Sun, 03 Mar 2024

Package RESET updated to version 0.2.2 with previous version 0.2.1 dated 2023-08-20

Title: Reconstruction Set Test
Description: Contains logic for sample-level variable set scoring using randomized reduced rank reconstruction error. Frost, H. Robert (2023) "Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error" <doi:10.1101/2023.04.03.535366>.
Author: H. Robert Frost [aut, cre]
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>

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Package greeks updated to version 1.3.5 with previous version 1.3.2 dated 2024-01-31

Title: Sensitivities of Prices of Financial Options and Implied Volatilities
Description: Methods to calculate sensitivities of financial option prices for European, geometric and arithmetic Asian, and American options, with various payoff functions in the Black Scholes model, and in more general jump diffusion models. A shiny app to interactively plot the results is included. Furthermore, methods to compute implied volatilities are provided for a wide range of option types and custom payoff functions. Classical formulas are implemented for European options in the Black Scholes Model, as is presented in Hull, J. C. (2017), Options, Futures, and Other Derivatives. In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American options, the Binomial Tree Method is implemented, as is presented in Hull, J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>

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Package stacomiR updated to version 0.6.1 with previous version 0.6.0.7 dated 2022-07-18

Title: Fish Migration Monitoring
Description: Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Author: Cedric Briand [aut, cre], Marion Legrand [aut], Beaulaton Laurent [ctb], Boulenger Clarisse [ctb], Lafage Denis [ctb], Grall Sebastien [ctb]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>

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Package runner updated to version 0.4.4 with previous version 0.4.3 dated 2023-03-21

Title: Running Operations for Vectors
Description: Lightweight library for rolling windows operations. Package enables full control over the window length, window lag and a time indices. With a runner one can apply any R function on a rolling windows. The package eases work with equally and unequally spaced time series.
Author: Dawid Kaledkowski [aut, cre]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@gmail.com>

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Package bWGR updated to version 2.2.6 with previous version 2.2.5 dated 2023-11-21

Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>), with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] , William Muir [aut], David Habier [aut], Kyle Kocak [aut], Shizhong Xu [aut], Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>

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Package nodbi updated to version 0.10.3 with previous version 0.10.2 dated 2024-02-24

Title: 'NoSQL' Database Connector
Description: Simplified 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]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Package UKFE updated to version 0.3.4 with previous version 0.3.3 dated 2024-01-21

Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 12.1. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood e [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>

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Package icr updated to version 0.6.5 with previous version 0.6.4 dated 2023-11-28

Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder reliability coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb]
Maintainer: Alexander Staudt <staudtlex@live.de>

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Package wdnet updated to version 1.2.3 with previous version 1.2.2 dated 2023-09-06

Title: Weighted and Directed Networks
Description: Assortativity coefficients, centrality measures, and clustering coefficients for weighted and directed networks. Rewiring unweighted networks with given assortativity coefficients. Generating general preferential attachment networks.
Author: Yelie Yuan [aut, cre], Tiandong Wang [aut], Jun Yan [aut], Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>

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Permanent link

Package IP updated to version 0.1.3 with previous version 0.1.2 dated 2024-01-10

Title: Classes and Methods for 'IP' Addresses
Description: Provides S4 classes for Internet Protocol (IP) versions 4 and 6 addresses and efficient methods for 'IP' addresses comparison, arithmetic, bit manipulation and lookup. Both 'IPv4' and 'IPv6' arbitrary ranges are also supported as well as internationalized (IDN) domain lookup with and 'whois' query.
Author: Thomas Soubiran [aut, cre]
Maintainer: Thomas Soubiran <thomas.soubiran@univ-lille.fr>

Diff between IP versions 0.1.2 dated 2024-01-10 and 0.1.3 dated 2024-03-03

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More information about IP at CRAN
Permanent link

New package geoAr with initial version 1.0.0
Package: geoAr
Title: Argentina's Spatial Data Toolbox
Version: 1.0.0
Description: Collection of tools that facilitates data access and workflow for spatial analysis of Argentina. Includes historical information from censuses, administrative limits at different levels of aggregation, location of human settlements, among others. Since it is expected that the majority of users will be Spanish-speaking, the documentation of the package prioritizes this language, although an effort is made to also offer annotations in English.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, gt, knitr, rmarkdown, geofacet, ggplot2, tibble
Depends: R (>= 2.10)
Imports: dplyr, sf, httr, assertthat, attempt, tidyr, stringr, magrittr, curl, glue, leaflet, jsonlite, purrr
URL: https://github.com/PoliticaArgentina/geoAr
BugReports: https://github.com/PoliticaArgentina/geoAr/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-03 00:36:15 UTC; UsuarioFundar
Author: Juan Pablo Ruiz Nicolini [aut, cre, cph] , Patricio Del Boca [aut], Juan Gabriel Juara [aut]
Maintainer: Juan Pablo Ruiz Nicolini <juanpabloruiznicolini@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-03 17:30:02 UTC

More information about geoAr at CRAN
Permanent link

Package KoboconnectR updated to version 1.2.2 with previous version 1.2.1 dated 2022-10-18

Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>

Diff between KoboconnectR versions 1.2.1 dated 2022-10-18 and 1.2.2 dated 2024-03-03

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Permanent link

Package sgsR updated to version 1.4.5 with previous version 1.4.4 dated 2023-06-13

Title: Structurally Guided Sampling
Description: Structurally guided sampling (SGS) approaches for airborne laser scanning (ALS; LIDAR). Primary functions provide means to generate data-driven stratifications & methods for allocating samples. Intermediate functions for calculating and extracting important information about input covariates and samples are also included. Processing outcomes are intended to help forest and environmental management practitioners better optimize field sample placement as well as assess and augment existing sample networks in the context of data distributions and conditions. ALS data is the primary intended use case, however any rasterized remote sensing data can be used, enabling data-driven stratifications and sampling approaches.
Author: Tristan RH Goodbody [aut, cre, cph] , Nicholas C Coops [aut] , Martin Queinnec [aut]
Maintainer: Tristan RH Goodbody <goodbody.t@gmail.com>

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Package RWsearch updated to version 5.1.4 with previous version 5.0.5 dated 2022-02-22

Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the package documentation (html index, README, NEWS, pdf manual, vignettes, source code, binaries) with a single instruction. Visualize the package dependencies and CRAN checks. Compare the package versions, unload and install the packages and their dependencies in a safe order. Explore CRAN archives. Use the above functions for task view maintenance. Access web search engines from the console thanks to 80+ bookmarks. All functions accept standard and non-standard evaluation.
Author: Patrice Kiener [aut, cre]
Maintainer: Patrice Kiener <rpackages@inmodelia.com>

Diff between RWsearch versions 5.0.5 dated 2022-02-22 and 5.1.4 dated 2024-03-03

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Package rcdklibs updated to version 2.9 with previous version 2.8 dated 2022-09-25

Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from <https://github.com/cdk/cdk>.
Author: Rajarshi Guha [aut] , Zachary Charlop-Powers [cre] , CDK Project [ctb, cph]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

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New package geostan with initial version 0.5.4
Package: geostan
Title: Bayesian Spatial Analysis
Version: 0.5.4
Date: 2024-03-01
URL: https://connordonegan.github.io/geostan/
BugReports: https://github.com/ConnorDonegan/geostan/issues
Description: For Bayesian inference with spatial data, provides exploratory spatial analysis tools, multiple spatial model specifications, spatial model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health surveillance data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.4)
Imports: spdep (>= 1.0), sf (>= 1.0-10), ggplot2 (>= 3.0.0), methods, graphics, stats, MASS, truncnorm, signs, gridExtra, utils, Matrix (>= 1.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.26.0), rstantools (>= 2.1.1)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>= 2.26.0)
Suggests: testthat, knitr, rmarkdown, bayesplot
SystemRequirements: GNU make
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-03-02 00:01:25 UTC; connor
Author: Connor Donegan [aut, cre] , Mitzi Morris [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-03 15:22:39 UTC

More information about geostan at CRAN
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Package FatTailsR updated to version 1.8-5 with previous version 1.8-0 dated 2021-03-12

Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3, K4 and K7 to characterize distributions with left and right, symmetric or asymmetric fat tails in market finance, neuroscience and other disciplines. Two algorithms to estimate with a high accuracy distribution parameters, quantiles, value-at-risk and expected shortfall. Include power hyperbolas and power hyperbolic functions.
Author: Patrice Kiener [aut, cre]
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>

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Package cryptotrackr updated to version 1.2.0 with previous version 1.1.0 dated 2023-12-07

Title: An Interface to Crypto Data Sources
Description: Allows you to connect to data sources across the crypto ecosystem. This data can enable a range of activity such as portfolio tracking, programmatic trading, or industry analysis.
Author: Trevor French [aut, cre]
Maintainer: Trevor French <FrenchTrevor@outlook.com>

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Package ETAS updated to version 0.6.1 with previous version 0.5.1 dated 2022-11-28

Title: Modeling Earthquake Data Using 'ETAS' Model
Description: Fits the space-time Epidemic Type Aftershock Sequence ('ETAS') model to earthquake catalogs using a stochastic 'declustering' approach. The 'ETAS' model is a 'spatio-temporal' marked point process model and a special case of the 'Hawkes' process. The package is based on a Fortran program by 'Jiancang Zhuang' (available at <http://bemlar.ism.ac.jp/zhuang/software.html>), which is modified and translated into C++ and C such that it can be called from R. Parallel computing with 'OpenMP' is possible on supported platforms.
Author: Abdollah Jalilian [aut, cre] , Jiancang Zhuang [ctb]
Maintainer: Abdollah Jalilian <stat4aj@gmail.com>

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Package stochvol updated to version 3.2.4 with previous version 3.2.3 dated 2023-11-26

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] , Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>

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Package lphom updated to version 0.3.5-5 with previous version 0.3.5-4 dated 2024-02-20

Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating, under the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices) using mainly aggregate data (from voting units). References: Pavía and Romero (2022) <doi:10.1177/00491241221092725>. Pavía (2023) <doi:10.1007/s43545-023-00658-y>. Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>. Pavía (2024) A local convergent ecological inference algorithm for RxC tables. Pavía and Penadés (2024). A bottom-up approach for ecological inference. Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>. Acknowledgements: The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Author: Jose M. Pavia [aut, cre] , Rafael Romero [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>

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Package rsimsum updated to version 0.13.0 with previous version 0.11.3 dated 2022-08-17

Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (White I.R., 2010 <https://www.stata-journal.com/article.html?article=st0200>), further extending it with additional performance measures and functionality.
Author: Alessandro Gasparini [aut, cre] , Ian R. White [aut]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>

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Package RAINBOWR updated to version 0.1.35 with previous version 0.1.33 dated 2023-09-12

Title: Genome-Wide Association Study with SNP-Set Methods
Description: By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.
Author: Kosuke Hamazaki [aut, cre], Hiroyoshi Iwata [aut, ctb]
Maintainer: Kosuke Hamazaki <hamazaki@ut-biomet.org>

Diff between RAINBOWR versions 0.1.33 dated 2023-09-12 and 0.1.35 dated 2024-03-03

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Package RcppArmadillo updated to version 0.12.8.1.0 with previous version 0.12.8.0.0 dated 2024-02-08

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package quickcode updated to version 0.7 with previous version 0.6 dated 2023-12-03

Title: A Compilation of Some Frequently Used R Functions
Description: The NOT functions and a simple compilation of various functions for easy usage. Shorthand code to save memory usage.
Author: Obinna Obianom [aut, cre], Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>

Diff between quickcode versions 0.6 dated 2023-12-03 and 0.7 dated 2024-03-03

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Package PolynomF updated to version 2.0-8 with previous version 2.0-5 dated 2022-05-01

Title: Polynomials in R
Description: Implements univariate polynomial operations in R, including polynomial arithmetic, finding zeros, plotting, and some operations on lists of polynomials.
Author: Bill Venables, with contribution by Kurt Hornik, Georgi Boshnakov and Brian Ripley.
Maintainer: Bill Venables <Bill.Venables@gmail.com>

Diff between PolynomF versions 2.0-5 dated 2022-05-01 and 2.0-8 dated 2024-03-03

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Sat, 02 Mar 2024

Package hdnom updated to version 6.0.3 with previous version 6.0.2 dated 2023-04-24

Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre] , Qing-Song Xu [aut], Miao-Zhu Li [aut], Frank Harrell [ctb] , Sergej Potapov [ctb] , Werner Adler [ctb] , Matthias Schmid [ctb]
Maintainer: Nan Xiao <me@nanx.me>

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Package NAIR updated to version 1.0.4 with previous version 1.0.3 dated 2024-01-09

Title: Network Analysis of Immune Repertoire
Description: Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.
Author: Brian Neal [aut, cre], Hai Yang [aut], Daniil Matveev [aut], Phi Long Le [aut], Li Zhang [cph, aut]
Maintainer: Brian Neal <Brian.Neal@ucsf.edu>

Diff between NAIR versions 1.0.3 dated 2024-01-09 and 1.0.4 dated 2024-03-02

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New package spnaf with initial version 0.3.1
Package: spnaf
Title: Spatial Network Autocorrelation for Flow Data
Version: 0.3.1
Description: Identify statistically significant flow clusters using the local spatial network autocorrelation statistic G_ij* proposed by 'Berglund' and 'Karlström' (1999) <doi:10.1007/s101090050013>. The metric, an extended statistic of 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>, detects a group of flows having similar traits in terms of directionality. You provide OD data and the associated polygon to get results with several parameters, some of which are defined by spdep package.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, magrittr, sf, spdep, tidyr, rlang
Suggests: knitr, rmarkdown, tmap
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-02 07:45:17 UTC; YB
Author: Youngbin Lee [aut, cre] , Hui Jeong Ha [aut] , Sohyun Park [aut] , Kyusik Kim [aut] , Jinhyung Lee [aut]
Maintainer: Youngbin Lee <youngbin@snu.ac.kr>
Repository: CRAN
Date/Publication: 2024-03-02 22:10:02 UTC

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Package secrdesign updated to version 2.9.0 with previous version 2.8.2 dated 2023-03-10

Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] , Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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New package RivRetrieve with initial version 0.1.4
Package: RivRetrieve
Title: Retrieve Global River Gauge Data
Version: 0.1.4
Description: Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.
License: MIT + file LICENSE
URL: https://github.com/Ryan-Riggs/RivRetrieve
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: BBmisc, dataRetrieval, devtools, dplyr, httr, jsonlite, lubridate, readr, rlang, rlist, RSelenium, rvest, stringr, tibble, tidyhydat, tidyr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-01 17:18:25 UTC; rriggs
Author: Ryan Riggs [aut, cre] , Simon Moulds [aut] , Michel Wortmann [aut] , Louise Slater [aut] , George Allen [aut]
Maintainer: Ryan Riggs <rriggs@tamu.edu>
Repository: CRAN
Date/Publication: 2024-03-02 22:32:42 UTC

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Package rdss updated to version 1.0.8 with previous version 1.0.6 dated 2024-02-20

Title: Companion Datasets and Functions for Research Design in the Social Sciences
Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book.
Author: Graeme Blair [aut, cre] , Alexander Coppock [aut] , Macartan Humphreys [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>

Diff between rdss versions 1.0.6 dated 2024-02-20 and 1.0.8 dated 2024-03-02

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Package RaMS updated to version 1.4.0 with previous version 1.3.4 dated 2023-12-13

Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages exist to process MS data, many of these make it difficult to access the underlying mass-to-charge ratio (m/z), intensity, and retention time of the files themselves. This package is designed to format MS data in a tidy fashion and allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph], Ricardo Cunha [ctb], Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>

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Package LikertMakeR updated to version 0.2.0 with previous version 0.1.5 dated 2022-12-22

Title: Synthesise and Correlate Rating-Scale Data
Description: Synthesise rating-scale data with predefined first & second moments (mean & standard deviation) and, optionally, correlate multiple vectors with predefined correlation matrix. Also generate synthetic rating-scale data with predefined Cronbach's Alpha.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>

Diff between LikertMakeR versions 0.1.5 dated 2022-12-22 and 0.2.0 dated 2024-03-02

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New package jmastats with initial version 0.2.1
Package: jmastats
Version: 0.2.1
Title: Download Weather Data from Japan Meteorological Agency Website
Description: Provides features that allow users to download weather data published by the Japan Meteorological Agency (JMA) website (<https://www.jma.go.jp/jma/index.html>). The data includes information dating back to 1976 and aligns with the categories available on the website. Additionally, users can process the best track data of typhoons and easily handle earthquake record files.
Depends: R (>= 4.1)
License: MIT + file LICENSE
BugReports: https://github.com/uribo/jmastats/issues
URL: https://uribo.github.io/jmastats/, https://github.com/uribo/jmastats
Imports: cli (>= 3.4.0), crayon (>= 1.3.4), dplyr (>= 1.1.0), forcats (>= 0.4.0), ggplot2 (>= 2.2.1), lifecycle (>= 1.0.3), lubridate (>= 1.7.4), purrr (>= 1.0.2), rappdirs (>= 0.3.3), readr (>= 1.1.1), rlang (>= 0.2.1), rvest (>= 0.3.2), sf (>= 0.6.3), stringr (>= 1.3.1), tibble (>= 3.0.0), tidyselect (>= 1.1.0), tidyr (>= 1.0.0), units (>= 0.5.1), xml2 (>= 1.2.0)
Suggests: knitr (>= 1.20), lwgeom (>= 0.1-4), rmarkdown (>= 1.9), testthat (>= 2.0.0)
Encoding: UTF-8
LazyData: true
ByteCompile: true
NeedsCompilation: no
Packaged: 2024-03-02 05:14:22 UTC; suryu
Author: Shinya Uryu [aut, cph, cre]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-02 22:30:06 UTC

More information about jmastats at CRAN
Permanent link

Package shinytest updated to version 1.5.4 with previous version 1.5.3 dated 2023-03-24

Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using a headless browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre], Gabor Csardi [aut], Hadley Wickham [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph, ccp]
Maintainer: Winston Chang <winston@posit.co>

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Package rcheology updated to version 4.3.3.0 with previous version 4.3.2.0 dated 2023-11-29

Title: Data on Base and Recommended Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package hdf5r updated to version 1.3.10 with previous version 1.3.9 dated 2024-01-14

Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre], Mario Annau [aut], Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>

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Package toastui updated to version 0.3.2 with previous version 0.3.1 dated 2024-02-09

Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package sdm updated to version 1.2-32 with previous version 1.1-8 dated 2021-11-12

Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>

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Package iNEXT.3D updated to version 1.0.2 with previous version 1.0.1 dated 2024-02-19

Title: Interpolation and Extrapolation for Three Dimensions of Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D) of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). This package provides functions to compute standardized 3D diversity estimates with a common sample size or sample coverage. A unified framework based on Hill numbers and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates are in the same units of species/lineage equivalents and can be meaningfully compared. The package features size- and coverage-based rarefaction and extrapolation sampling curves to facilitate rigorous comparison of 3D diversity across individual assemblages. Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021) <doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre], KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>

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Package coxme updated to version 2.2-19 with previous version 2.2-18.1 dated 2022-10-03

Title: Mixed Effects Cox Models
Description: Fit Cox proportional hazards models containing both fixed and random effects. The random effects can have a general form, of which familial interactions (a "kinship" matrix) is a particular special case. Note that the simplest case of a mixed effects Cox model, i.e. a single random per-group intercept, is also called a "frailty" model. The approach is based on Ripatti and Palmgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau.terry@mayo.edu>

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Package bdsmatrix updated to version 1.3-7 with previous version 1.3-6 dated 2022-06-03

Title: Routines for Block Diagonal Symmetric Matrices
Description: This is a special case of sparse matrices, used by coxme.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>

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Package tinycodet updated to version 0.4.5 with previous version 0.4.1 dated 2024-02-17

Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette. 'tinycodet' primarily focuses on 4 aspects. 1) Safer decimal (in)equality testing, safer atomic conversions, and other functions for safer coding. 2) A new package import system, that attempts to combine the benefits of using a package without attaching it, with the benefits of attaching a package. 3) Extending the string manipulation capabilities of the 'stringi' R package. 4) Reducing repetitive code. Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>

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Package mwcsr updated to version 0.1.8 with previous version 0.1.7 dated 2023-05-16

Title: Solvers for Maximum Weight Connected Subgraph Problem and Its Variants
Description: Algorithms for solving various Maximum Weight Connected Subgraph Problems, including variants with budget constraints, cardinality constraints, weighted edges and signals. The package represents an R interface to high-efficient solvers based on relax-and-cut approach (Álvarez-Miranda E., Sinnl M. (2017) <doi:10.1016/j.cor.2017.05.015>) mixed-integer programming (Loboda A., Artyomov M., and Sergushichev A. (2016) <doi:10.1007/978-3-319-43681-4_17>) and simulated annealing.
Author: Alexander Loboda [aut, cre], Nikolay Poperechnyi [aut], Eduardo Alvarez-Miranda [aut], Markus Sinnl [aut], Alexey Sergushichev [aut], Paul Hosler Jr. [cph] , www.hamcrest.org [cph] , Barak Naveh and Contributors [cph] , The Apache Software Foundation [...truncated...]
Maintainer: Alexander Loboda <aleks.loboda@gmail.com>

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Package CAGR updated to version 1.1.0 with previous version 0.1.0 dated 2023-11-09

Title: Compound Annual Growth Rate
Description: A time series usually does not have a uniform growth rate. Compound Annual Growth Rate measures the average annual growth over a given period. More details can be found in Bardhan et al. (2022) <DOI:10.18805/ag.D-5418>.
Author: Debopam Rakshit [aut, cre], Dwaipayan Bardhan [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>

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Package MR.RGM updated to version 0.0.2 with previous version 0.0.1 dated 2024-02-28

Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In the process, causal effects, adjacency matrices, and other essential parameters of the complex biological networks, [...truncated...]
Author: Bitan Sarkar [aut, cre], Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>

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Package GPCERF updated to version 0.2.3 with previous version 0.2.2 dated 2024-02-16

Title: Gaussian Processes for Estimating Causal Exposure Response Curves
Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <arXiv:2105.03454>.
Author: Naeem Khoshnevis [aut, cre] , Boyu Ren [aut] , Tanujit Dey [ctb] , Danielle Braun [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>

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Package fabletools updated to version 0.4.1 with previous version 0.4.0 dated 2024-02-09

Title: Core Tools for Packages in the 'fable' Framework
Description: Provides tools, helpers and data structures for developing models and time series functions for 'fable' and extension packages. These tools support a consistent and tidy interface for time series modelling and analysis.
Author: Mitchell O'Hara-Wild [aut, cre] , Rob Hyndman [aut], Earo Wang [aut] , Di Cook [ctb], George Athanasopoulos [ctb], David Holt [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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Package survivalmodels (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:

2022-03-25 0.1.13
2022-03-11 0.1.12
2022-02-16 0.1.11
2021-09-11 0.1.9
2021-04-17 0.1.8
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2020-11-18 0.1.4
2020-11-11 0.1.3
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2020-10-20 0.1.1
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Package EvalEst (with last version 2024.2-1) was removed from CRAN

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

2024-02-18 2024.2-1
2021-03-02 2021.2-1

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Package survivalSL (with last version 0.93) was removed from CRAN

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2024-02-23 0.93
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Package eiCompare (with last version 3.0.4) was removed from CRAN

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2023-08-31 3.0.4

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Package dse (with last version 2020.2-1) was removed from CRAN

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

2020-02-26 2020.2-1
2015-12-16 2015.12-1
2014-11-25 2014.11-1
2013-03-07 2013.3-2
2012-09-20 2012.6-1
2012-05-02 2012.4-1
2011-11-28 2011.11-2
2011-11-03 2011.11-1
2011-03-23 2011.3-1
2011-01-20 2009.12-1
2009-10-18 2009.10-2
2009-10-13 2009.10-1
2009-07-26 2009.7-1
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2007-05-13 2007.5-2

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Package showtext updated to version 0.9-7 with previous version 0.9-6 dated 2023-05-03

Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as 'Ghostscript' is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package R2SWF updated to version 0.9-9 with previous version 0.9-8 dated 2022-11-17

Title: Convert R Graphics to Flash Animations
Description: Using the 'Ming' library <https://github.com/libming/libming> to create Flash animations. Users can either use the 'SWF' device swf() to generate 'SWF' file directly through plotting functions like plot() and lines(), or convert images of other formats ('SVG', 'PNG', 'JPEG') into 'SWF'.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package ggsci updated to version 3.0.1 with previous version 3.0.0 dated 2023-03-08

Title: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre] , Joshua Cook [ctb], Clara Jegousse [ctb], Miaozhu Li [ctb]
Maintainer: Nan Xiao <me@nanx.me>

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Package Qval updated to version 0.1.5 with previous version 0.1.4 dated 2024-02-04

Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>. Different research methods during Q-matrix validating are available.
Author: Haijiang Qin [aut, cre, cph], Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>

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Fri, 01 Mar 2024

Package sysfonts updated to version 0.8.9 with previous version 0.8.8 dated 2022-03-13

Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package melt updated to version 1.11.1 with previous version 1.11.0 dated 2024-02-17

Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests. It offers an easy-to-use interface and flexibility in specifying hypotheses and calibration methods, extending the framework to simultaneous inferences. The core computational routines are implemented using the 'Eigen' 'C++' library and 'RcppEigen' interface, with 'OpenMP' for parallel computation. Details of the testing procedures are provided in Kim, MacEachern, and Peruggia (2023) <doi:10.1080/10485252.2023.2206919>. A companion paper by Kim, MacEachern, and Peruggia (2024) <doi:10.18637/jss.v108.i05> is available for further information. This work was supported by the U.S. National Science Foundation under Grants No. SES-1921523 and DMS-2015552.
Author: Eunseop Kim [aut, cph, cre], Steven MacEachern [ctb, ths], Mario Peruggia [ctb, ths], Pierre Chausse [rev], Alex Stringer [rev]
Maintainer: Eunseop Kim <markean@pm.me>

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Package GPArotation updated to version 2024.3-1 with previous version 2024.2-1 dated 2024-02-04

Title: Gradient Projection Factor Rotation
Description: Gradient Projection Algorithms for Factor Rotation. For details see ?GPArotation. When using this package, please cite: Bernaards and Jennrich (2005) <doi:10.1177/0013164404272507>. "Gradient Projection Algorithms and Software for Arbitrary Rotation Criteria in Factor Analysis".
Author: Coen Bernaards [aut, cre], Paul Gilbert [aut], Robert Jennrich [aut]
Maintainer: Coen Bernaards <cab.gparotation@gmail.com>

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Package choroplethr updated to version 3.7.3 with previous version 3.7.2 dated 2023-07-06

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.
Author: Ari Lamstein [aut, cre], Brian Johnson [ctb], Trulia, Inc. [cph]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>

Diff between choroplethr versions 3.7.2 dated 2023-07-06 and 3.7.3 dated 2024-03-01

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Package sarima updated to version 0.9.2 with previous version 0.9.1 dated 2022-08-11

Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA and related models. The aim of the package is to provide consistent interface for the user. For example, a single function autocorrelations() computes various kinds of theoretical and sample autocorrelations. This is work in progress, see the documentation and vignettes for the current functionality. Function sarima() fits extended multiplicative seasonal ARIMA models with trends, exogenous variables and arbitrary roots on the unit circle, which can be fixed or estimated (for the algebraic basis for this see <arXiv:2208.05055>, a paper on the methodology is being prepared). The suggested package 'FitARMA' can be installed with 'remotes::install_github("cran/FitARMA")' if necessary but is no longer needed in normal use.
Author: Georgi N. Boshnakov [aut, cre], Jamie Halliday [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package pvda updated to version 0.0.3 with previous version 0.0.2 dated 2024-01-18

Title: Disproportionality Functions for Pharmacovigilance
Description: Tools for performing disproportionality analysis using the information component, proportional reporting rate and the reporting odds ratio. The anticipated use is passing data to the da() function, which executes the disproportionality analysis. See Norén et al (2011) <doi:10.1177/0962280211403604> and Montastruc et al (2011) <doi:10.1111/j.1365-2125.2011.04037.x> for further details.
Author: Oskar Gauffin [aut, cre]
Maintainer: Oskar Gauffin <oskar.gauffin@hotmail.com>

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Package ipanema updated to version 1.1.0 with previous version 0.6.7 dated 2024-01-30

Title: Read Data from 'LimeSurvey'
Description: Read data from 'LimeSurvey' (<https://www.limesurvey.org/>) in a comfortable way. Heavily inspired by 'limer' (<https://github.com/cloudyr/limer/>), which lacked a few comfort features for me.
Author: Maximilian Hagspiel [aut, cre, cph]
Maintainer: Maximilian Hagspiel <maxhag@mailbox.org>

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Package curl updated to version 5.2.1 with previous version 5.2.0 dated 2023-12-08

Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other 'libcurl' goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] , Hadley Wickham [ctb], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package nominatimlite updated to version 0.3.0 with previous version 0.2.1 dated 2023-08-15

Title: Interface with 'Nominatim' API Service
Description: Lite interface for getting data from 'OSM' service 'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract coordinates from addresses, find places near a set of coordinates and return spatial objects on 'sf' format.
Author: Diego Hernangomez [aut, cre, cph] , Jindra Lacko [ctb, rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

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Package mlr3mbo updated to version 0.2.2 with previous version 0.2.1 dated 2023-06-05

Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox providing both ready-to-use optimization algorithms as well as their fundamental building blocks allowing for straightforward implementation of custom algorithms. Single- and multi-objective optimization is supported as well as mixed continuous, categorical and conditional search spaces. Moreover, using 'mlr3mbo' for hyperparameter optimization of machine learning models within the 'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use optimization algorithms include Efficient Global Optimization by Jones et al. (1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006) <doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008) <doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] , Jakob Richter [aut] , Marc Becker [aut] , Michel Lang [aut] , Bernd Bischl [aut] , Florian Pfisterer [aut] , Martin Binder [aut], Sebastian Fischer [aut] , Michael H. Buselli [cph], Wessel Dankers [cph], Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>

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Package locfit updated to version 1.5-9.9 with previous version 1.5-9.8 dated 2023-06-11

Title: Local Regression, Likelihood and Density Estimation
Description: Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Author: Catherine Loader [aut], Jiayang Sun [ctb], Lucent Technologies [cph], Andy Liaw [cre]
Maintainer: Andy Liaw <andy_liaw@merck.com>

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Package fda updated to version 6.1.7 with previous version 6.1.4 dated 2023-05-23

Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: James Ramsay [aut, cre], Giles Hooker [ctb], Spencer Graves [ctb]
Maintainer: James Ramsay <ramsay@psych.mcgill.ca>

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Package eRm updated to version 1.0-5 with previous version 1.0-4 dated 2023-09-28

Title: Extended Rasch Modeling
Description: Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, simulation module for various binary data matrices.
Author: Patrick Mair [cre, aut], Thomas Rusch [aut], Reinhold Hatzinger [aut], Marco J. Maier [aut], Rudolf Debelak [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package rts2 updated to version 0.7.1 with previous version 0.6.1 dated 2024-01-25

Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts, and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2020) <arXiv:2004.11408> and the nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>. 'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>

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Package nhstplot updated to version 1.3.0 with previous version 1.2.0 dated 2023-04-11

Title: Plot Null Hypothesis Significance Tests
Description: Illustrate graphically the most common Null Hypothesis Significance Testing procedures. More specifically, this package provides functions to plot Chi-Squared, F, t (one- and two-tailed) and z (one- and two-tailed) tests, by plotting the probability density under the null hypothesis as a function of the different test statistic values. Although highly flexible (color theme, fonts, etc.), only the minimal number of arguments (observed test statistic, degrees of freedom) are necessary for a clear and useful graph to be plotted, with the observed test statistic and the p value, as well as their corresponding value labels. The axes are automatically scaled to present the relevant part and the overall shape of the probability density function. This package is especially intended for education purposes, as it provides a helpful support to help explain the Null Hypothesis Significance Testing process, its use and/or shortcomings.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>

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Package nanonext updated to version 0.13.2 with previous version 0.13.0 dated 2024-02-07

Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library implementing 'Scalability Protocols', a reliable, high-performance standard for common communications patterns including publish/subscribe, request/reply and service discovery, over in-process, IPC, TCP, WebSocket and secure TLS transports. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing, with intuitive 'aio' objects which resolve automatically upon completion of asynchronous operations, and synchronisation primitives allowing R to wait upon events signalled by concurrent threads.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph], R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package csmpv updated to version 1.0.3 with previous version 1.0.1 dated 2024-01-10

Title: Biomarker Confirmation, Selection, Modelling, Prediction, and Validation
Description: There are diverse purposes such as biomarker confirmation, novel biomarker discovery, constructing predictive models, model-based prediction, and validation. It handles binary, continuous, and time-to-event outcomes at the sample or patient level. - Biomarker confirmation utilizes established functions like glm() from 'stats', coxph() from 'survival', surv_fit(), and ggsurvplot() from 'survminer'. - Biomarker discovery and variable selection are facilitated by three LASSO-related functions LASSO2(), LASSO_plus(), and LASSO2plus(), leveraging the 'glmnet' R package with additional steps. - Eight versatile modeling functions are offered, each designed for predictive models across various outcomes and data types. 1) LASSO2(), LASSO_plus(), LASSO2plus(), and LASSO2_reg() perform variable selection using LASSO methods and construct predictive models based on selected variables. 2) XGBtraining() employs 'XGBoost' for model building and is the only function not involving variable selection. 3 [...truncated...]
Author: Aixiang Jiang [aut, cre, cph]
Maintainer: Aixiang Jiang <aijiang@bccrc.ca>

Diff between csmpv versions 1.0.1 dated 2024-01-10 and 1.0.3 dated 2024-03-01

 DESCRIPTION                   |   28 
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Package smacof updated to version 2.1-6 with previous version 2.1-5 dated 2022-05-06

Title: Multidimensional Scaling
Description: Implements the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): ratio/interval/ordinal/spline MDS on symmetric dissimilarity matrices, MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal), MDS with spherical restrictions, and ratio/interval/ordinal/spline unfolding (circular restrictions, row-conditional). Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Patrick J. F. Groenen [aut], Ingwer Borg [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

Diff between smacof versions 2.1-5 dated 2022-05-06 and 2.1-6 dated 2024-03-01

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Package expowo updated to version 2.0 with previous version 1.0 dated 2023-02-22

Title: Data Mining of Plant Diversity and Distribution
Description: Produces diversity estimates and species lists with associated global distribution for any vascular plant family and genus from 'Plants of the World Online' database <https://powo.science.kew.org/>, by interacting with the source code of each plant taxon page. It also creates global maps of species richness, graphics of species discoveries and nomenclatural changes over time.
Author: Debora Zuanny [aut, cre, cph] , Domingos Cardoso [aut, ctb, cph]
Maintainer: Debora Zuanny <deborazuanny@gmail.com>

Diff between expowo versions 1.0 dated 2023-02-22 and 2.0 dated 2024-03-01

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New package wordbankr with initial version 1.0.3
Package: wordbankr
Title: Accessing the Wordbank Database
Description: Connecting to Wordbank, an open repository for developmental vocabulary data. For more information on the underlying data, see <http://wordbank.stanford.edu>.
Version: 1.0.3
Depends: R (>= 4.0)
License: GPL-3
URL: https://langcog.github.io/wordbankr/, https://github.com/langcog/wordbankr/
BugReports: https://github.com/langcog/wordbankr/issues/
Imports: assertthat (>= 0.2.1), DBI (>= 1.1.3), dbplyr (>= 2.3.4), dplyr (>= 1.1.3), glue (>= 1.6.2), jsonlite (>= 1.8.7), lifecycle (>= 1.0.3), purrr (>= 1.0.2), quantregGrowth (>= 1.7-0), rlang (>= 1.1.1), RMySQL (>= 0.10.26), robustbase (>= 0.99-0), stringr (>= 1.5.0), tidyr (>= 1.3.0)
Suggests: ggplot2, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-02-14 18:52:31 UTC; mikabr
Author: Mika Braginsky [aut, cre], Daniel Yurovsky [ctb], Michael Frank [ctb], Danielle Kellier [ctb], Alvin Tan [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-01 16:50:02 UTC

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Package dslabs updated to version 0.8.0 with previous version 0.7.6 dated 2023-07-16

Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>

Diff between dslabs versions 0.7.6 dated 2023-07-16 and 0.8.0 dated 2024-03-01

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Package DIDmultiplegtDYN updated to version 1.0.5 with previous version 1.0.4 dated 2024-02-23

Title: Estimation in Difference-in-Difference Designs with Multiple Groups and Periods
Description: Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.
Author: Diego Ciccia [aut, cre], Felix Knau [aut], Melitine Malezieux [aut], Doulo Sow [aut], Clement de Chaisemartin [aut]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>

Diff between DIDmultiplegtDYN versions 1.0.4 dated 2024-02-23 and 1.0.5 dated 2024-03-01

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 MD5                          |   14 ++++++++------
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 9 files changed, 58 insertions(+), 20 deletions(-)

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New package TropFishR with initial version 1.6.4
Package: TropFishR
Title: Tropical Fisheries Analysis
Version: 1.6.4
Date: 2024-01-29
Author: Tobias K. Mildenberger, Marc H. Taylor, Matthias Wolff
Maintainer: Tobias K. Mildenberger <t.k.mildenberger@gmail.com>
Depends: R (>= 3.0.0)
Imports: Matrix, msm, reshape2, MASS, GenSA, GA, stats, utils, propagate, parallel, doParallel
LazyData: true
Description: A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<https://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.
License: GPL-3
NeedsCompilation: no
BugReports: https://github.com/tokami/TropFishR/issues
URL: https://github.com/tokami/TropFishR
Encoding: UTF-8
Suggests: graphics, grDevices, knitr, rmarkdown, plyr
VignetteBuilder: knitr
Packaged: 2024-02-29 10:59:19 UTC; tobm
Repository: CRAN
Date/Publication: 2024-03-01 15:22:40 UTC

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New package TestsSymmetry with initial version 1.0.0
Package: TestsSymmetry
Title: Tests for Symmetry when the Center of Symmetry is Unknown
Version: 1.0.0
Date: 2024-02-22
Maintainer: Jiaojiao Zhou <woerge99@gmail.com>
Description: Provides functionality of a statistical testing implementation whether a dataset comes from a symmetric distribution when the center of symmetry is unknown, including Wilcoxon test and sign test procedure. In addition, sample size determination for both tests is provided. The Wilcoxon test procedure is described in Vexler et al. (2023) <https://www.sciencedirect.com/science/article/abs/pii/S0167947323000579>, and the sign test is outlined in Gastwirth (1971) <https://www.jstor.org/stable/2284233>.
License: GPL-3
Encoding: UTF-8
Imports: Rcpp, MASS, e1071, rpart
LinkingTo: Rcpp
Depends: R (>= 3.5.0)
LazyData: true
NeedsCompilation: yes
Packaged: 2024-02-29 19:58:36 UTC; jzhou54
Author: Jiaojiao Zhou [aut, cre], Xinyu Gao [aut], Albert Vexler [aut]
Repository: CRAN
Date/Publication: 2024-03-01 15:02:40 UTC

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Package StanHeaders updated to version 2.32.6 with previous version 2.32.5 dated 2024-01-10

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between StanHeaders versions 2.32.5 dated 2024-01-10 and 2.32.6 dated 2024-03-01

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 8 files changed, 23 insertions(+), 22 deletions(-)

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Package shinyWidgets updated to version 0.8.2 with previous version 0.8.1 dated 2024-01-10

Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], David Granjon [aut], Ian Fellows [ctb] , Wil Davis [ctb] , Spencer Matthews [ctb] , JavaScript and CSS libraries authors [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinyWidgets versions 0.8.1 dated 2024-01-10 and 0.8.2 dated 2024-03-01

 DESCRIPTION                                                   |    8 
 MD5                                                           |   79 
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 R/bootstrap-utils.R                                           |  264 +-
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 R/input-airDatepicker.R                                       |    2 
 R/input-awesomeradio.R                                        |   55 
 R/input-search.R                                              |    1 
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 R/module-pickerGroup.R                                        |  606 ++--
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 41 files changed, 5485 insertions(+), 4564 deletions(-)

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New package OmicsQC with initial version 1.1.0
Package: OmicsQC
Title: Nominating Quality Control Outliers in Genomic Profiling Studies
Version: 1.1.0
Description: A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.
Depends: R (>= 2.10)
Imports: stats, utils, fitdistrplus, lsa, BoutrosLab.plotting.general
Suggests: knitr, rmarkdown, kableExtra, dplyr, testthat (>= 3.0.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-29 22:17:18 UTC; helenzhu
Author: Anders Hugo Frelin [aut], Helen Zhu [aut], Paul C. Boutros [aut, cre]
Maintainer: Paul C. Boutros <PBoutros@mednet.ucla.edu>
Repository: CRAN
Date/Publication: 2024-03-01 15:02:43 UTC

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New package habtools with initial version 1.0.5
Package: habtools
Title: Tools and Metrics for 3D Surfaces and Objects
Version: 1.0.5
Description: A collection of functions for sampling and simulating 3D surfaces and objects and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity, second moments of area and volume, and more.
License: MIT + file LICENSE
URL: https://jmadinlab.github.io/habtools/
BugReports: https://github.com/jmadinlab/habtools/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: raster (>= 3.5), terra, methods, Rvcg, sp, geometry, concaveman, magrittr, purrr, dplyr
Suggests: knitr, rmarkdown, rgl, parallel, ggplot2, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-01 00:40:18 UTC; nina
Author: Joshua Madin [aut] , Nina Schiettekatte [aut, cre]
Maintainer: Nina Schiettekatte <nina.schiettekatte@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-01 15:20:02 UTC

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New package ggsankeyfier with initial version 0.1.7
Package: ggsankeyfier
Title: Create Sankey and Alluvial Diagrams Using 'ggplot2'
Version: 0.1.7
Date: 2024-02-29
Author: Pepijn de Vries [aut, cre, dtc] , Gerjan Piet [dtc] , Ruud Jongbloed [dtc] , Anne Grundlehner [dtc] , Jacqueline Tamis [dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Description: Sankey and alluvial diagrams visualise flows of quantities across stages in stacked bars. This package makes it easy to create such diagrams using 'ggplot2'.
Depends: R (>= 4.1.0)
Imports: dplyr, ggplot2 (>= 3.4.4), grid (>= 4.1.0), gridBezier, methods, rlang, scales, stats, tidyr, vwline
Suggests: knitr, rmarkdown, stringr, svglite, testthat (>= 3.0.0), vdiffr
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
URL: https://pepijn-devries.github.io/ggsankeyfier/, https://github.com/pepijn-devries/ggsankeyfier/
BugReports: https://github.com/pepijn-devries/ggsankeyfier/issues
NeedsCompilation: no
Packaged: 2024-02-29 22:38:56 UTC; vries171
Repository: CRAN
Date/Publication: 2024-03-01 15:02:37 UTC

More information about ggsankeyfier at CRAN
Permanent link

Package sonicscrewdriver updated to version 0.0.6 with previous version 0.0.5 dated 2024-02-22

Title: Bioacoustic Analysis and Publication Tools
Description: Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.
Author: Ed Baker [aut, cre] , Quentin Geissman [ctb]
Maintainer: Ed Baker <ed@ebaker.me.uk>

Diff between sonicscrewdriver versions 0.0.5 dated 2024-02-22 and 0.0.6 dated 2024-03-01

 DESCRIPTION                              |    6 
 MD5                                      |  348 ++++++------
 NAMESPACE                                |  350 ++++++-------
 NEWS.md                                  |    7 
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More information about sonicscrewdriver at CRAN
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Package snvecR updated to version 3.9.0 with previous version 3.8.0 dated 2024-01-26

Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the C-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the C-routine is snvec, which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph] , Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>

Diff between snvecR versions 3.8.0 dated 2024-01-26 and 3.9.0 dated 2024-03-01

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New package sccca with initial version 0.1.0
Package: sccca
Title: Single-Cell Correlation Based Cell Type Annotation
Version: 0.1.0
Maintainer: Mohamed Soudy <Mohmedsoudy2009@gmail.com>
Description: Performing cell type annotation based on cell markers from a unified database. The approach utilizes correlation-based approach combined with association analysis using Fisher-exact and phyper statistical tests (Upton, Graham JG. (1992) <DOI:10.2307/2982890>).
License: GPL-3
Encoding: UTF-8
Imports: Seurat, dplyr, plyr
NeedsCompilation: no
Packaged: 2024-02-29 11:16:18 UTC; mohamed.soudy
Author: Mohamed Soudy [aut, cre], Sophie LE BARS [aut], Enrico Glaab [aut]
Repository: CRAN
Date/Publication: 2024-03-01 14:00:06 UTC

More information about sccca at CRAN
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Package readmet updated to version 1.7.1 with previous version 1.6.9 dated 2023-02-11

Title: Read some less Popular Formats Used in Meteorology
Description: Contains tools for reading and writing data from or to files in the formats: akterm, dmna, Scintec Format-1, and Campbell Scientific TOA5.
Author: Clemens Druee, Universitaet Trier
Maintainer: Clemens Druee <druee@uni-trier.de>

Diff between readmet versions 1.6.9 dated 2023-02-11 and 1.7.1 dated 2024-03-01

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New package geneHapR with initial version 1.2.4
Package: geneHapR
Title: Gene Haplotype Statistics, Phenotype Association and Visualization
Description: Import genome variants data and perform gene haplotype Statistics, visualization and phenotype association with 'R'.
Encoding: UTF-8
Maintainer: Zhang Renliang <zhang_renliang@163.com>
Version: 1.2.4
LazyData: True
Imports: ape, Biostrings, ggpubr, genetics, GenomicRanges, lolliplot, maps, methods, IRanges, pegas, reshape2, rlang, rtracklayer, shiny, shinyjs, stats, stringdist, stringr, tibble, sf, tidyr, utils, vcfR
Depends: ggplot2, R (>= 4.0.0)
Suggests: mapdata, knitr, rmarkdown, testthat (>= 3.0.0)
License: GPL-3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-01 12:29:13 UTC; zhang
Author: Zhang Renliang [aut, cre], Jia Guanqing [aut]
Repository: CRAN
Date/Publication: 2024-03-01 14:32:40 UTC

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Permanent link

Package bvhar updated to version 2.0.1 with previous version 2.0.0 dated 2024-02-14

Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to research Bayesian Vector heterogeneous autoregressive (VHAR) model, referring to Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>). 'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph] , Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>

Diff between bvhar versions 2.0.0 dated 2024-02-14 and 2.0.1 dated 2024-03-01

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Package admtools updated to version 0.2.0 with previous version 0.1.0 dated 2023-12-06

Title: Estimate and Manipulate Age-Depth Models
Description: Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>

Diff between admtools versions 0.1.0 dated 2023-12-06 and 0.2.0 dated 2024-03-01

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Package sdetorus updated to version 0.1.10 with previous version 0.1.9 dated 2023-08-20

Title: Statistical Tools for Toroidal Diffusions
Description: Implementation of statistical methods for the estimation of toroidal diffusions. Several diffusive models are provided, most of them belonging to the Langevin family of diffusions on the torus. Specifically, the wrapped normal and von Mises processes are included, which can be seen as toroidal analogues of the Ornstein-Uhlenbeck diffusion. A collection of methods for approximate maximum likelihood estimation, organized in four blocks, is given: (i) based on the exact transition probability density, obtained as the numerical solution to the Fokker-Plank equation; (ii) based on wrapped pseudo-likelihoods; (iii) based on specific analytic approximations by wrapped processes; (iv) based on maximum likelihood of the stationary densities. The package allows the replicability of the results in García-Portugués et al. (2019) <doi:10.1007/s11222-017-9790-2>.
Author: Eduardo Garcia-Portugues [aut, cre]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>

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Package IOHanalyzer updated to version 0.1.8.10 with previous version 0.1.8.6 dated 2023-12-04

Title: Data Analysis Part of 'IOHprofiler'
Description: The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Author: Hao Wang [aut] , Diederick Vermetten [cre, aut] , Carola Doerr [aut] , Thomas Baeck [aut]
Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>

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Package BalancedSampling updated to version 2.0.6 with previous version 2.0.5 dated 2024-02-23

Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method by Grafström, Lundström and Schelin (2012) <doi:10.1111/j.1541-0420.2011.01699.x> and spatially correlated Poisson sampling by Grafström (2012) <doi:10.1016/j.jspi.2011.07.003> are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included, see Grafström and Tillé (2013) <doi:10.1002/env.2194>.
Author: Anton Grafstroem, Jonathan Lisic, Wilmer Prentius
Maintainer: Anton Grafstroem <anton.grafstrom@gmail.com>

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Package SheetReader updated to version 1.2.0 with previous version 1.1.0 dated 2023-05-09

Title: Parse xlsx Files
Description: Uses C++ via the 'Rcpp' package to parse modern Excel files ('.xlsx'). Memory usage is kept minimal by decompressing only parts of the file at a time, while employing multiple threads to achieve significant runtime reduction. Uses <https://github.com/richgel999/miniz> and <https://github.com/lemire/fast_double_parser>.
Author: Felix Henze [aut, cre], Rich Geldreich [ctb, cph] , Daniel Lemire [ctb, cph]
Maintainer: Felix Henze <felixhenze0@gmail.com>

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Package sequoia updated to version 2.9.0 with previous version 2.8.3 dated 2023-12-19

Title: Pedigree Inference from SNPs
Description: Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>

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Package causalBatch updated to version 1.2.0 with previous version 1.1 dated 2024-02-12

Title: Causal Batch Effects
Description: Software which provides numerous functionalities for detecting and removing group-level effects from high-dimensional scientific data which, when combined with additional assumptions, allow for causal conclusions, as-described in our manuscripts Bridgeford et al. (2024) <doi:10.1101/2021.09.03.458920> and Bridgeford et al. (2023) <arXiv:2307.13868>. Also provides a number of useful utilities for generating simulations and balancing covariates across multiple groups/batches of data via matching and propensity trimming for more than two groups.
Author: Eric W. Bridgeford [aut, cre], Michael Powell [ctb], Brian Caffo [ctb], Joshua T. Vogelstein [ctb]
Maintainer: Eric W. Bridgeford <ericwb95@gmail.com>

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Package CalibrationCurves updated to version 2.0.1 with previous version 2.0.0 dated 2023-09-20

Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <arXiv:2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre], Nieboer Daan [aut], Van Calster Ben [aut], Steyerberg Ewout [aut], Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>

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Package CADStat (with last version 3.0.8) was removed from CRAN

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

2017-05-09 3.0.8
2017-04-17 3.0.7

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Package wavScalogram updated to version 1.1.3 with previous version 1.1.2 dated 2022-12-12

Title: Wavelet Scalogram Tools for Time Series Analysis
Description: Provides scalogram based wavelet tools for time series analysis: wavelet power spectrum, scalogram, windowed scalogram, windowed scalogram difference (see Bolos et al. (2017) <doi:10.1016/j.amc.2017.05.046>), scale index and windowed scale index (Benitez et al. (2010) <doi:10.1016/j.camwa.2010.05.010>).
Author: Vicente J. Bolos and Rafael Benitez
Maintainer: Vicente J. Bolos <vicente.bolos@uv.es>

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Package GPUmatrix updated to version 1.0.2 with previous version 1.0.1 dated 2023-12-01

Title: Basic Linear Algebra with GPU
Description: GPUs are great resources for data analysis, especially in statistics and linear algebra. Unfortunately, very few packages connect R to the GPU, and none of them are transparent enough to run the computations on the GPU without substantial changes to the code. The maintenance of these packages is cumbersome: several of the earlier attempts have been removed from their respective repositories. It would be desirable to have a properly maintained R package that takes advantage of the GPU with minimal changes to the existing code. We have developed the GPUmatrix package (available on CRAN). GPUmatrix mimics the behavior of the Matrix package and extends R to use the GPU for computations. It includes single(FP32) and double(FP64) precision data types, and provides support for sparse matrices. It is easy to learn, and requires very few code changes to perform the operations on the GPU. GPUmatrix relies on either the Torch or Tensorflow R packages to perform the GPU operations. We have demonst [...truncated...]
Author: Cesar Lobato-Fernandez [aut, cre], Juan A.Ferrer-Bonsoms [aut], Angel Rubio [aut, ctb]
Maintainer: Cesar Lobato-Fernandez <clobatofern@unav.es>

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Package ggside updated to version 0.3.1 with previous version 0.3.0 dated 2024-02-25

Title: Side Grammar Graphics
Description: The grammar of graphics as shown in 'ggplot2' has provided an expressive API for users to build plots. 'ggside' extends 'ggplot2' by allowing users to add graphical information about one of the main panel's axis using a familiar 'ggplot2' style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.
Author: Justin Landis [aut, cre]
Maintainer: Justin Landis <jtlandis314@gmail.com>

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Package SUMMER updated to version 1.4.0 with previous version 1.3.0 dated 2022-07-08

Title: Small-Area-Estimation Unit/Area Models and Methods for Estimation in R
Description: Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <arXiv:2007.05117>.
Author: Zehang R Li [cre, aut], Bryan D Martin [aut], Yuan Hsiao [aut], Jessica Godwin [aut], John Paige [aut], Peter Gao [aut], Jon Wakefield [aut], Samuel J Clark [aut], Geir-Arne Fuglstad [aut], Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>

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Package shinyMobile updated to version 1.0.1 with previous version 1.0.0 dated 2022-11-25

Title: Mobile Ready 'shiny' Apps with Standalone Capabilities
Description: Develop outstanding 'shiny' apps for 'iOS', 'Android', desktop as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).
Author: David Granjon [aut, cre], Victor Perrier [aut], John Coene [ctb], Isabelle Rudolf [aut], Dieter Menne [ctb], Marvelapp [ctb, cph] , Vladimir Kharlampidi [ctb, cph]
Maintainer: David Granjon <dgranjon@ymail.com>

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More information about shinyMobile at CRAN
Permanent link

Package pointblank updated to version 0.12.0 with previous version 0.11.4 dated 2023-04-25

Title: Data Validation and Organization of Metadata for Local and Remote Tables
Description: Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.
Author: Richard Iannone [aut, cre] , Mauricio Vargas [aut] , June Choe [aut]
Maintainer: Richard Iannone <rich@posit.co>

Diff between pointblank versions 0.11.4 dated 2023-04-25 and 0.12.0 dated 2024-03-01

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 pointblank-0.12.0/pointblank/DESCRIPTION                                           |   25 
 pointblank-0.12.0/pointblank/LICENSE                                               |    4 
 pointblank-0.12.0/pointblank/MD5                                                   |  405 ++++-----
 pointblank-0.12.0/pointblank/NAMESPACE                                             |   10 
 pointblank-0.12.0/pointblank/NEWS.md                                               |   30 
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 pointblank-0.12.0/pointblank/R/col_count_match.R                                   |   86 +-
 pointblank-0.12.0/pointblank/R/col_exists.R                                        |  140 ++-
 pointblank-0.12.0/pointblank/R/col_is_character.R                                  |  111 +-
 pointblank-0.12.0/pointblank/R/col_is_date.R                                       |  111 +-
 pointblank-0.12.0/pointblank/R/col_is_factor.R                                     |  113 +-
 pointblank-0.12.0/pointblank/R/col_is_integer.R                                    |  111 +-
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 pointblank-0.12.0/pointblank/R/col_is_posix.R                                      |  115 +-
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 pointblank-0.12.0/pointblank/R/col_vals_between.R                                  |  152 ++-
 pointblank-0.12.0/pointblank/R/col_vals_decreasing.R                               |  145 ++-
 pointblank-0.12.0/pointblank/R/col_vals_equal.R                                    |  125 +--
 pointblank-0.12.0/pointblank/R/col_vals_expr.R                                     |   85 +-
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 pointblank-0.12.0/pointblank/R/column_roles.R                                      |   32 
 pointblank-0.12.0/pointblank/R/conjointly.R                                        |  167 ++--
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 pointblank-0.12.0/pointblank/R/interrogate.R                                       |  279 +++---
 pointblank-0.12.0/pointblank/R/logging.R                                           |   81 +
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 pointblank-0.12.0/pointblank/R/pipe.R                                              |   32 
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 pointblank-0.12.0/pointblank/R/regex.R                                             |   32 
 pointblank-0.12.0/pointblank/R/remove_deactivate.R                                 |  101 +-
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 pointblank-0.12.0/pointblank/R/scan_data.R                                         |  125 +--
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More information about pointblank at CRAN
Permanent link

Package mclustAddons updated to version 0.8 with previous version 0.7.2 dated 2023-01-06

Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian finite mixture modeling by including: density estimation for data with bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal clustering using MEM (Modal EM) algorithm for Gaussian mixtures (Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via Gaussian mixture modeling (Robin & Scrucca, 2023 <doi:10.1016/j.csda.2022.107582>).
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

Diff between mclustAddons versions 0.7.2 dated 2023-01-06 and 0.8 dated 2024-03-01

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Package secretbase updated to version 0.3.0.1 with previous version 0.3.0 dated 2024-02-21

Title: Cryptographic Hash and Extendable-Output Functions
Description: SHA-256, SHA-3 cryptographic hash and SHAKE256 extendable-output functions (XOF). The SHA-3 Secure Hash Standard was published by the National Institute of Standards and Technology (NIST) in 2015 at <doi:10.6028/NIST.FIPS.202>. The SHA-256 Secure Hash Standard was published by NIST in 2002 at <https://csrc.nist.gov/publications/fips/fips180-2/fips180-2.pdf>. Fast and memory-efficient implementation using the core algorithms from 'Mbed TLS' under the Trusted Firmware Project <https://www.trustedfirmware.org/projects/mbed-tls/>.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

Diff between secretbase versions 0.3.0 dated 2024-02-21 and 0.3.0.1 dated 2024-03-01

 DESCRIPTION   |    6 
 MD5           |   11 -
 NEWS.md       |    4 
 README.md     |   13 -
 src/secret.c  |  391 +---------------------------------------------------------
 src/secret.h  |   15 +-
 src/secret2.c |only
 7 files changed, 35 insertions(+), 405 deletions(-)

More information about secretbase at CRAN
Permanent link

Package filibustr updated to version 0.2.0 with previous version 0.1.1 dated 2024-02-13

Title: Data Utilities for Congressional Research
Description: Provides easy-to-understand and consistent interfaces for accessing data on the U.S. Congress. The functions in 'filibustr' streamline the process for importing data on Congress into R, removing the need to download and work from CSV files and the like. Data sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate website (<https://www.senate.gov/>), and more.
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>

Diff between filibustr versions 0.1.1 dated 2024-02-13 and 0.2.0 dated 2024-03-01

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Package assertive.reflection (with last version 0.0-5) was removed from CRAN

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

2020-07-30 0.0-5

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Package mixreg (with last version 2.0-10) was removed from CRAN

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

2021-10-14 2.0-10
2018-03-31 0.0-6
2014-02-20 0.0-5
2011-11-04 0.0-4
2009-11-04 0.0-3
2006-09-12 0.0-2

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Package rmangal (with last version 2.1.3) was removed from CRAN

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

2023-03-30 2.1.3

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Package coxphMIC (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:

2017-04-26 0.1.0

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Package FamEvent (with last version 3.0) was removed from CRAN

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

2022-11-17 3.0

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Package SCCS (with last version 1.6) was removed from CRAN

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

2022-07-05 1.6

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Package bnClustOmics (with last version 1.1.1) was removed from CRAN

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

2022-08-05 1.1.1
2022-06-10 1.0.9

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Thu, 29 Feb 2024

Package port4me updated to version 0.7.1 with previous version 0.7.0 dated 2024-01-15

Title: Get the Same, Personal, Free 'TCP' Port over and over
Description: An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.
Author: Henrik Bengtsson [aut, cre, cph] , Jeroen Ooms [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package FastJM updated to version 1.4.2 with previous version 1.4.1 dated 2024-01-09

Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>. The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre], Ning Li [ctb], Hong Wang [ctb], Jin Zhou [ctb], Hua Zhou [ctb], Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>

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Package epidatr updated to version 1.1.0 with previous version 1.0.0 dated 2023-09-19

Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut], Dmitry Shemetov [aut], Samuel Gratzl [aut], David Weber [ctb, cre], Alex Reinhart [ctb], Daniel McDonald [ctb], Kean Ming Tan [ctb], Will Townes [ctb], George Haff [ctb], Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>

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Package One4All updated to version 0.4 with previous version 0.3 dated 2024-02-04

Title: Validate, Share, and Download Data
Description: Designed to enhance data validation and management processes by employing a set of functions that read a set of rules from a 'CSV' or 'Excel' file and apply them to a dataset. Funded by the National Renewable Energy Laboratory and Possibility Lab, maintained by the Moore Institute for Plastic Pollution Research.
Author: Hannah Sherrod [cre, aut] , Nick Leong [aut] , Hannah Hapich [aut] , Fabian Gomez [aut], Shelly Moore [aut], Win Cowger [aut] , Scott Coffin [ctb], Tony Hale [ctb], Diana Lin [ctb], Gemma Shusterman [ctb], Rebecca Sutton [ctb], Adam Wong [ctb], Haig [...truncated...]
Maintainer: Hannah Sherrod <hannah@mooreplasticresearch.org>

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Package secr updated to version 4.6.6 with previous version 4.6.5 dated 2024-02-17

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] , Philipp Jund [ctb] ), David Fletcher [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Package qrnn updated to version 2.1.1 with previous version 2.1 dated 2023-04-27

Title: Quantile Regression Neural Network
Description: Fit quantile regression neural network models with optional left censoring, partial monotonicity constraints, generalized additive model constraints, and the ability to fit multiple non-crossing quantile functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005> and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.
Author: Alex J. Cannon [aut, cre]
Maintainer: Alex J. Cannon <alex.cannon@ec.gc.ca>

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Package yuima updated to version 1.15.27 with previous version 1.15.22 dated 2022-12-20

Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>

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Package Surrogate updated to version 3.2.4 with previous version 3.2.2 dated 2024-02-20

Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration (Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut], Florian Stijven [aut], Fenny Ong [aut], Paul Meyvisch [aut], Alvaro Poveda [aut], Ariel Alonso [aut], Hannah Ensor [aut], Christoper Weir [aut], Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>

Diff between Surrogate versions 3.2.2 dated 2024-02-20 and 3.2.4 dated 2024-02-29

 DESCRIPTION                                                                         |    6 
 MD5                                                                                 |   50 
 NEWS.md                                                                             |    9 
 R/CbC.R                                                                             |    2 
 R/ITCI-Dvine-inference-utils.R                                                      |   86 -
 R/fit_model_BinCont_copula.R                                                        |    1 
 R/fit_model_SurvSurv.R                                                              |    2 
 R/goodness_of_fit_SurvSurv.R                                                        |    7 
 R/sensitivity_analysis_BinCont_copula.R                                             |  674 +++++-----
 R/sensitivity_analysis_SurvSurv.R                                                   |   17 
 R/sensitivity_intervals.R                                                           |   21 
 man/fit_copula_model_BinCont.Rd                                                     |    1 
 man/fit_model_SurvSurv.Rd                                                           |    2 
 man/sample_copula_parameters.Rd                                                     |    6 
 man/sensitivity_analysis_BinCont_copula.Rd                                          |   14 
 man/sensitivity_analysis_SurvSurv_copula.Rd                                         |   15 
 man/sensitivity_intervals_Dvine.Rd                                                  |    9 
 man/summary_level_bootstrap_ICA.Rd                                                  |    7 
 tests/testthat/_snaps/fit_model_SurvSurv/plot-function-for-gof.svg                  |    9 
 tests/testthat/_snaps/goodness_of_fit_SurvSurv/mean-surrogate-before-dying-gof.svg  |   10 
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 tests/testthat/test-ITCI-Dvine-inference-utils.R                                    |   17 
 tests/testthat/test-fit_model_SurvSurv.R                                            |    8 
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 tests/testthat/test-sensitivity_analysis_SurvSurv.R                                 |   30 
 tests/testthat/test-sensitivity_intervals.R                                         |   57 
 26 files changed, 646 insertions(+), 505 deletions(-)

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New package specs with initial version 1.0.1
Package: specs
Title: Single-Equation Penalized Error-Correction Selector (SPECS)
Version: 1.0.1
Description: Implementation of SPECS, your favourite Single-Equation Penalized Error-Correction Selector developed in Smeekes and Wijler (2021) <doi:10.1016/j.jeconom.2020.07.021>. SPECS provides a fully automated estimation procedure for large and potentially (co)integrated datasets. The dataset in levels is converted to a conditional error-correction model, either by the user or by means of the functions included in this package, and various specialised forms of penalized regression can be applied to the model. Automated options for initializing and selecting a sequence of penalties, as well as the construction of penalty weights via an initial estimator, are available. Moreover, the user may choose from a number of pre-specified deterministic configurations to further simplify the model building process.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
NeedsCompilation: yes
Packaged: 2024-02-29 19:48:32 UTC; Etienne
Author: Etienne Wijler [aut, cre], Stephan Smeekes [aut]
Maintainer: Etienne Wijler <e.j.j.wijler@vu.nl>
Repository: CRAN
Date/Publication: 2024-02-29 21:10:02 UTC

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Package simhelpers updated to version 0.2.1 with previous version 0.2.0 dated 2024-02-23

Title: Helper Functions for Simulation Studies
Description: Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies. Our derivation and explanation of formulas and our general simulation workflow is closely aligned with the approach described by Morris, White, and Crowther (2019) <DOI:10.1002/sim.8086>.
Author: Megha Joshi [aut, cre] , James Pustejovsky [aut]
Maintainer: Megha Joshi <megha.j456@gmail.com>

Diff between simhelpers versions 0.2.0 dated 2024-02-23 and 0.2.1 dated 2024-02-29

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 8 files changed, 102 insertions(+), 17 deletions(-)

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Package RcppCWB updated to version 0.6.4 with previous version 0.6.3 dated 2023-11-30

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 <http://www.pcre.org/licence.txt>) 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 0.6.3 dated 2023-11-30 and 0.6.4 dated 2024-02-29

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 11 files changed, 420 insertions(+), 287 deletions(-)

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Package namer updated to version 0.1.8 with previous version 0.1.6 dated 2022-10-06

Title: Names Your 'R Markdown' Chunks
Description: It names the 'R Markdown' chunks of files based on the filename.
Author: Colin Gillespie [aut, cre], Steph Locke [aut], Maelle Salmon [aut] , Ellis Valentiner [ctb], Charlie Hadley [ctb] , Jumping Rivers [fnd] , Han Oostdijk [ctb] , Patrick Schratz [ctb]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>

Diff between namer versions 0.1.6 dated 2022-10-06 and 0.1.8 dated 2024-02-29

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Package minimaxApprox updated to version 0.4.1 with previous version 0.4.0 dated 2024-02-26

Title: Implementation of Remez Algorithm for Polynomial and Rational Function Approximation
Description: Implements the algorithm of Remez (1962) for polynomial minimax approximation and of Cody et al. (1968) <doi:10.1007/BF02162506> for rational minimax approximation.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between minimaxApprox versions 0.4.0 dated 2024-02-26 and 0.4.1 dated 2024-02-29

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 6 files changed, 23 insertions(+), 12 deletions(-)

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Package kit updated to version 0.0.16 with previous version 0.0.15 dated 2023-10-01

Title: Data Manipulation Functions Implemented in C
Description: Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.
Author: Morgan Jacob [aut, cre, cph], Sebastian Krantz [ctb]
Maintainer: Morgan Jacob <morgan.emailbox@gmail.com>

Diff between kit versions 0.0.15 dated 2023-10-01 and 0.0.16 dated 2024-02-29

 DESCRIPTION              |    8 ++++----
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 6 files changed, 30 insertions(+), 14 deletions(-)

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Package DIDmultiplegt updated to version 0.1.3 with previous version 0.1.2 dated 2024-02-03

Title: Estimation in DID with Multiple Groups and Periods
Description: Estimate the effect of a treatment on an outcome in sharp Difference-in-Difference designs with multiple groups and periods. It computes the DIDM estimator introduced in Section 4 of "Two-Way Fixed Effects Estimators with Heterogeneous Treatment Effects" (Chaisemartin, D'Haultfoeuille (2020) <doi:10.1257/aer.20181169>), which generalizes the standard DID estimator with two groups, two periods and a binary treatment to situations with many groups,many periods and a potentially non-binary treatment. For each pair of consecutive time periods t-1 and t and for each value of the treatment d, the package computes a DID estimator comparing the outcome evolution among the switchers, the groups whose treatment changes from d to some other value between t-1 and t, to the same evolution among control groups whose treatment is equal to d both in t-1 and t. Then the DIDM estimator is equal to the average of those DIDs across all pairs of consecutive time periods and across all values of the [...truncated...]
Author: Shuo Zhang [aut], Clement de Chaisemartin [aut], Diego Ciccia [cre]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>

Diff between DIDmultiplegt versions 0.1.2 dated 2024-02-03 and 0.1.3 dated 2024-02-29

 DESCRIPTION           |    6 +++---
 MD5                   |    6 +++---
 R/did_multiplegt.R    |    4 ++++
 man/did_multiplegt.Rd |    4 +++-
 4 files changed, 13 insertions(+), 7 deletions(-)

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New package ao with initial version 0.3.3
Package: ao
Title: Alternating Optimization
Version: 0.3.3
Description: Alternating optimization of (high-dimensional) functions is an iterative procedure for optimizing jointly over all parameters by alternately optimizing parameter subsets.
URL: https://loelschlaeger.de/ao/, https://github.com/loelschlaeger/ao/
BugReports: https://github.com/loelschlaeger/ao/issues
License: GPL-3
Encoding: UTF-8
Imports: checkmate, cli, oeli, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 4.0.0), optimizeR (>= 1.0.4)
NeedsCompilation: no
Packaged: 2024-02-29 20:05:27 UTC; Oelschlaeger
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Repository: CRAN
Date/Publication: 2024-02-29 21:12:46 UTC

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New package SemiPar.depCens with initial version 0.1.1
Package: SemiPar.depCens
Title: Copula Based Cox Proportional Hazards Models for Dependent Censoring
Version: 0.1.1
Date: 2024-02-27
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Description: Copula based Cox proportional hazards models for survival data subject to dependent censoring. This approach does not assume that the parameter defining the copula is known. The dependency parameter is estimated with other finite model parameters by maximizing a Pseudo likelihood function. The cumulative hazard function is estimated via estimating equations derived based on martingale ideas. Available copula functions include Frank, Gumbel and Normal copulas. Only Weibull and lognormal models are allowed for the censoring model, even though any parametric model that satisfies certain identifiability conditions could be used. Implemented methods are described in the article "Copula based Cox proportional hazards models for dependent censoring" by Deresa and Van Keilegom (2023) <doi:10.1080/01621459.2022.2161387>.
Imports: survival, copula, stats, foreach, parallel, doParallel, pbivnorm
License: GPL-3
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0)
URL: https://github.com/Nago2020/SemiPar.depCens
BugReports: https://github.com/Nago2020/SemiPar.depCens/issues
NeedsCompilation: no
Packaged: 2024-02-28 23:13:41 UTC; lucp11636
Author: Negera Wakgari Deresa [aut, cre] , Ingrid Van Keilegom [aut]
Repository: CRAN
Date/Publication: 2024-02-29 20:42:46 UTC

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New package roxytypes with initial version 0.1.0
Package: roxytypes
Title: Typed Parameter Tags for Integration with 'roxygen2'
Version: 0.1.0
Description: Provides typed parameter documentation tags for integration with 'roxygen2'. Typed parameter tags provide a consistent interface for annotating expected types for parameters and returned values. Tools for converting from existing styles are also provided to easily adapt projects which implement typed documentation by convention rather than tag. Use the default format or provide your own.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/openpharma/roxytypes, https://openpharma.github.io/roxytypes/
BugReports: https://github.com/openpharma/roxytypes/issues
Imports: utils, cli, glue, roxygen2
Suggests: mockery, testthat
Enhances: roxylint
NeedsCompilation: no
Packaged: 2024-02-28 18:25:38 UTC; root
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Repository: CRAN
Date/Publication: 2024-02-29 20:30:02 UTC

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New package metaConvert with initial version 1.0.0
Package: metaConvert
Title: An Automatic Suite for Estimation of Various Effect Size Measures
Version: 1.0.0
Maintainer: Corentin J. Gosling <corentin.gosling@parisnanterre.fr>
Description: Automatically estimate 11 effect size measures from a well-formatted dataset. Various other functions can help, for example, removing dependency between several effect sizes, or identifying differences between two datasets. This package is mainly designed to assist in conducting a systematic review with a meta-analysis but can be useful to any researcher interested in estimating an effect size.
Imports: compareDF, metafor, estimraw, mvtnorm, numDeriv, rio, utils
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Suggests: testthat (>= 3.0.0), metaumbrella, TOSTER, esc, epiR, compute.es, meta, effectsize, MetaUtility, knitr, DT, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-28 21:57:11 UTC; Corentin Gosling
Author: Corentin J. Gosling [aut, cre], Samuele Cortese [aut], Marco Solmi [aut], Belen Haza [aut], Eduard Vieta [aut], Richard Delorme [aut], Paolo Fusar-Poli [aut], Joaquim Radua [aut]
Repository: CRAN
Date/Publication: 2024-02-29 20:40:02 UTC

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New package JSDNE with initial version 4.2.2
Package: JSDNE
Title: Estimating the Age using Auricular Surface by DNE
Version: 4.2.2
Maintainer: Jisun Jang <jisun.jang.19@ucl.ac.uk>
Description: The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), principal component regression analysis (PCR), and principal component logistic regression analysis (PCLR) methods. The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Imports: dplyr, MASS, molaR, nnet, Rvcg
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-28 20:38:38 UTC; jangj
Author: Jisun Jang [aut, cre]
Repository: CRAN
Date/Publication: 2024-02-29 20:32:39 UTC

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New package dlim with initial version 0.1.0
Package: dlim
Date: 2024-02-25
Title: Distributed Lag Interaction Model
Version: 0.1.0
Description: Collection of functions for fitting and interpreting distributed lag interaction models (DLIM). A DLIM regresses a scalar outcome on repeated measures of exposure and allows for modification by a continuous variable. Includes a dlim() function for fitting, predict() function for inference, and plotting functions for visualization. Details on methodology are described in Demateis et al. (2024) <doi:10.1002/env.2843>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dlnm, ggplot2, mgcv, reshape2, rlang, splines, tsModel, viridis
Depends: R (>= 2.10)
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-29 00:31:34 UTC; ddema
Author: Danielle Demateis [aut, cre] , Kayleigh Keller [aut] , Ander Wilson [aut]
Maintainer: Danielle Demateis <Danielle.Demateis@colostate.edu>
Repository: CRAN
Date/Publication: 2024-02-29 20:42:42 UTC

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New package agcounts with initial version 0.6.6
Package: agcounts
Title: Calculate 'ActiGraph' Counts from Accelerometer Data
Version: 0.6.6
Description: Calculate 'ActiGraph' counts from the X, Y, and Z axes of a triaxial accelerometer. This work was inspired by Neishabouri et al. who published the article "Quantification of Acceleration as Activity Counts in 'ActiGraph' Wearables" on February 24, 2022. The link to the article (<https://pubmed.ncbi.nlm.nih.gov/35831446>) and 'python' implementation of this code (<https://github.com/actigraph/agcounts>).
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Imports: data.table, gsignal, lubridate, magrittr, Rcpp, GGIR, stats, utils, zoo, reticulate, dplyr, stringr, ggplot2, reactable, shiny, bslib, read.gt3x, DBI, RSQLite
Suggests: parallel, devtools, foreach, testthat (>= 3.0.0), shinytest2, covr
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-02-28 18:57:14 UTC; bhelsel
Author: Brian C. Helsel [aut, cre], Paul R. Hibbing [ctb], Robert N. Montgomery [ctb], Eric D. Vidoni [ctb], Jonathan Clutton [ctb], University of Kansas [cph]
Maintainer: Brian C. Helsel <bhelsel@kumc.edu>
Repository: CRAN
Date/Publication: 2024-02-29 20:12:36 UTC

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New package SINRELEF.LD with initial version 1.0.3
Package: SINRELEF.LD
Title: Reliability and Relative Efficiency in Locally-Dependent Measures
Version: 1.0.3
Date: 2024-02-28
Description: Implements an approach aimed at assessing the accuracy and effectiveness of raw scores obtained in scales that contain locally dependent items. The program uses as input the calibration (structural) item estimates obtained from fitting extended unidimensional factor-analytic solutions in which the existing local dependencies are included. Measures of reliability (Omega) and information are proposed at three levels: (a) total score, (b) bivariate-doublet, and (c) item-by-item deletion, and are compared to those that would be obtained if all the items had been locally independent. All the implemented procedures can be obtained from: (a) linear factor-analytic solutions in which the item scores are treated as approximately continuous, and (b) non-linear solutions in which the item scores are treated as ordered-categorical.
Depends: R (>= 3.5)
Imports: stats
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
Packaged: 2024-02-28 13:48:43 UTC; dnava
Author: David Navarro-Gonzalez [aut, cre], Fabia Morales-Vives [aut], Pere J. Ferrando [aut]
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>
Repository: CRAN
Date/Publication: 2024-02-29 19:22:51 UTC

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New package rnaCrosslinkOO with initial version 0.1.2
Package: rnaCrosslinkOO
Title: Analysis of RNA Crosslinking Data
Version: 0.1.2
Maintainer: Jonathan Price <jlp76@cam.ac.uk>
Description: Analysis of RNA crosslinking data for RNA structure prediction. The package is suitable for the analysis of RNA structure cross-linking data and chemical probing data.
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/JLP-BioInf/rnaCrosslinkOO/issues
Depends: seqinr, GenomicRanges, stats
Imports: ggplot2, reshape2, MASS, mixtools, utils, S4Vectors, patchwork, doParallel, igraph, R4RNA, RColorBrewer, IRanges, foreach,grDevices, heatmap3, TopDom, tidyverse, RRNA, ggrepel, methods, parallel, ClassDiscovery
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-28 14:05:35 UTC; jp
Author: Jonathan Price [aut, cre] , Andrew Lim [ctb]
Repository: CRAN
Date/Publication: 2024-02-29 19:20:02 UTC

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New package paleobioDB with initial version 1.0.0
Package: paleobioDB
Title: Download and Process Data from the Paleobiology Database
Version: 1.0.0
Maintainer: Adrian Castro Insua <adrian.castro.insua@uvigo.gal>
Description: Includes functions to wrap most endpoints of the 'PaleobioDB' API and functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>.
License: GPL-2
URL: https://docs.ropensci.org/paleobioDB/, https://github.com/ropensci/paleobioDB
BugReports: https://github.com/ropensci/paleobioDB/issues
Imports: curl, graphics, grDevices, gtools, maps, rjson, terra
Suggests: roxygen2, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-02-28 10:18:18 UTC; aci
Author: Sara Varela [aut] , Javier Gonzalez Hernandez [aut], Luciano Fabris Sgarbi [aut] , Adrian Castro Insua [cre, ctb]
Repository: CRAN
Date/Publication: 2024-02-29 19:20:07 UTC

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Package FactoMineR updated to version 2.10 with previous version 2.9 dated 2023-10-12

Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@institut-agro.fr>

Diff between FactoMineR versions 2.9 dated 2023-10-12 and 2.10 dated 2024-02-29

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 vignettes/FactoMineR.html |  250 +++++++++++--------------------------
 22 files changed, 415 insertions(+), 540 deletions(-)

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New package chouca with initial version 0.0.999
Package: chouca
Title: A Stochastic Cellular Automaton Engine
Version: 0.0.999
Description: An engine for stochastic cellular automata. It provides a high-level interface to declare a model, which can then be simulated by various backends (Genin et al. (2023) <doi:10.1101/2023.11.08.566206>).
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.0.0)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, plyr, digest, stats, graphics, grDevices
Suggests: covr, testthat (>= 3.0.0), deSolve, igraph, knitr, rmarkdown, ggplot2, spatialwarnings
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-02-28 13:38:10 UTC; alex
Author: Alexandre Genin [aut, cre]
Maintainer: Alexandre Genin <a.a.h.genin@uu.nl>
Repository: CRAN
Date/Publication: 2024-02-29 19:22:47 UTC

More information about chouca at CRAN
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Package zdeskR updated to version 0.4.0 with previous version 0.3.0 dated 2023-05-02

Title: Connect to Your 'Zendesk' Data
Description: Facilitates making a connection to the 'Zendesk' API and executing various queries. You can use it to get ticket, ticket metrics, and user data. The 'Zendesk' documentation is available at <https://developer.zendesk.com/rest_api /docs/support/introduction>. This package is not supported by 'Zendesk' (owner of the software).
Author: Chris Umphlett [aut, cre], Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>

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Package lpcde updated to version 0.1.2 with previous version 0.1.1 dated 2023-09-01

Title: Boundary Adaptive Local Polynomial Conditional Density Estimator
Description: Tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024).
Author: Rajita Chandak [aut, cre]
Maintainer: Rajita Chandak <rchandak@princeton.edu>

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Package aRxiv updated to version 0.10 with previous version 0.8 dated 2024-01-22

Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv', a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics.
Author: Karthik Ram [aut] , Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>

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Package r2dii.plot updated to version 0.4.0 with previous version 0.3.1 dated 2023-05-23

Title: Visualize the Climate Scenario Alignment of a Financial Portfolio
Description: Create plots to visualize the alignment of a corporate lending financial portfolio to climate change scenarios based on climate indicators (production and emission intensities) across key climate relevant sectors of the 'PACTA' methodology (Paris Agreement Capital Transition Assessment; <https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre] , Mauro Lepore [aut, ctr] , Alex Axthelm [aut, ctr] , Rocky Mountain Institute [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>

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Package gmvarkit updated to version 2.1.2 with previous version 2.1.1 dated 2024-01-22

Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t mixture vector autoregressive models, quantile residual tests, graphical diagnostics, simulations, forecasting, and estimation of generalized impulse response function and generalized forecast error variance decomposition. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>, Savi Virolainen (forthcoming) <doi:10.1080/07350015.2024.2322090>, Savi Virolainen (2022) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

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Package intendo updated to version 0.1.1 with previous version 0.1 dated 2023-02-22

Title: A Group of Fun Datasets of Various Sizes and Differing Levels of Quality
Description: Four datasets are provided here from the 'Intendo' game 'Super Jetroid'. It is data from the 2015 year of operation and it comprises a revenue table ('all_revenue'), a daily users table ('users_daily'), a user summary table ('user_summary'), and a table with data on all user sessions ('all_sessions'). These core datasets come in different sizes, and, each of them has a variant that was intentionally made faulty (totally riddled with errors and inconsistencies). This suite of tables is useful for testing with packages that focus on data validation and data documentation.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>

Diff between intendo versions 0.1 dated 2023-02-22 and 0.1.1 dated 2024-02-29

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Package hdflex updated to version 0.2.1 with previous version 0.2.0 dated 2023-10-31

Title: High-Dimensional Aggregate Density Forecasts
Description: Provides a forecasting method that maps vast numbers of (scalar-valued) signals of any type into an aggregate density forecast in a time-varying and computationally fast manner. The method proceeds in two steps: First, it transforms a predictive signal into a density forecast. Second, it combines the generated candidate density forecasts into an ultimate density forecast. The methods are explained in detail in Adaemmer et al. (2023) <doi:10.2139/ssrn.4342487>.
Author: Sven Lehmann [aut, cre, cph], Philipp Adaemmer [aut], Rainer Schuessler [aut]
Maintainer: Sven Lehmann <sven.lehmann@uni-rostock.de>

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Package svSocket updated to version 1.1.5 with previous version 1.1.0 dated 2022-05-10

Title: 'SciViews' - Socket Server
Description: A socket server allows to connect clients to R.
Author: Philippe Grosjean [aut, cre] , Matthew Dowle [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>

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Package qrng updated to version 0.0-10 with previous version 0.0-9 dated 2023-04-20

Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in high dimensions.
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>

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Package noise updated to version 1.0.2 with previous version 1.0.1 dated 2021-01-07

Title: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data
Description: Functions to calculate estimates of intrinsic and extrinsic noise from the two-reporter single-cell experiment, as in Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. Functions implement multiple estimators developed for unbiasedness or min Mean Squared Error (MSE) in Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Statistical Applications in Genetics and Molecular Biology, 15(6), 447-471.
Author: Audrey Qiuyan Fu and Lior Pachter
Maintainer: Audrey Q. Fu <audreyqyfu@gmail.com>

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New package tidyheatmaps with initial version 0.2.1
Package: tidyheatmaps
Title: Heatmaps from Tidy Data
Version: 0.2.1
Description: The goal of 'tidyheatmaps' is to simplify the generation of publication-ready heatmaps from tidy data. By offering an interface to the powerful 'pheatmap' package, it allows for the effortless creation of intricate heatmaps with minimal code.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, pheatmap, rlang, grDevices, tidyr, tibble, RColorBrewer
Suggests: testthat (>= 2.1.0), knitr, rmarkdown
URL: https://github.com/jbengler/tidyheatmaps, https://jbengler.github.io/tidyheatmaps/
BugReports: https://github.com/jbengler/tidyheatmaps/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-28 12:54:41 UTC; janbroderengler
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Repository: CRAN
Date/Publication: 2024-02-29 13:00:02 UTC

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Package PUMP updated to version 1.0.3 with previous version 1.0.2 dated 2023-05-22

Title: Power Under Multiplicity Project
Description: Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Author: Kristin Porter [aut], Luke Miratrix [aut, cre] , Kristen Hunter [aut] , Zarni Htet [aut], MDRC [cph], Institute of Education Sciences [fnd]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>

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New package OptGS with initial version 1.2
Package: OptGS
Title: Near-Optimal Group-Sequential Designs for Continuous Outcomes
Version: 1.2
Date: 2024-02-27
Maintainer: James Wason <james.wason@newcastle.ac.uk>
Description: Optimal group-sequential designs minimise some function of the expected and maximum sample size whilst controlling the type I error rate and power at a specified level. 'OptGS' provides functions to quickly search for near-optimal group-sequential designs for normally distributed outcomes. The methods used are described in Wason, JMS (2015) <doi:10.18637/jss.v066.i02>.
License: GPL-2
NeedsCompilation: yes
Packaged: 2024-02-28 13:18:08 UTC; njw228
Author: James Wason [aut, cre], John Burkardt [ctb], R O'Neill [ctb]
Repository: CRAN
Date/Publication: 2024-02-29 13:02:48 UTC

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New package moderate.mediation with initial version 0.0.8
Package: moderate.mediation
Version: 0.0.8
Date: 2024-02-12
Title: Causal Moderated Mediation Analysis
Maintainer: Xu Qin <xuqin@pitt.edu>
Depends: R (>= 3.5.0)
Imports: stats, mvtnorm, cowplot, distr, graphics, ggplot2, reshape2, doSNOW, scales, foreach, earth
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
License: GPL-2
NeedsCompilation: no
Packaged: 2024-02-12 23:32:03 UTC; XUQIN
Author: Xu Qin [aut, cre, cph], Lijuan Wang [ctb]
Repository: CRAN
Date/Publication: 2024-02-29 13:00:05 UTC

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Package Directional updated to version 6.5 with previous version 6.4 dated 2023-12-09

Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <d [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

Diff between Directional versions 6.4 dated 2023-12-09 and 6.5 dated 2024-02-29

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Package Compositional updated to version 6.7 with previous version 6.6 dated 2023-12-09

Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions). The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include: a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. d) Tsagris M. (2015). "Regression analysis with compositional data containing zero values". Chilean Journa [...truncated...]
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut], Abdulaziz Alenazi [ctb], Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

Diff between Compositional versions 6.6 dated 2023-12-09 and 6.7 dated 2024-02-29

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New package SlicedLHD with initial version 1.0
Package: SlicedLHD
Version: 1.0
Date: 2024-02-28
Title: Sliced Latin Hypercube Designs
Author: A Anil Kumar [aut], Baidya Nath Mandal [aut, cre], Rajender Parsad [aut], Sukanta Dash [aut], Mukesh Kumar [aut]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Depends: R (>= 4.3.0)
Description: A facility to generate sliced (orthogonal) Latin hypercube designs with four and five slices. For details about sliced and orthogonal Latin hypercube designs, see Yang, J. F., Lin, C. D., Qian, P. Z., and Lin, D. K. (2013). "Construction of sliced orthogonal Latin hypercube designs". Statistica Sinica, 1117-1130, <doi:10.5705/ss.2012.037>.
Note: This package is developed as part of ongoing Ph.D. (Agricultural Statistics) thesis research work of first author at ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-02-28 12:10:51 UTC; PC
Repository: CRAN
Date/Publication: 2024-02-29 12:42:40 UTC

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New package Lifertable with initial version 0.0.1
Package: Lifertable
Title: Life and Fertility Tables Specially for Insects
Version: 0.0.1
Description: Life and Fertility Tables are appropriate to study the dynamics of arthropods populations. This package provides utilities for constructing Life Tables and Fertility Tables, related demographic parameters, and some simple graphs of interest. It also offers functions to transform the obtained data into a known format for better manipulation. This document is based on the article by Maia, Luiz, and Campanhola "Statistical Inference on Associated Fertility Life Table Parameters Using Jackknife Technique Computational Aspects" (April 2000, Journal of Economic Entomology, Volume 93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Imports: ggplot2, methods, stats, tidyr
Suggests: openxlsx
Depends: R (>= 2.10)
Author: Carlos Abimael Sarmiento Sanchez [aut, cre]
Maintainer: Carlos Abimael Sarmiento Sanchez <cass9918@hotmail.com>
NeedsCompilation: no
Packaged: 2024-02-28 02:07:19 UTC; CASS
Repository: CRAN
Date/Publication: 2024-02-29 12:02:37 UTC

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New package GeneNMF with initial version 0.4.0
Package: GeneNMF
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Version: 0.4.0
Description: A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Depends: R (>= 4.3.0)
Imports: RcppML, NMF, stats, Seurat (>= 4.3.0), cluster, pheatmap, viridis
Suggests: knitr, rmarkdown, fgsea, dplyr, msigdbr
VignetteBuilder: knitr
URL: https://github.com/carmonalab/GeneNMF
BugReports: https://github.com/carmonalab/GeneNMF/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-02-28 08:27:05 UTC; mass
Author: Massimo Andreatta [aut, cre] , Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>
Repository: CRAN
Date/Publication: 2024-02-29 12:22:40 UTC

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Package gausscov updated to version 1.1.0 with previous version 1.0.3 dated 2023-10-11

Title: The Gaussian Covariate Method for Variable Selection
Description: The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper, it is intuitive and requires only four simple equations. Its overwhelming advantage compared with a standard F P-value is that is is exact and valid whatever the data. In contrast F P [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>

Diff between gausscov versions 1.0.3 dated 2023-10-11 and 1.1.0 dated 2024-02-29

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New package COAP with initial version 1.1
Package: COAP
Title: High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model
Version: 1.1
Date: 2024-02-28
Author: Wei Liu [aut, cre], Qingzhi Zhong [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Description: A covariate-augmented overdispersed Poisson factor model is proposed to jointly perform a high-dimensional Poisson factor analysis and estimate a large coefficient matrix for overdispersed count data. More details can be referred to Liu et al. (2024) <doi:10.48550/arXiv.2402.15071>.
License: GPL-3
Depends: irlba, R (>= 3.5.0)
Imports: MASS, stats, Rcpp (>= 1.0.10)
URL: https://github.com/feiyoung/COAP
BugReports: https://github.com/feiyoung/COAP/issues
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-02-28 06:04:26 UTC; Liuxianju
Repository: CRAN
Date/Publication: 2024-02-29 12:22:43 UTC

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Package bbotk updated to version 0.8.0 with previous version 0.7.3 dated 2023-11-13

Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox' package and optimizes every user-defined objective function. The package includes several optimization algorithms e.g. Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning', 'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] , Jakob Richter [aut] , Michel Lang [aut] , Bernd Bischl [aut] , Martin Binder [aut], Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between bbotk versions 0.7.3 dated 2023-11-13 and 0.8.0 dated 2024-02-29

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Package spatstat.random updated to version 3.2-3 with previous version 3.2-2 dated 2023-11-29

Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] , Rolf Turner [aut, cph] , Ege Rubak [aut, cph] , Tilman Davies [aut, cph] , Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.random versions 3.2-2 dated 2023-11-29 and 3.2-3 dated 2024-02-29

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New package normaliseR with initial version 0.1.2
Package: normaliseR
Title: Re-Scale Vectors and Time-Series Features
Version: 0.1.2
Date: 2024-02-28
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Description: Provides standardized access to a range of re-scaling methods for numerical vectors and time-series features calculated within the 'theft' ecosystem.
BugReports: https://github.com/hendersontrent/normaliseR/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: rlang, stats, dplyr, scales
Suggests: knitr, markdown, rmarkdown, pkgdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://hendersontrent.github.io/normaliseR/
NeedsCompilation: no
Packaged: 2024-02-28 00:25:29 UTC; trenthenderson
Author: Trent Henderson [cre, aut]
Repository: CRAN
Date/Publication: 2024-02-29 11:50:02 UTC

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New package multilevelmediation with initial version 0.3.1
Package: multilevelmediation
Title: Utility Functions for Multilevel Mediation Analysis
Version: 0.3.1
Date: 2024-02-27
Maintainer: Carl F. Falk <carl.falk@mcgill.ca>
BugReports: https://github.com/falkcarl/multilevelmediation
Description: The ultimate goal is to support 2-2-1, 2-1-1, and 1-1-1 models for multilevel mediation, the option of a moderating variable for either the a, b, or both paths, and covariates. Currently the 1-1-1 model is supported and several options of random effects; the initial code for bootstrapping was evaluated in simulations by Falk, Vogel, Hammami, and Miočević (2024) <doi:10.3758/s13428-023-02079-4>. Support for Bayesian estimation using 'brms' comprises ongoing work. Currently only continuous mediators and outcomes are supported. Factors for any predictors must be numerically represented.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: furrr, future, matrixcalc, MCMCpack, nlme, parallel, parallelly, stats, tidyr, brms, posterior
Suggests: testthat (>= 3.0.0), boot
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-02-28 00:21:41 UTC; CarlFalkMcGill
Author: Carl F. Falk [cre, aut], Todd Vogel [aut], Sarah Hammami [aut], Milica Miocevic [aut]
Repository: CRAN
Date/Publication: 2024-02-29 11:50:05 UTC

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Package lfe updated to version 3.0-0 with previous version 2.9-0 dated 2023-02-13

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024> Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>). Since version 3.0, it provides dedicated functions to estimate Poisson models.
Author: Simen Gaure [aut] , Grant McDermott [ctb], Mauricio Vargas Sepulveda [ctb, cre] , Karl Dunkle Werner [ctb], Matthieu Stigler [ctb] , Daniel Luedecke [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>

Diff between lfe versions 2.9-0 dated 2023-02-13 and 3.0-0 dated 2024-02-29

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Package predictmeans updated to version 1.1.0 with previous version 1.0.9 dated 2023-10-20

Title: Predicted Means for Linear and Semiparametric Models
Description: Providing functions to diagnose and make inferences from various linear models, such as those obtained from 'aov', 'lm', 'glm', 'gls', 'lme', 'lmer', 'glmmTMB' and 'semireg'. Inferences include predicted means and standard errors, contrasts, multiple comparisons, permutation tests, adjusted R-square and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>

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Package BioM2 updated to version 1.0.4 with previous version 1.0.3 dated 2024-01-10

Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <arXiv:1712.0036v1>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang and Junfang Chen
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>

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Package multilevelcoda (with last version 1.2.1) was removed from CRAN

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

2023-08-13 1.2.1
2023-08-12 1.2.0
2023-06-16 1.1.0

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Package MSoutcomes updated to version 0.2.0 with previous version 0.1.0 dated 2023-09-13

Title: CORe Multiple Sclerosis Outcomes Toolkit
Description: Enable operationalized evaluation of disease outcomes in multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded clinical data structured in long format. The package is based on the research developed at Clinical Outcomes Research unit (CORe), University of Melbourne and Neuroimmunology Centre, Royal Melbourne Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>. Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al. (2022) <doi:10.1111/ene.15406>. Dzau et al. (2023) <doi:10.1136/jnnp-2023-331748>.
Author: Sifat Sharmin [aut], Johannes Lorscheider [aut], Nathaniel Lizak [aut], Sam Harding-Forrester [aut], Winston Dzau [aut], Tomas Kalincik [aut, cre, cph]
Maintainer: Tomas Kalincik <tomas.kalincik@unimelb.edu.au>

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Package AmigaFFH updated to version 0.4.5 with previous version 0.4.3 dated 2023-08-27

Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This package intends to handle many file formats that were native to the antiquated Commodore Amiga machine. This package focuses on file types from the older Amiga operating systems (<= 3.0). It will read and write specific file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

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Package jmastats (with last version 0.2.0) was removed from CRAN

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2023-09-11 0.2.0

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2023-11-24 0.5.3
2023-10-04 0.5.2
2023-06-03 0.5.1
2023-05-29 0.5.0
2022-12-04 0.4.1
2022-09-19 0.4.0
2022-07-11 0.3.0
2022-02-09 0.2.1

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Package RivRetrieve (with last version 0.1.3) was removed from CRAN

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2023-11-14 0.1.3
2023-11-03 0.1.2

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Package jlmerclusterperm (with last version 1.1.2) was removed from CRAN

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2024-02-17 1.1.2
2024-02-08 1.1.1
2023-10-07 1.1.0
2023-09-18 1.0.6
2023-09-10 1.0.5
2023-09-06 1.0.4
2023-07-19 1.0.3
2023-07-15 1.0.2
2023-07-02 1.0.1
2023-06-27 1.0.0

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2024-02-01 2024.1.31
2024-01-24 2024.1.24
2023-04-03 2023.3.31
2023-03-31 2023.3.30
2022-09-19 2022.9.16
2022-08-27 2022.8.25

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Package QTLEMM updated to version 1.5.1 with previous version 1.5.0 dated 2024-01-22

Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, this package comprises several functions designed to execute diverse tasks, such as simulating or analyzing data, calculating significance thresholds, and visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables the fitting and comparison of various statistical models, is employed to analyze the data for estimating QTL parameters. The models encompass linear regression, permutation tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic process is utilized to compute significance thresholds for QTL detection on a genetic linkage map within experimental populations. Two types of data, complete genotyping, and selective genotyping data from various experimental populations, including backcross, F2, recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can be developed based on either utilizin [...truncated...]
Author: Ping-Yuan Chung [cre], Chen-Hung Kao [aut], Y.-T. Guo [aut], H.-N. Ho [aut], H.-I. Lee [aut], P.-Y. Wu [aut], M.-H. Yang [aut], M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>

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Package parallelly updated to version 1.37.1 with previous version 1.37.0 dated 2024-02-14

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

Diff between parallelly versions 1.37.0 dated 2024-02-14 and 1.37.1 dated 2024-02-29

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Package data.table updated to version 1.15.2 with previous version 1.15.0 dated 2024-01-30

Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre], Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut], Toby Hocking [aut] , Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonag [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>

Diff between data.table versions 1.15.0 dated 2024-01-30 and 1.15.2 dated 2024-02-29

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More information about data.table at CRAN
Permanent link

Package VGAM updated to version 1.1-10 with previous version 1.1-9 dated 2023-09-19

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (100+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecolog [...truncated...]
Author: Thomas Yee [aut, cre] , Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

Diff between VGAM versions 1.1-9 dated 2023-09-19 and 1.1-10 dated 2024-02-29

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More information about VGAM at CRAN
Permanent link

Wed, 28 Feb 2024

Package growthPheno updated to version 2.1.24 with previous version 2.1.23 dated 2023-10-24

Title: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
Description: Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

Diff between growthPheno versions 2.1.23 dated 2023-10-24 and 2.1.24 dated 2024-02-28

 DESCRIPTION                        |    9 
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Package farr updated to version 0.3.0 with previous version 0.2.39 dated 2023-12-13

Title: Data and Code for Financial Accounting Research
Description: Handy functions and data to support a course book for accounting research. Gow, Ian and Tongqing Ding (2022) 'Accounting Research: An Introductory Course' <https://iangow.github.io/far_book/>.
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>

Diff between farr versions 0.2.39 dated 2023-12-13 and 0.3.0 dated 2024-02-28

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Package sdmTMB updated to version 0.4.3 with previous version 0.4.2 dated 2024-01-17

Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2022) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] , Eric J. Ward [aut] , Philina A. English [aut] , Lewis A. K. Barnett [aut] , James T. Thorson [aut, cph] , Joe Watson [ctb] , Julia Indivero [ctb] , Jillian C. Dunic [ctb] , Cole C. Monnahan [ctb, cph] , Mollie Brooks [ct [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>

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Package saros updated to version 1.0.4 with previous version 1.0.1 dated 2024-01-26

Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Produces highly customized reports, primarily intended for survey research. Building on 'Quarto' (<https://quarto.org>), it generates draft chapters of all specified dependent/independent variables, which can be further edited by hand, containing figures, tables and analyses (currently only uni-/bivariate tests of equivalent means/proportions). The feature 'mesos'-reports offer tailor-made batch report production where e.g. an institution can compare itself to all other participants. Publication tools are also included, such as password generation for 'mesos'-report sections on a 'Quarto' Website.
Author: Stephan Daus [aut, cre, cph] , Nordic Institute for The Studies of Innovation, Research and Education [fnd], Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>

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Package renv updated to version 1.0.5 with previous version 1.0.4 dated 2024-02-21

Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] , Hadley Wickham [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between renv versions 1.0.4 dated 2024-02-21 and 1.0.5 dated 2024-02-28

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Package tidyclust updated to version 0.2.1 with previous version 0.2.0 dated 2023-09-25

Title: A Common API to Clustering
Description: A common interface to specifying clustering models, in the same style as 'parsnip'. Creates unified interface across different functions and computational engines.
Author: Emil Hvitfeldt [aut, cre] , Kelly Bodwin [aut], Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>

Diff between tidyclust versions 0.2.0 dated 2023-09-25 and 0.2.1 dated 2024-02-28

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Package Seurat updated to version 5.0.2 with previous version 5.0.1 dated 2023-11-17

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] , Saket Choudhary [ctb] , Charlotte Darby [ctb] , Jeff Farrell [ctb], Isabella Grabski [ctb] , Christoph Hafemeister [ctb] , Yuhan Hao [ctb] , Austin Hartman [ctb] , Paul Hoffman [ctb] , Jaison Jain [ctb] , Longda Jiang [ctb] , Ma [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>

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Package gompertztrunc updated to version 0.1.2 with previous version 0.1.1 dated 2022-12-23

Title: Conducting Maximum Likelihood Estimation with Truncated Mortality Data
Description: Estimates hazard ratios and mortality differentials for doubly-truncated data without population denominators. This method is described in Goldstein et al. (2023) <doi:10.1007/s11113-023-09785-z>.
Author: Casey Breen [aut] , Maria Osborne [aut, cre], Joshua R. Goldstein [aut]
Maintainer: Maria Osborne <mariaosborne@berkeley.edu>

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Package DrugUtilisation updated to version 0.5.1 with previous version 0.5.0 dated 2024-02-10

Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] , Mike Du [aut] , Yuchen Guo [aut] , Kim Lopez-Guell [aut] , Edward Burn [ctb] , Xintong Li [ctb] , Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>

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Package colorednoise updated to version 1.1.2 with previous version 1.1.1 dated 2023-09-22

Title: Simulate Temporally Autocorrelated Populations
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one. This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.
Author: July Pilowsky [aut, cre]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>

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Package scCustomize updated to version 2.1.2 with previous version 2.1.1 dated 2024-02-24

Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] , Ming Tang [ctb], Velina Kozareva [ctb], Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>

Diff between scCustomize versions 2.1.1 dated 2024-02-24 and 2.1.2 dated 2024-02-28

 DESCRIPTION                    |    8 ++++----
 MD5                            |   10 +++++-----
 NEWS.md                        |   14 ++++++++++++++
 R/Nebulosa_Plotting.R          |   14 ++++++++++++--
 man/Plot_Density_Custom.Rd     |    2 +-
 man/Plot_Density_Joint_Only.Rd |    2 +-
 6 files changed, 37 insertions(+), 13 deletions(-)

More information about scCustomize at CRAN
Permanent link

Package RcppEigen updated to version 0.3.4.0.0 with previous version 0.3.3.9.4 dated 2023-11-02

Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
Description: R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu; the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppEigen versions 0.3.3.9.4 dated 2023-11-02 and 0.3.4.0.0 dated 2024-02-28

 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/Half.h                                          |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/MathFunctions.h                                 |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/PacketMath.h                                    |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h                                |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/TypeCasting.h                                   |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h                                   |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/LU/arch/Inverse_SSE.h                                          |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSycl.h                          |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclConvertToDeviceExpression.h |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExprConstructor.h           |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractAccessor.h           |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractFunctors.h           |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclLeafCount.h                 |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclPlaceHolderExpr.h           |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclRun.h                       |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclTuple.h                     |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/SimpleThreadPool.h                |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/EmulateCXX11Meta.h                      |only
 RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/CUDA                         |only
 RcppEigen-0.3.4.0.0/RcppEigen/ChangeLog                                                                             |   18 
 RcppEigen-0.3.4.0.0/RcppEigen/DESCRIPTION                                                                           |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/MD5                                                                                   |  812 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/NEWS.Rd                                                                          |   10 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf                                                   |binary
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Cholesky                                                           |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/CholmodSupport                                                     |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Core                                                               |  378 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Eigenvalues                                                        |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Geometry                                                           |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Householder                                                        |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Jacobi                                                             |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/KLUSupport                                                         |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/LU                                                                 |    7 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/OrderingMethods                                                    |    3 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/PaStiXSupport                                                      |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/QR                                                                 |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/QtAlignedMalloc                                                    |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SVD                                                                |    1 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Sparse                                                             |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SparseCholesky                                                     |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SparseLU                                                           |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h                                                |   69 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h                                                 |   62 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h                                |  141 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArithmeticSequence.h                                      |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Array.h                                                   |  110 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArrayBase.h                                               |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArrayWrapper.h                                            |   42 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Assign.h                                                  |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/AssignEvaluator.h                                         |  175 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Assign_MKL.h                                              |   20 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/BandMatrix.h                                              |   32 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Block.h                                                   |  116 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/BooleanRedux.h                                            |   60 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CommaInitializer.h                                        |   10 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CoreEvaluators.h                                          |  597 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CoreIterators.h                                           |    5 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseBinaryOp.h                                           |   43 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseNullaryOp.h                                          |  171 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryOp.h                                            |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryView.h                                          |   22 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseBase.h                                               |  167 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseCoeffsBase.h                                         |   46 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseStorage.h                                            |  218 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Diagonal.h                                                |   44 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalMatrix.h                                          |   52 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalProduct.h                                         |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Dot.h                                                     |   20 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/EigenBase.h                                               |   19 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ForceAlignedAccess.h                                      |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Fuzzy.h                                                   |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GeneralProduct.h                                          |   30 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GenericPacketMath.h                                       |  744 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GlobalFunctions.h                                         |   73 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/IO.h                                                      |   47 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/IndexedView.h                                             |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Inverse.h                                                 |   19 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Map.h                                                     |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h                                                 |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctions.h                                           |  876 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctionsImpl.h                                       |  137 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Matrix.h                                                  |  156 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MatrixBase.h                                              |   21 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NestByValue.h                                             |   75 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NoAlias.h                                                 |    7 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NumTraits.h                                               |  127 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PartialReduxEvaluator.h                                   |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PermutationMatrix.h                                       |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PlainObjectBase.h                                         |  199 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Product.h                                                 |   57 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ProductEvaluators.h                                       |  325 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Random.h                                                  |   38 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Redux.h                                                   |  350 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Ref.h                                                     |  139 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Replicate.h                                               |   16 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Reshaped.h                                                |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ReturnByValue.h                                           |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Reverse.h                                                 |   30 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Select.h                                                  |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SelfAdjointView.h                                         |   53 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Solve.h                                                   |   28 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SolveTriangular.h                                         |   26 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SolverBase.h                                              |   44 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/StableNorm.h                                              |  170 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/StlIterators.h                                            |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Stride.h                                                  |   13 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Swap.h                                                    |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Transpose.h                                               |  113 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Transpositions.h                                          |   34 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/TriangularMatrix.h                                        |  160 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/VectorBlock.h                                             |   10 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/VectorwiseOp.h                                            |  229 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Visitor.h                                                 |  166 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/Complex.h                                        |  179 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/MathFunctions.h                                  |  467 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/PacketMath.h                                     | 1247 ++
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/TypeCasting.h                                    |   66 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/Complex.h                                     |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h                               |  397 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h                                  | 1508 ++-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/TypeCasting.h                                 |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/Complex.h                                    |  317 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MathFunctions.h                              |  270 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProduct.h                              |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h                        |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h                           |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h                                 | 2344 ++++-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/Complex.h                                       |  315 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/BFloat16.h                                   |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/ConjHelper.h                                 |  116 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h                 |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h              |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/Half.h                                       |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/Settings.h                                   |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/TypeCasting.h                                |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/GPU                                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/HIP                                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/MSA                                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h                                       |  536 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h                       |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/MathFunctions.h                                 |  122 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h                                    | 4639 +++++++++-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/TypeCasting.h                                   |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/Complex.h                                        |  238 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h                                  |  495 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/PacketMath.h                                     | 1192 +-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h                                    |   65 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SVE                                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SYCL                                                 |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/Complex.h                                    |  395 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/MathFunctions.h                              |  106 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/PacketMath.h                                 |  883 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/AssignmentFunctors.h                             |   13 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/BinaryFunctors.h                                 |  158 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/NullaryFunctors.h                                |   61 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/StlFunctors.h                                    |   34 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/UnaryFunctors.h                                  |  369 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h                        | 1652 ++-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h                            |   36 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h                  |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h             |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h                            |  895 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/Parallelizer.h                                   |   32 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h                        |   29 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h                        |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointProduct.h                             |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointRank2Update.h                         |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h                         |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h                         |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverVector.h                         |   23 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/BlasUtil.h                                           |  332 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ConfigureVectorization.h                             |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Constants.h                                          |   34 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h                              |   19 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ForwardDeclarations.h                                |   32 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/IndexedViewHelper.h                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/IntegralConstant.h                                   |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/MKL_support.h                                        |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h                                             |  911 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h                                             |  274 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Meta.h                                               |  458 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h                             |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ReshapedHelper.h                                     |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/StaticAssert.h                                       |   13 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/SymbolicIndex.h                                      |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/XprHelper.h                                          |   78 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h                               |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h                                     |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenSolver.h                                      |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h                |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h                          |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h                            |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h                                           |   15 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur.h                                        |   15 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h                           |  117 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h                               |   35 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/AlignedBox.h                                          |  104 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/AngleAxis.h                                           |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/EulerAngles.h                                         |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Homogeneous.h                                         |   26 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Hyperplane.h                                          |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/OrthoMethods.h                                        |    5 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/ParametrizedLine.h                                    |   41 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Quaternion.h                                          |   66 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h                                          |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Scaling.h                                             |   26 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Transform.h                                           |  151 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Translation.h                                         |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SIMD.h                                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h                                 |   11 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/Householder.h                                      |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/HouseholderSequence.h                              |  173 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h                  |   30 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h                              |   30 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h                     |   27 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h                    |   88 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h                         |  111 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h                   |   90 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h          |   22 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h                        |   20 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Jacobi/Jacobi.h                                                |   41 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/KLUSupport                                                     |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/Determinant.h                                               |   54 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/FullPivLU.h                                                 |   72 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/InverseImpl.h                                               |   33 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU.h                                              |  124 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/arch/InverseSize4.h                                         |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Amd.h                                          |   24 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h                                 |  582 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Ordering.h                                     |   16 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h                                  |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/PardisoSupport/PardisoSupport.h                                |   19 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h                                       |   61 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/CompleteOrthogonalDecomposition.h                           |  127 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/FullPivHouseholderQR.h                                      |   81 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR.h                                             |   71 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h                             |   28 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/BDCSVD.h                                                   |  187 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h                                                |   36 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/SVDBase.h                                                  |  103 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/UpperBidiagonalization.h                                   |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h                            |   24 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h                       |   47 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/CompressedStorage.h                                 |   16 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h                   |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h                                      |  108 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseBlock.h                                       |   82 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCompressedBase.h                              |   51 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h                               |   26 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h                                |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h                                |   38 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrix.h                                      |  134 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrixBase.h                                  |   17 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseProduct.h                                     |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseRef.h                                         |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h                             |    3 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseUtil.h                                        |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseVector.h                                      |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU.h                                            |  170 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_Memory.h                                     |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h                           |   78 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_column_dfs.h                                 |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h                                |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h                                 |    2 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseQR/SparseQR.h                                            |   25 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdDeque.h                                          |   16 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdList.h                                           |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdVector.h                                         |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h                                |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h                                |  214 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/misc/lapacke.h                                                 |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h                                  |   28 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h                                   |  166 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/BlockMethods.h                                         |  926 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseUnaryOps.h                                  |   14 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/IndexedViewMethods.h                                   |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h                                 |    8 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h                                  |   10 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ReshapedMethods.h                                      |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AdolcForward                                           |    5 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AlignedVector3                                         |   12 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/ArpackSupport                                          |    9 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AutoDiff                                               |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/BVH                                                    |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/Tensor                                           |   77 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/TensorSymmetry                                   |    6 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/ThreadPool                                       |   21 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/README.md                             |  371 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/Tensor.h                              |   29 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h                        |   78 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h                        |   94 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h                          |  268 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h                         |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h                  |  767 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h                      |  278 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h                 |   84 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h                   |  623 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h           |   41 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h               | 1393 ---
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h                |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h             |  238 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h               |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h         | 1578 ++-
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h                    |  269 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h                   |  190 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h               |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h                     |   10 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h                      |   90 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h                        |   69 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h                    |  337 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h                 |   33 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h                     |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h                    | 1070 ++
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h              |  347 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h                    |  162 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h                        |  111 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h                     |  634 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h                      |  695 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h                          |   23 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h                           |   86 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h                     |   34 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h                    |  190 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h           |   90 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h                      |  191 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h                     |  149 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h             |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h           |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h                    |  164 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h                     |  203 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h                     |   28 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h                   |    4 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h                        |   28 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h                    |   71 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h                        |   52 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h                           |  114 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h                          |  129 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h                      |  568 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h                       |  375 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h                         |   32 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h                        |  198 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h                     |  383 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h                 |  750 -
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h                  |only
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h                 |  746 +
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h                           |   37 
 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h                       |  263 
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 RcppEigen-0.3.4.0.0/RcppEigen/src/fastLm.cpp                                                                        |    4 
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Package ibmsunburst updated to version 0.1.4 with previous version 0.1.3 dated 2023-10-30

Title: Generate Personality Insights Sunburst Diagrams
Description: Generates Personality Insights sunburst diagrams based on 'IBM Watson' Personality Insights service output.
Author: Colin Gillespie [aut, cre], Steph Locke [aut] , IBM [cph] , Hendrik Feddersen [fnd] , Kent Russell [aut], Maelle Salmon [ctb] , Jumping Rivers [fnd]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>

Diff between ibmsunburst versions 0.1.3 dated 2023-10-30 and 0.1.4 dated 2024-02-28

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 MD5                       |    8 ++---
 NEWS.md                   |    4 ++
 build/vignette.rds        |binary
 inst/doc/ibmsunburst.html |   64 +++++++++++++++++++++++-----------------------
 5 files changed, 46 insertions(+), 42 deletions(-)

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New package gscramble with initial version 1.0.1
Package: gscramble
Title: Simulating Admixed Genotypes Without Replacement
Version: 1.0.1
Description: A genomic simulation approach for creating biologically informed individual genotypes from empirical data that 1) samples alleles from populations without replacement, 2) segregates alleles based on species-specific recombination rates. 'gscramble' is a flexible simulation approach that allows users to create pedigrees of varying complexity in order to simulate admixed genotypes. Furthermore, it allows users to track haplotype blocks from the source populations through the pedigrees.
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: dplyr, ggplot2, glue, magrittr, purrr, readr, rlang, stats, stringr, tibble, tidyr
Suggests: cowplot, knitr, rmarkdown, tidyverse
VignetteBuilder: knitr
URL: https://github.com/eriqande/gscramble
BugReports: https://github.com/eriqande/gscramble/issues
NeedsCompilation: no
Packaged: 2024-02-27 23:41:47 UTC; eriq
Author: Eric C. Anderson [aut, cre] , Rachael M. Giglio [aut] , Matt G. DeSaix [aut] , Timothy J. Smyser [aut]
Maintainer: Eric C. Anderson <eric.anderson@noaa.gov>
Repository: CRAN
Date/Publication: 2024-02-28 19:10:05 UTC

More information about gscramble at CRAN
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