(1-alpha)% global envelope is a band bounded by two vectors such that the probability that T falls outside this envelope in any of the d points is equal to alpha. Global means that the probability is controlled simultaneously for all the d elements of the vectors. The global envelopes can be used for graphical Monte Carlo and permutation tests where the test statistic is a multivariate vector or function (e.g. goodness-of-fit testing for point patterns and random sets, functional analysis of variance, functional general linear model, n-sample test of correspondence of distribution functions), for central regions of functional or multivariate data (e.g. outlier detection, functional boxplot) and for global confidence and prediction bands (e.g. confidence band in polynomial regression, Bayesian posterior prediction). See Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre], Tomas Mrkvicka [aut], Mikko Kuronen [ctb], Jiri Dvorak [ctb], Pavel Grabarnik [ctb], Ute Hahn [ctb], Michael Rost [ctb], Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>

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Package nodbi updated to version 0.12.0 with previous version 0.11.0 dated 2024-11-10

Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] , Scott Chamberlain [aut] , Rich FitzJohn [aut], Jeroen Ooms [aut], Ivan Tarbakou [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Package GWASinspector updated to version 1.7.3 with previous version 1.7.1 dated 2024-05-06

Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre], Peter J. van der Most [aut], Ahmad Vaez [aut], Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>

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Package RcppZiggurat updated to version 0.1.8 with previous version 0.1.7 dated 2025-03-22

Title: 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations
Description: The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>) has been improved upon a few times starting with Leong et al (2005, <doi:10.18637/jss.v012.i07>). This package provides an aggregation in order to compare different implementations in order to provide a 'faster but good enough' alternative for use with R and C++ code. See the 'zigg' package for a lighter implementation for much easier use in other packages.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package keyATM updated to version 0.5.3 with previous version 0.5.2 dated 2024-04-24

Title: Keyword Assisted Topic Models
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) <doi:10.1111/ajps.12779>.
Author: Shusei Eshima [aut, cre] , Tomoya Sasaki [aut], Kosuke Imai [aut], Chung-hong Chan [ctb] , Romain Francois [ctb] , Martin Feldkircher [ctb] , William Lowe [ctb], Seo-young Silvia Kim [ctb]
Maintainer: Shusei Eshima <shuseieshima@gmail.com>

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Package PsychWordVec updated to version 2025.3 with previous version 2023.9 dated 2023-09-27

Title: Word Embedding Research Framework for Psychological Science
Description: An integrative toolbox of word embedding research that provides: (1) a collection of 'pre-trained' static word vectors in the '.RData' compressed format <https://psychbruce.github.io/WordVector_RData.pdf>; (2) a group of functions to process, analyze, and visualize word vectors; (3) a range of tests to examine conceptual associations, including the Word Embedding Association Test <doi:10.1126/science.aal4230> and the Relative Norm Distance <doi:10.1073/pnas.1720347115>, with permutation test of significance; and (4) a set of training methods to locally train (static) word vectors from text corpora, including 'Word2Vec' <doi:10.48550/arXiv.1301.3781>, 'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <doi:10.48550/arXiv.1607.04606>.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>

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Package AQuality updated to version 1.3 with previous version 1.2 dated 2025-03-21

Title: Water and Measurements Quality
Description: The functions proposed in this package allows to evaluate the process of measurement of the chemical components of water numerically or graphically. TSSS(), ICHS and datacheck() functions are useful to control the quality of measurements of chemical components of a sample of water. If one or more measurements include an error, the generated graph will indicate it with a position of the point that represents the sample outside the confidence interval. The function CI allows to evaluate the possibility of contamination of a water sample after being obtained.
Author: Maela Lupo [aut, cre], Andrea Porpatto [aut], Rosa Marzullo [aut], Alfredo Rigalli [aut]
Maintainer: Maela Lupo <maela.lupo@gmail.com>

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Package RcppPlanc (with last version 2.0.0) was removed from CRAN

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

2025-03-25 2.0.0

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Package pema updated to version 0.1.4 with previous version 0.1.3 dated 2023-03-16

Title: Penalized Meta-Analysis
Description: Conduct penalized meta-analysis, see Van Lissa, Van Erp, & Clapper (2023) <doi:10.31234/osf.io/6phs5>. In meta-analysis, there are often between-study differences. These can be coded as moderator variables, and controlled for using meta-regression. However, if the number of moderators is large relative to the number of studies, such an analysis may be overfit. Penalized meta-regression is useful in these cases, because it shrinks the regression slopes of irrelevant moderators towards zero.
Author: Caspar J van Lissa [aut, cre] , Sara J van Erp [aut]
Maintainer: Caspar J van Lissa <c.j.vanlissa@tilburguniversity.edu>

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Package rim (with last version 0.7.0) was removed from CRAN

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2024-10-18 0.7.0
2023-08-24 0.6.4
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Package RITCH (with last version 0.1.26) was removed from CRAN

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

2024-01-15 0.1.26
2024-01-13 0.1.25
2024-01-11 0.1.24

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Package salso updated to version 0.3.51 with previous version 0.3.42 dated 2024-09-16

Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] , Devin J. Johnson [aut] , Peter Mueller [aut], Andres Felipe Barrientos [aut], Garritt Page [aut], David Dunson [aut], Alex Crichton [ctb] , Brendan Zabarauskas [ctb] , David B. Dahl [ctb] , David Tolnay [ctb] , Jim Turner [c [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

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Package rarestR updated to version 1.1.1 with previous version 1.1.0 dated 2024-09-26

Title: Rarefaction-Based Species Richness Estimator
Description: Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.
Author: Peng Zhao [aut, cre] , Yi Zou [aut]
Maintainer: Peng Zhao <pengzhao20@outlook.com>

Diff between rarestR versions 1.1.0 dated 2024-09-26 and 1.1.1 dated 2025-03-30

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Package caviarpd updated to version 0.3.14 with previous version 0.3.13 dated 2024-09-06

Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates. An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] , R. Jacob Andros [aut] , J. Brandon Carter [aut] , Alex Crichton [ctb] , Brendan Zabarauskas [ctb] , David B. Dahl [ctb] , David Tolnay [ctb] , Jim Turner [ctb] , Jorge Aparicio [ctb] , Josh Stone [ctb] , Mikhail Vorotilov [ [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between caviarpd versions 0.3.13 dated 2024-09-06 and 0.3.14 dated 2025-03-30

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