CRANberries

Thu, 23 Jan 2025

New package undidR with initial version 1.0.0
Package: undidR
Title: Difference-in-Differences with Unpoolable Data
Version: 1.0.0
Maintainer: Eric Jamieson <ericbrucejamieson@gmail.com>
Description: A framework for estimating difference-in-differences with unpoolable data, based on Karim, Webb, Austin, and Strumpf (2024) <doi:10.48550/arXiv.2403.15910>. Supports common or staggered adoption, multiple groups, and the inclusion of covariates. Also computes p-values for the aggregate average treatment effect on the treated via the randomization inference procedure described in MacKinnon and Webb (2020) <doi:10.1016/j.jeconom.2020.04.024>.
License: MIT + file LICENSE
Depends: R (>= 4.0)
Imports: graphics, grDevices, stats, utils
Encoding: UTF-8
URL: https://github.com/ebjamieson97/undidR, https://ebjamieson97.github.io/undidR/
BugReports: https://github.com/ebjamieson97/undidR/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-22 00:13:41 UTC; Eric Bruce Jamieson
Author: Eric Jamieson [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-01-23 17:30:05 UTC

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New package SlideCNA with initial version 0.1.0
Package: SlideCNA
Title: Calls Copy Number Alterations from Slide-Seq Data
Version: 0.1.0
Description: This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").
Imports: data.table, reshape2, dplyr, ggplot2, scales, pheatmap, cluster, factoextra, dendextend, Seurat, tidyselect, stringr, magrittr, tibble, futile.logger, mltools, utils
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), enrichR (>= 3.0)
NeedsCompilation: no
Packaged: 2025-01-22 04:05:22 UTC; dzhang
Author: Diane Zhang [aut, cre] , Johanna Klughammer [aut] , Jan Watter [aut] , Broad Institute of MIT and Harvard [cph, fnd]
Maintainer: Diane Zhang <dkzhang711@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-23 17:40:05 UTC

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New package pattern.checks with initial version 0.1.0
Package: pattern.checks
Title: Identifies Patterned Responses in Scales
Version: 0.1.0
Description: Identifies the entries with patterned responses for psychometric scales. The patterns included in the package are identical (a, a, a), ascending (a, b, c), descending (c, b, a), alternative (a, b, a, b / a, b, c, a, b, c).
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-22 04:48:03 UTC; JZL
Author: JASEEL C K [aut, cre]
Maintainer: JASEEL C K <jzlckclt@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-23 17:40:01 UTC

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New package ncaavolleyballr with initial version 0.4.1
Package: ncaavolleyballr
Title: Extract Data from NCAA Women's and Men's Volleyball Website
Version: 0.4.1
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Description: Extracts team records/schedules and player statistics for the 2020-2024 National Collegiate Athletic Association (NCAA) women's and men's divisions I, II, and III volleyball teams from <https://stats.ncaa.org>. Functions can aggregate statistics for teams, conferences, divisions, or custom groups of teams.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
Imports: cli, curl, dplyr, httr2, lifecycle, purrr, rlang, rvest, stringr, tibble, tidyr, xml2
Suggests: knitr, quarto, testthat (>= 3.0.0)
URL: https://github.com/JeffreyRStevens/ncaavolleyballr, https://jeffreyrstevens.github.io/ncaavolleyballr/
BugReports: https://github.com/JeffreyRStevens/ncaavolleyballr/issues
VignetteBuilder: quarto
NeedsCompilation: no
Packaged: 2025-01-21 23:47:24 UTC; jstevens
Author: Jeffrey R. Stevens [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-01-23 17:30:09 UTC

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New package grec with initial version 1.6.1
Package: grec
Title: Gradient-Based Recognition of Spatial Patterns in Environmental Data
Version: 1.6.1
Date: 2025-01-22
URL: https://github.com/LuisLauM/grec
BugReports: https://github.com/LuisLauM/grec/issues
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Description: Provides algorithms for detection of spatial patterns from oceanographic data using image processing methods based on Gradient Recognition.
License: GPL (>= 3)
Depends: R (>= 3.2.0)
Imports: utils, imagine (>= 2.1.2), raster, terra, abind, lifecycle
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-22 09:09:09 UTC; llaumedr
Author: Wencheng Lau-Medrano [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-23 09:30:02 UTC

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New package depower with initial version 2025.1.20
Package: depower
Title: Power Analysis for Differential Expression Studies
Version: 2025.1.20
Description: Provides a convenient framework to simulate, test, power, and visualize data for differential expression studies with lognormal or negative binomial outcomes. Supported designs are two-sample comparisons of independent or dependent outcomes. Power may be summarized in the context of controlling the per-family error rate or family-wise error rate. Negative binomial methods are described in Yu, Fernandez, and Brock (2017) <doi:10.1186/s12859-017-1648-2> and Yu, Fernandez, and Brock (2020) <doi:10.1186/s12859-020-3541-7>.
URL: https://brettklamer.com/work/depower/, https://bitbucket.org/bklamer/depower/
License: MIT + file LICENSE
Depends: R (>= 4.2.0)
Imports: Rdpack, stats, mvnfast, glmmTMB, dplyr, multidplyr, ggplot2, scales
Suggests: tinytest, rmarkdown
Language: en-US
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-21 00:00:00 UTC; x
Author: Brett Klamer [aut, cre] , Lianbo Yu [aut]
Maintainer: Brett Klamer <code@brettklamer.com>
Repository: CRAN
Date/Publication: 2025-01-23 09:50:02 UTC

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Wed, 22 Jan 2025

New package bootStateSpace with initial version 1.0.1
Package: bootStateSpace
Title: Bootstrap for State Space Models
Version: 1.0.1
Description: Provides a streamlined and user-friendly framework for bootstrapping in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
URL: https://github.com/jeksterslab/bootStateSpace, https://jeksterslab.github.io/bootStateSpace/
BugReports: https://github.com/jeksterslab/bootStateSpace/issues
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: stats, simStateSpace, dynr
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2025-01-21 17:10:18 UTC; root
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-22 18:30:02 UTC

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New package retimer with initial version 0.1.3
Package: retimer
Title: Retime and Analyse Speech Signals
Version: 0.1.3
Description: Retime speech signals with a native Waveform Similarity Overlap-Add (WSOLA) implementation translated from the 'TSM toolbox' by Driedger & Müller (2014) <https://www.audiolabs-erlangen.de/content/resources/MIR/TSMtoolbox/2014_DriedgerMueller_TSM-Toolbox_DAFX.pdf>. Design retimings and pitch (f0) transformations with tidy data and apply them via 'Praat' interface. Produce spectrograms, spectra, and amplitude envelopes. Includes implementation of vocalic speech envelope analysis (fft_spectrum) technique and example data (mm1) from Tilsen, S., & Johnson, K. (2008) <doi:10.1121/1.2947626>.
Depends: R (>= 4.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: rPraat, purrr, dplyr, tibble, tidyr, tuneR, ggplot2, stringr, signal, gsignal, methods, seewave, phonTools
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-21 11:55:20 UTC; alistairbeith
Author: Alistair Beith [aut, cre, cph]
Maintainer: Alistair Beith <alistair.beith@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-22 17:20:02 UTC

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New package presmoothedTP with initial version 0.1.0
Package: presmoothedTP
Title: Presmoothed Landmark Aalen-Johansen Estimator of Transition Probabilities for Complex Multi-State Models
Version: 0.1.0
Description: Multi-state models are essential tools in longitudinal data analysis. One primary goal of these models is the estimation of transition probabilities, a critical metric for predicting clinical prognosis across various stages of diseases or medical conditions. Traditionally, inference in multi-state models relies on the Aalen-Johansen (AJ) estimator which is consistent under the Markov assumption. However, in many practical applications, the Markovian nature of the process is often not guaranteed, limiting the applicability of the AJ estimator in more complex scenarios. This package extends the landmark Aalen-Johansen estimator (Putter, H, Spitoni, C (2018) <doi:10.1177/0962280216674497>) incorporating presmoothing techniques described by Soutinho, Meira-Machado and Oliveira (2020) <doi:10.1080/03610918.2020.1762895>, offering a robust alternative for estimating transition probabilities in non-Markovian multi-state models with multiple states and potential reversible transiti [...truncated...]
License: GPL-3
Depends: R (>= 3.5.0)
Imports: survival, mstate, plyr
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
Packaged: 2025-01-20 21:07:03 UTC; AEFH
Author: Gustavo Soutinho [aut, cre] , Luis Meira-Machado [aut]
Maintainer: Gustavo Soutinho <gustavosoutinho@sapo.pt>
Repository: CRAN
Date/Publication: 2025-01-22 17:10:02 UTC

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New package heiscore.data with initial version 0.0.1
Package: heiscore.data
Title: Data Only Package to 'heiscore'
Version: 0.0.1
Description: Contains the National Health and Nutrition Examination Survey 24-hour dietary recall data and Healthy Eating Index scoring standards used by the 'heiscore' package.
License: CC0
Depends: R (>= 3.5)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2025-01-21 01:15:58 UTC; vijetharamdas
Author: Vijetha Ramdas [aut, cre], Berkeley Ho [aut], Abhra Sarkar [aut]
Maintainer: Vijetha Ramdas <vramdas06@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-22 17:10:05 UTC

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New package pxmake with initial version 0.14.2
Package: pxmake
Title: Make PX-Files in R
Version: 0.14.2
Description: Create PX-files from scratch or read and modify existing ones. Includes a function for every PX keyword, making metadata manipulation simple and human-readable.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: arrow, dplyr, furrr, magrittr, methods, openxlsx, purrr, readxl, rlang, stats, stringi, stringr, tibble, tidyr, tools, utils, vctrs
Suggests: knitr, rmarkdown, withr, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
LazyData: true
URL: https://github.com/StatisticsGreenland/pxmake, https://statisticsgreenland.github.io/pxmake/
BugReports: https://github.com/StatisticsGreenland/pxmake/issues
NeedsCompilation: no
Packaged: 2025-01-20 14:30:22 UTC; Johan Ejstrud
Author: Johan Ejstrud [cre, aut], Lars Pedersen [aut], Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Repository: CRAN
Date/Publication: 2025-01-22 16:50:02 UTC

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New package finna with initial version 0.1.1
Package: finna
Title: Access the 'Finna' API
Version: 0.1.1
Date: 2025-01-10
Maintainer: Akewak Jeba <akjeba@utu.fi>
Description: Provides functions to access and retrieve metadata from the 'Finna' API <https://api.finna.fi/>, which aggregates content from Finnish archives, libraries, and museums.
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
Imports: dplyr, glue, httr, xml2, jsonlite, ggplot2, readr, tibble, curl, progress, purrr
Suggests: testthat (>= 3.0.0), rmarkdown, knitr
URL: https://ropengov.github.io/finna/, https://CRAN.R-project.org/package=finna
BugReports: https://github.com/rOpenGov/finna/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-20 16:01:40 UTC; akasia
Author: Akewak Jeba [aut, cre] , Leo Lahti [aut]
Repository: CRAN
Date/Publication: 2025-01-22 16:50:07 UTC

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New package sacRebleu with initial version 0.2.0
Package: sacRebleu
Title: Metrics for Assessing the Quality of Generated Text
Version: 0.2.0
Date: 2025-01-19
Description: Implementation of the BLEU-Score in 'C++' to evaluate the quality of generated text. The BLEU-Score, introduced by Papineni et al. (2002) <doi:10.3115/1073083.1073135>, is a metric for evaluating the quality of generated text. It is based on the n-gram overlap between the generated text and reference texts. Additionally, the package provides some smoothing methods as described in Chen and Cherry (2014) <doi:10.3115/v1/W14-3346>.
License: GPL (>= 2)
SystemRequirements: libclang/llvm-config
Depends: R (>= 4.2.0)
Imports: checkmate, Rcpp (>= 1.0.12)
LinkingTo: Rcpp
URL: https://github.com/LazerLambda/sacRebleu
BugReports: https://github.com/LazerLambda/sacRebleu/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vctrs, withr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2025-01-21 18:15:29 UTC; philko
Author: Philipp Koch [aut, cre]
Maintainer: Philipp Koch <PhillKoch@protonmail.com>
Repository: CRAN
Date/Publication: 2025-01-22 08:10:02 UTC

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New package blockTools with initial version 0.6.6
Package: blockTools
Title: Block, Assign, and Diagnose Potential Interference in Randomized Experiments
Version: 0.6.6
Date: 2025-01-21
Description: Blocks units into experimental blocks, with one unit per treatment condition, by creating a measure of multivariate distance between all possible pairs of units. Maximum, minimum, or an allowable range of differences between units on one variable can be set. Randomly assign units to treatment conditions. Diagnose potential interference between units assigned to different treatment conditions. Write outputs to .tex and .csv files. For more information on the methods implemented, see Moore (2012) <doi:10.1093/pan/mps025>.
License: GPL (>= 2) | file LICENSE
Encoding: UTF-8
Imports: dplyr, MASS, tibble
Suggests: nbpMatching, RItools, testthat (>= 3.0.0), xtable
Depends: R (>= 3.5.0)
URL: https://www.ryantmoore.org/html/software.blockTools.html
NeedsCompilation: yes
Packaged: 2025-01-21 16:37:19 UTC; rtm
Author: Ryan T. Moore [aut, cre] , Keith Schnakenberg [aut]
Maintainer: Ryan T. Moore <rtm@american.edu>
Repository: CRAN
Date/Publication: 2025-01-22 08:10:05 UTC

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Tue, 21 Jan 2025

New package setariaviridis with initial version 0.1.0
Package: setariaviridis
Title: Field-Collected Data of Green Foxtail
Version: 0.1.0
Description: Setaria viridis (green foxtail) is a common weed. This package contains measurements from individual branches of a wild Setaria viridis plant collected near the author's home. The data is intended for use in data analysis practice.
License: MIT + file LICENSE
URL: https://github.com/NONONOexe/setariaviridis, https://nononoexe.github.io/setariaviridis/
BugReports: https://github.com/NONONOexe/setariaviridis/issues
Depends: R (>= 3.5)
Encoding: UTF-8
LazyData: true
Suggests: spelling
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-20 11:20:29 UTC; nononoexe
Author: Keisuke Ando [aut, cre]
Maintainer: Keisuke Ando <ando@maslab.aitech.ac.jp>
Repository: CRAN
Date/Publication: 2025-01-21 16:00:02 UTC

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New package readapra with initial version 0.2.0
Package: readapra
Title: Download and Tidy Data from the Australian Prudential Regulation Authority
Version: 0.2.0
Description: Download the latest data from the Australian Prudential Regulation Authority <https://www.apra.gov.au/> and import it into R as a tidy data frame.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: openxlsx, readr, testthat (>= 3.0.0), webmockr, withr
URL: https://github.com/javanderwal/readapra
BugReports: https://github.com/javanderwal/readapra/issues
Imports: cli (>= 3.0.0), dplyr (>= 1.0.0), httr (>= 1.0.0), janitor, lubridate (>= 1.0.0), memoise, polite (>= 0.1.0), purrr (>= 1.0.0), ratelimitr, rlang (>= 1.0.0), robotstxt, rvest (>= 1.0.0), stringdist, stringr (>= 1.0.0), tibble (>= 2.0.0), tidyr (>= 1.0.0), tidyselect (>= 1.0.0), tidyxl (>= 1.0.0), utils
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2025-01-20 02:01:30 UTC; jarva
Author: Jarrod van der Wal [aut, cre, cph]
Maintainer: Jarrod van der Wal <jarvanderwal@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-21 15:50:02 UTC

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New package MiscMath with initial version 1.0
Package: MiscMath
Title: Miscellaneous Mathematical Tools
Version: 1.0
Description: Some basic math calculators for finding angles for triangles and for finding the greatest common divisor of two numbers and so on.
LazyLoad: true
License: GPL (>= 2)
Depends: randomForest
NeedsCompilation: yes
Author: W.J. Braun [aut, cre]
Maintainer: W.J. Braun <john.braun@ubc.ca>
Packaged: 2025-01-19 01:17:55 UTC; johbraun
Repository: CRAN
Date/Publication: 2025-01-21 15:30:06 UTC

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New package metabodecon with initial version 1.2.6
Package: metabodecon
Title: Deconvolution and Alignment of 1d NMR Spectra
Version: 1.2.6
Description: A framework for deconvolution, alignment and postprocessing of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in a data matrix of aligned signal integrals. The deconvolution part uses the algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>. The alignment part is based on functions from the 'speaq' package, described in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al. (2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in Haeckl et al. (2021) <doi:10.3390/metabo11070452>.
License: GPL (>= 3)
URL: https://github.com/spang-lab/metabodecon/, https://spang-lab.github.io/metabodecon/
BugReports: https://github.com/spang-lab/metabodecon/issues
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: data.table, mathjaxr, readJDX, speaq, toscutil (>= 2.8.0), withr
Suggests: devtools, digest, knitr, lifecycle, microbenchmark, pkgload, rmarkdown, usethis, vdiffr, testthat (>= 3.0.0)
LazyData: true
BuildManual: TRUE
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-20 12:14:18 UTC; tschmidt
Author: Tobias Schmidt [aut, cre, cph], Martina Haeckl [aut, cph], Yanren Linda Hu [ctb], Wolfram Gronwald [aut, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-21 16:00:06 UTC

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New package dMrs with initial version 1.0.0
Package: dMrs
Title: Competing Risk in Dependent Net Survival Analysis
Version: 1.0.0
Date: 2025-01-09
Description: Provides statistical tools for analyzing net and relative survival, with a key feature of relaxing the assumption of independent censoring and incorporating the effect of dependent competing risks. It employs a copula-based methodology, specifically the Archimedean copula, to simulate data, conduct survival analysis, and offer comparisons with other methods. This approach is detailed in the work of Adatorwovor et al. (2022) <doi:10.1515/ijb-2021-0016>.
Encoding: UTF-8
Imports: methods, Rcpp, Rmpfr, copula, gplots, ggplot2, viridis, sqldf, data.table, relsurv
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, markdown
VignetteBuilder: knitr
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2025-01-19 06:03:35 UTC; Admin
Author: Reuben Adatorwovor [aut], Paul Little [cre]
Maintainer: Paul Little <pllittle321@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-21 15:40:05 UTC

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New package bdsm with initial version 0.1.0
Package: bdsm
Title: Bayesian Dynamic Systems Modeling
Version: 0.1.0
Description: Implements methods for building and analyzing models based on panel data as described in the paper by Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>). The package provides functions to estimate dynamic panel data models and analyze the results of the estimation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: spelling, testthat (>= 3.0.0)
Imports: dplyr, magrittr, optimbase, parallel, rje, rlang, rootSolve, stats, tidyr, tidyselect
Depends: R (>= 2.10)
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-18 20:49:43 UTC; marcindubel
Author: Mateusz Wyszynski [aut], Marcin Dubel [ctb, cre], Krzysztof Beck [ctb]
Maintainer: Marcin Dubel <marcindubel@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-21 15:30:02 UTC

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New package streetscape with initial version 1.0.5
Package: streetscape
Title: Collect and Investigate Street Views for Urban Science
Version: 1.0.5
Description: A collection of functions to search and download street view imagery ('Mapilary' <https://www.mapillary.com/developer/api-documentation>) and to extract, quantify, and visualize visual features. Moreover, there are functions provided to generate Qualtrics survey in TXT format using the collection of street views for various research purposes.
License: GPL-3
Depends: R (>= 4.1)
Language: en-US
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Imports: rlang, cli, methods, dplyr, sf, sp, httr, reticulate, osmdata, quickPWCR, mapview, SuperpixelImageSegmentation, OpenImageR, pbmcapply, parallelly
NeedsCompilation: no
Packaged: 2025-01-21 14:10:34 UTC; yangxiaohao
Author: Xiaohao Yang [aut, cre, cph], Derek Van Berkel [aut], Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Repository: CRAN
Date/Publication: 2025-01-21 14:50:03 UTC

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New package BOJ with initial version 0.3.4
Package: BOJ
Title: Interface to Bank of Japan Statistics
Version: 0.3.4
Description: Provides an interface to Bank of Japan <https://www.boj.or.jp> statistics.
License: MIT + file LICENSE
URL: https://github.com/stefanangrick/BOJ
BugReports: https://github.com/stefanangrick/BOJ/issues
Suggests: knitr, rmarkdown, ggplot2, zoo
Imports: dplyr, readr, tidyr, tidyselect, rvest, xml2
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-02 08:05:31 UTC; qwerty
Author: Stefan Angrick [aut, cre, cph]
Maintainer: Stefan Angrick <contact@stefanangrick.net>
Repository: CRAN
Date/Publication: 2025-01-19 11:10:02 UTC

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Mon, 20 Jan 2025

New package micer with initial version 0.2.0
Package: micer
Title: Map Image Classification Efficacy
Version: 0.2.0
Date: 2025-01-05
Maintainer: Aaron Maxwell <Aaron.Maxwell@mail.wvu.edu>
Description: Map image classification efficacy (MICE) adjusts the accuracy rate relative to a random classification baseline (Shao et al. (2021)<doi:10.1109/ACCESS.2021.3116526> and Tang et al. (2024)<doi:10.1109/TGRS.2024.3446950>). Only the proportions from the reference labels are considered, as opposed to the proportions from the reference and predictions, as is the case for the Kappa statistic. This package offers means to calculate MICE and adjusted versions of class-level user's accuracy (i.e., precision) and producer's accuracy (i.e., recall) and F1-scores. Class-level metrics are aggregated using macro-averaging. Functions are also made available to estimate confidence intervals using bootstrapping and statistically compare two classification results.
Depends: R (>= 2.10)
Imports: dplyr (>= 1.1.3),
License: GPL (>= 3)
URL: https://github.com/maxwell-geospatial/micer
BugReports: https://github.com/maxwell-geospatial/micer/issues
NeedsCompilation: no
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2025-01-18 02:30:32 UTC; vidcg
Author: Aaron Maxwell [aut, cre, cph], Sarah Farhadpour [aut]
Repository: CRAN
Date/Publication: 2025-01-20 21:00:01 UTC

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New package flexFitR with initial version 1.0.0
Package: flexFitR
Title: Flexible Non-Linear Least Square Model Fitting
Version: 1.0.0
Maintainer: Johan Aparicio <aparicioarce@wisc.edu>
Description: Provides tools for flexible non-linear least squares model fitting using general-purpose optimization techniques. The package supports a variety of optimization algorithms, including those provided by the 'optimx' package, making it suitable for handling complex non-linear models. Features include parallel processing support via the 'future' and 'foreach' packages, comprehensive model diagnostics, and visualization capabilities. Implements methods described in Nash and Varadhan (2011, <doi:10.18637/jss.v043.i09>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Author: Johan Aparicio [cre, aut], Jeffrey Endelman [aut], University of Wisconsin Madison [cph]
Imports: agriutilities, doFuture, dplyr, foreach, future, ggplot2, numDeriv, optimx, progressr, rlang, subplex, tibble, tidyr
URL: https://apariciojohan.github.io/flexFitR/, https://github.com/AparicioJohan/flexFitR
BugReports: https://github.com/AparicioJohan/flexFitR/issues
Suggests: BB, dfoptim, ggpubr, kableExtra, knitr, lbfgsb3c, marqLevAlg, purrr, rmarkdown, ucminf
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-17 19:54:01 UTC; johan
Repository: CRAN
Date/Publication: 2025-01-20 17:01:56 UTC

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New package sysAgNPs with initial version 1.0.0
Package: sysAgNPs
Title: Systematic Quantification of AgNPs to Unleash their Potential for Applicability
Version: 1.0.0
Description: There is variation across AgNPs due to differences in characterization techniques and testing metrics employed in studies. To address this problem, we have developed a systematic evaluation framework called 'sysAgNPs'. Within this framework, Distribution Entropy (DE) is utilized to measure the uncertainty of feature categories of AgNPs, Proclivity Entropy (PE) assesses the preference of these categories, and Combination Entropy (CE) quantifies the uncertainty of feature combinations of AgNPs. Additionally, a Markov chain model is employed to examine the relationships among the sub-features of AgNPs and to determine a Transition Score (TS) scoring standard that is based on steady-state probabilities. The 'sysAgNPs' framework provides metrics for evaluating AgNPs, which helps to unravel their complexity and facilitates effective comparisons among different AgNPs, thereby advancing the scientific research and application of these AgNPs.
License: GPL (>= 3)
Language: en-US
Encoding: UTF-8
LazyData: true
URL: https://github.com/xitingwang-ida/sysAgNPs
Imports: dplyr, expm, ggplot2, ggpubr, magrittr, patchwork, purrr, rio, tibble, tidyr, rlang, RColorBrewer, forcats, stats
NeedsCompilation: no
Packaged: 2025-01-17 14:46:13 UTC; pc
Author: Xiting Wang [aut, cre] , Longfei Mao [aut, cph] , Jiamin Hu [ctb]
Maintainer: Xiting Wang <XitingWang2023@outlook.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-01-20 16:20:02 UTC

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New package SLOS with initial version 1.0.0
Package: SLOS
Title: ICU Length of Stay Prediction and Efficiency Evaluation
Version: 1.0.0
Maintainer: Joana da Matta <joana.damatta02@gmail.com>
Description: Provides tools for predicting ICU length of stay and assessing ICU efficiency. It is based on the methodologies proposed by Peres et al. (2022, 2023), which utilize data-driven approaches for modeling and validation, offering insights into ICU performance and patient outcomes. References: Peres et al. (2022)<https://pubmed.ncbi.nlm.nih.gov/35988701/>, Peres et al. (2023)<https://pubmed.ncbi.nlm.nih.gov/37922007/>. More information: <https://github.com/igor-peres/ICU-Length-of-Stay-Prediction>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, MLmetrics, ems, dplyr, ggplot2, magrittr, caretEnsemble, ranger
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-01-17 12:12:52 UTC; jodamatta
Depends: R (>= 3.5.0)
Author: Igor Peres [aut], Joana da Matta [cre]
Repository: CRAN
Date/Publication: 2025-01-20 16:02:03 UTC

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New package rollupTree with initial version 0.1.0
Package: rollupTree
Title: Perform Recursive Computations
Version: 0.1.0
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
Imports: igraph
Depends: R (>= 3.5)
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://jsjuni.github.io/rollupTree/, https://github.com/jsjuni/rollupTree
BugReports: https://github.com/jsjuni/rollupTree/issues
NeedsCompilation: no
Packaged: 2025-01-17 14:40:46 UTC; sjenkins
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Repository: CRAN
Date/Publication: 2025-01-20 16:20:05 UTC

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New package gomp with initial version 1.0
Package: gomp
Title: The gamma-OMP Feature Selection Algorithm
Version: 1.0
Date: 2025-01-11
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: doParallel, foreach, Hmisc, MASS, nnet, ordinal, parallel, quantreg, Rfast, Rfast2, stats, survival
Suggests: dcorVS
Description: The gamma-Orthogonal Matching Pursuit (gamma-OMP) is a recently suggested modification of the OMP feature selection algorithm for a wide range of response variables. The package offers many alternative regression models, such linear, robust, survival, multivariate etc., including k-fold cross-validation. References: Tsagris M., Papadovasilakis Z., Lakiotaki K. and Tsamardinos I. (2018). "Efficient feature selection on gene expression data: Which algorithm to use?" BioRxiv. <doi:10.1101/431734>. Tsagris M., Papadovasilakis Z., Lakiotaki K. and Tsamardinos I. (2022). "The gamma-OMP algorithm for feature selection with application to gene expression data". IEEE/ACM Transactions on Computational Biology and Bioinformatics 19(2): 1214--1224. <doi:10.1109/TCBB.2020.3029952>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-01-11 11:49:10 UTC; mtsag
Repository: CRAN
Date/Publication: 2025-01-20 16:02:00 UTC

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New package EHRmuse with initial version 0.0.2.0
Package: EHRmuse
Title: Multi-Cohort Selection Bias Correction using IPW and AIPW Methods
Version: 0.0.2.0
Description: Comprehensive toolkit for addressing selection bias in binary disease models across diverse non-probability samples, each with unique selection mechanisms. It utilizes Inverse Probability Weighting (IPW) and Augmented Inverse Probability Weighting (AIPW) methods to reduce selection bias effectively in multiple non-probability cohorts by integrating data from either individual-level or summary-level external sources. The package also provides a variety of variance estimation techniques. Please refer to Kundu et al. <doi:10.48550/arXiv.2412.00228>.
License: GPL (>= 2)
URL: https://github.com/Ritoban1/EHRmuse
BugReports: https://github.com/Ritoban1/EHRmuse/issues
Depends: R (>= 4.0.0)
Imports: dplyr (>= 1.0.0), magrittr, MASS, nleqslv (>= 3.3.2), xgboost (>= 1.4.1), survey (>= 4.1.0), stats, nnet (>= 7.3-17), simplexreg (>= 0.1.6)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-17 14:47:35 UTC; mk
Author: Ritoban Kundu [aut], Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Repository: CRAN
Date/Publication: 2025-01-20 16:20:13 UTC

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New package ComBatFamQC with initial version 1.0.2
Package: ComBatFamQC
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Version: 1.0.2
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
License: MIT + file LICENSE
URL: https://github.com/Zheng206/ComBatFamQC, https://zheng206.github.io/ComBatQC-Web/
BugReports: https://github.com/Zheng206/ComBatFamQC/issues
Encoding: UTF-8
Imports: tidyr, dplyr, magrittr, ggplot2, DT, shiny, car, broom, pbkrtest, parallel, Rtsne, MDMR, gamlss, lme4, mgcv, bslib, shinydashboard, methods, gamlss.dist, invgamma, openxlsx
Depends: R (>= 3.5.0)
LazyData: true
Suggests: knitr, rmarkdown, devtools, testthat (>= 3.0.0), remotes, shinytest2, plotly, quarto, spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-17 22:55:37 UTC; zhengren
Author: Zheng Ren [aut, cre, cph] , Andrew Chen [aut, cph] , Elizabeth Horwath [ctb]
Maintainer: Zheng Ren <zren1422@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-20 16:44:12 UTC

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New package CoDaLoMic with initial version 0.1.0
Package: CoDaLoMic
Title: Compositional Models to Longitudinal Microbiome Data
Version: 0.1.0
Author: Irene Creus Marti [aut, cre]
Maintainer: Irene Creus Marti <ircrmar@mat.upv.es>
Description: Implementation of models to analyse compositional microbiome time series taking into account the interaction between groups of bacteria. The models implemented are described in Creus-Martí et al (2018, ISBN:978-84-09-07541-6), Creus-Martí et al (2021) <doi:10.1155/2021/9951817> and Creus-Martí et al (2022) <doi:10.1155/2022/4907527>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: xtable, ggplot2, reshape2, compositions, MASS, broom, R2jags, ggbiplot, zCompositions
Suggests: testthat (>= 3.0.0), gtools, knitr, parallel, base
NeedsCompilation: no
Packaged: 2025-01-17 18:53:04 UTC; IRENE
Repository: CRAN
Date/Publication: 2025-01-20 16:44:16 UTC

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New package AMISforInfectiousDiseases with initial version 0.1.0
Package: AMISforInfectiousDiseases
Title: Implement the AMIS Algorithm for Infectious Disease Models
Version: 0.1.0
Description: Implements the Adaptive Multiple Importance Sampling (AMIS) algorithm, as described by Retkute et al. (2021, <doi:10.1214/21-AOAS1486>), to estimate key epidemiological parameters by combining outputs from a geostatistical model of infectious diseases (such as prevalence, incidence, or relative risk) with a disease transmission model. Utilising the resulting posterior distributions, the package enables forward projections at the local level.
Acknowledgements: This work was supported by the NTD Modelling Consortium grant INV-030046, funded by the Bill & Melinda Gates Foundation.
Encoding: UTF-8
Imports: Hmisc, mclust, mnormt, Rcpp, weights
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.1)
Suggests: knitr, ggplot2, patchwork, rmarkdown, sf, viridis
VignetteBuilder: knitr
URL: https://github.com/drsimonspencer/AMISforInfectiousDiseases-dev
BugReports: https://github.com/drsimonspencer/AMISforInfectiousDiseases-dev/issues
License: MIT + file LICENSE
NeedsCompilation: yes
Packaged: 2025-01-17 05:58:43 UTC; evandro
Author: Evandro Konzen [aut] , Renata Retkute [aut] , Raiha Browning [aut] , Thilbault Lestang [aut], Simon Spencer [aut, cre] , University of Warwick [cph], Oxford Research Software Engineering [cph]
Maintainer: Simon Spencer <s.e.f.spencer@warwick.ac.uk>
Repository: CRAN
Date/Publication: 2025-01-20 16:02:05 UTC

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New package admiralmetabolic with initial version 0.1.0
Package: admiralmetabolic
Title: Metabolism Extension Package for ADaM in 'R' Asset Library
Version: 0.1.0
Description: A toolbox for programming Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>). The package is an extension package of the 'admiral' package focusing on the metabolism therapeutic area.
License: Apache License (>= 2)
URL: https://pharmaverse.github.io/admiralmetabolic/, https://github.com/pharmaverse/admiralmetabolic
BugReports: https://github.com/pharmaverse/admiralmetabolic/issues
Depends: R (>= 4.1)
Imports: admiral (>= 1.1.1), admiraldev (>= 1.0.0), cli (>= 3.6.2), dplyr (>= 0.8.4), stringr (>= 1.4.0), lifecycle (>= 0.1.0), lubridate (>= 1.7.4), magrittr (>= 1.5), purrr (>= 0.3.3), rlang (>= 0.4.4), tidyselect (>= 1.0.0)
Suggests: diffdf, DT, htmltools, knitr, methods, pharmaversesdtm (>= 1.0.0), rmarkdown, testthat (>= 3.0.0), tibble, usethis (>= 2.2.3)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-17 13:57:46 UTC; IAKD
Author: Anders Askeland [aut, cre] , Andrii Yurovskyi [aut] , Kathrin Flunkert [aut], Edoardo Mancini [aut] , Shunsuke Goto [aut], Siddhesh Pujari [aut] , Sonali Das [aut], Olga Starostecka [aut], Vang Le-Quy [aut]
Maintainer: Anders Askeland <iakd@novonordisk.com>
Repository: CRAN
Date/Publication: 2025-01-20 16:20:09 UTC

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Sat, 18 Jan 2025

New package windfarmGA with initial version 4.0.0
Package: windfarmGA
Title: Genetic Algorithm for Wind Farm Layout Optimization
Version: 4.0.0
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Description: The genetic algorithm is designed to optimize wind farms of any shape. It requires a predefined amount of turbines, a unified rotor radius and an average wind speed value for each incoming wind direction. A terrain effect model can be included that downloads an 'SRTM' elevation model and loads a Corine Land Cover raster to approximate surface roughness.
Depends: R (>= 4.1.0)
Imports: Rcpp, terra, sf, RColorBrewer, calibrate, grDevices, graphics, magrittr, methods, stats, utils
LinkingTo: Rcpp
LazyData: TRUE
License: MIT + file LICENSE
URL: https://ysosirius.github.io/windfarmGA/index.html
BugReports: https://github.com/YsoSirius/windfarmGA/issues
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), foreach, parallel, doParallel, progress, stars, raster, leaflet, elevatr (>= 0.99.0), ggplot2, gstat, rworldmap
NeedsCompilation: yes
Packaged: 2025-01-18 09:24:17 UTC; kona1
Author: Sebastian Gatscha [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-01-18 11:00:02 UTC

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Fri, 17 Jan 2025

New package tidyfit with initial version 0.7.3
Package: tidyfit
Title: Regularized Linear Modeling with Tidy Data
Date: 2025-01-14
Version: 0.7.3
Author: Johann Pfitzinger [aut, cre]
Maintainer: Johann Pfitzinger <johann.pfitzinger@gmail.com>
Description: An extension to the 'R' tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://tidyfit.residualmetrics.com, https://github.com/jpfitzinger/tidyfit
Depends: R (>= 3.5)
Imports: broom, crayon, dials, dplyr, furrr, generics, magrittr, MASS, methods, progressr, purrr, rlang, rsample, stats, tibble, tidyr, utils, vctrs, yardstick
Suggests: arm, bestglm, BMS, BoomSpikeSlab, CORElearn, e1071, gaselect, gets, gglasso, ggplot2, glmnet, hfr, iml, kableExtra, knitr, lme4, lmtest, lubridate, markdown, mboost, monomvn, mRMRe, MSwM, nnet, pls, quantreg, quantregForest, randomForest, sandwich, sensitivity, shrinkTVP, stringr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-14 19:48:21 UTC; johann
Repository: CRAN
Date/Publication: 2025-01-17 15:00:02 UTC

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New package unhcrdown with initial version 0.6.0
Package: unhcrdown
Title: UNHCR Branded Templates for R Markdown Documents
Version: 0.6.0
Description: Create United Nations High Commissioner for Refugees (UNHCR) branded documents, presentations, and reports using R Markdown templates. This package provides customized formats that align with UNHCR's official brand guidelines for creating professional PDF reports, Word documents, PowerPoint presentations, and HTML outputs.
License: MIT + file LICENSE
URL: https://github.com/unhcr-dataviz/unhcrdown, https://unhcr-dataviz.github.io/unhcrdown/
BugReports: https://github.com/unhcr-dataviz/unhcrdown/issues
Imports: bslib, magick, officedown, pagedown, rmarkdown, xaringan
Suggests: fontawesome, knitr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-17 09:09:16 UTC; cvidonne
Author: Cedric Vidonne [aut, cre], Ahmadou Dicko [aut], Edouard Legoupil [aut], UNHCR [cph]
Maintainer: Cedric Vidonne <cedric@vidonne.me>
Repository: CRAN
Date/Publication: 2025-01-17 12:10:05 UTC

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New package veesa with initial version 0.1.6
Package: veesa
Title: Pipeline for Explainable Machine Learning with Functional Data
Version: 0.1.6
Description: Implements the Variable importance Explainable Elastic Shape Analysis pipeline for explainable machine learning with functional data inputs. Converts training and testing data functional inputs to elastic shape analysis principal components that account for vertical and/or horizontal variability. Computes feature importance to identify important principal components and visualizes variability captured by functional principal components. See Goode et al. (2025) <doi:10.48550/arXiv.2501.07602> for technical details about the methodology.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: dplyr, fdasrvf, forcats, ggplot2, purrr, stats, stringr, tidyr
Suggests: randomForest, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-01-16 21:07:54 UTC; kjgoode
Author: Katherine Goode [cre, aut], J. Derek Tucker [aut], Sandia National Laboratories [cph, fnd]
Maintainer: Katherine Goode <kjgoode@sandia.gov>
Repository: CRAN
Date/Publication: 2025-01-17 10:10:01 UTC

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New package rtables.officer with initial version 0.0.2
Package: rtables.officer
Title: Exporting Tools for 'rtables'
Version: 0.0.2
Date: 2025-01-14
Description: Designed to create and display complex tables with R, the 'rtables' R package allows cells in an 'rtables' object to contain any high-dimensional data structure, which can then be displayed with cell-specific formatting instructions. Additionally, the 'rtables.officer' package supports export formats related to the Microsoft Office software suite, including Microsoft Word ('docx') and Microsoft PowerPoint ('pptx').
License: Apache License 2.0
URL: https://github.com/insightsengineering/rtables.officer, https://insightsengineering.github.io/rtables.officer/
BugReports: https://github.com/insightsengineering/rtables.officer/issues
Depends: formatters (>= 0.5.10), magrittr (>= 1.5), methods, R (>= 2.10), rtables (>= 0.6.11)
Imports: checkmate (>= 2.1.0), flextable (>= 0.9.6), lifecycle (>= 0.2.0), officer (>= 0.6.6), stats, stringi (>= 1.6)
Suggests: broom (>= 1.0.5), car (>= 3.0-13), dplyr (>= 1.0.5), knitr (>= 1.42), r2rtf (>= 0.3.2), rmarkdown (>= 2.23), survival (>= 3.3-1), testthat (>= 3.0.4), tibble (>= 3.2.1), tidyr (>= 1.1.3), withr (>= 2.0.0), xml2 (>= 1.1.0)
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-17 01:47:22 UTC; rstudio
Author: Gabriel Becker [ctb], Davide Garolini [aut], Emily de la Rua [aut], Abinaya Yogasekaram [aut], Joe Zhu [aut, cre] , F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Repository: CRAN
Date/Publication: 2025-01-17 10:50:01 UTC

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New package MonotonicityTest with initial version 1.0
Package: MonotonicityTest
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Version: 1.0
Description: Implements nonparametric bootstrap tests for detecting monotonicity in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363> Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports efficient computation with 'C++'.
License: GPL
Encoding: UTF-8
LinkingTo: Rcpp, RcppEigen
Imports: Rcpp (>= 1.0.13-1), parallel, stats, graphics, ggplot2 (>= 3.0.0), rlang
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2025-01-16 22:04:57 UTC; dylanh
Repository: CRAN
Date/Publication: 2025-01-17 10:30:02 UTC

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New package zephyr with initial version 0.1.0
Package: zephyr
Title: Structured Messages and Options
Version: 0.1.0
Description: Provides a structured framework for consistent user communication and configuration management for package developers.
License: Apache License (>= 2)
URL: https://novonordisk-opensource.github.io/zephyr/, https://github.com/novonordisk-opensource/zephyr
BugReports: https://github.com/novonordisk-opensource/zephyr/issues
Depends: R (>= 4.1)
Imports: cli, glue, rlang (>= 1.0.0)
Suggests: callr, checkmate, devtools, knitr, rmarkdown, testthat (>= 3.1.5), usethis, withr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-16 13:15:02 UTC; oath
Author: Aksel Thomsen [aut, cre], Mathias Lerbech Jeppesen [aut], Cervan Girard [aut], Kristian Troejelsgaard [aut], Lovemore Gakava [aut], Steffen Falgreen Larsen [aut], Vladimir Obucina [aut], Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Repository: CRAN
Date/Publication: 2025-01-17 09:10:02 UTC

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New package chartreview with initial version 1.0
Package: chartreview
Title: Adaptive Multi-Wave Sampling for Efficient Chart Validation
Version: 1.0
Date: 2025-01-14
Author: Georg Hahn [aut, cre], Sebastian Schneeweiss [ctb], Shirley Wang [ctb]
Maintainer: Georg Hahn <ghahn@bwh.harvard.edu>
Description: Functionality to perform adaptive multi-wave sampling for efficient chart validation. Code allows one to define strata, adaptively sample using several types of confidence bounds for the quantity of interest (Lai's confidence bands, Bayesian credible intervals, normal confidence intervals), and sampling strategies (random sampling, stratified random sampling, Neyman's sampling, see Neyman (1934) <doi:10.2307/2342192> and Neyman (1938) <doi:10.1080/01621459.1938.10503378>).
License: GPL (>= 2)
Encoding: UTF-8
Imports: Rdpack, anesrake, weights, grDevices, graphics, methods, stats
NeedsCompilation: no
Packaged: 2025-01-16 15:52:10 UTC; acer
Repository: CRAN
Date/Publication: 2025-01-17 09:20:02 UTC

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New package SeedMaker with initial version 1.0.0
Package: SeedMaker
Title: Generate a Collection of Seeds from a Single Seed
Version: 1.0.0
Description: A mechanism for easily generating and organizing a collection of seeds from a single seed, which may be subsequently used to ensure reproducibility in processes/pipelines that utilize multiple random components (e.g., trial simulation).
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: devtools (>= 2.4.5), knitr (>= 1.45), rmarkdown (>= 2.25), testthat (>= 3.2.0), usethis (>= 2.2.2)
Imports: checkmate (>= 2.3.0), dplyr (>= 1.1.4), rlang (>= 1.1.2), tibble (>= 3.2.1), tidyr (>= 1.3.0)
URL: https://github.com/hdhshowalter/SeedMaker
BugReports: https://github.com/hdhshowalter/SeedMaker/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-16 12:10:26 UTC; r865461
Author: Hollins Showalter [aut, cre], Eli Lilly and Company [cph, fnd]
Maintainer: Hollins Showalter <hollins.showalter@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-17 09:00:02 UTC

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New package duet with initial version 0.1.1
Package: duet
Title: Analysing Non-Verbal Communication in Dyadic Interactions from Video Data
Version: 0.1.1
Description: Analyzes non-verbal communication by processing data extracted from video recordings of dyadic interactions. It supports integration with open source tools, currently limited to 'OpenPose' (Cao et al. (2019) <doi:10.1109/TPAMI.2019.2929257>), converting its outputs into CSV format for further analysis. The package includes functions for data pre-processing, visualization, and computation of motion indices such as velocity, acceleration, and jerkiness (Cook et al. (2013) <doi:10.1093/brain/awt208>), facilitating the analysis of non-verbal cues in paired interactions and contributing to research on human communication dynamics.
License: MIT + file LICENSE
SystemRequirements: FFmpeg (https://ffmpeg.org/)
Imports: dplyr, ggplot2, ggthemes, graphics, grDevices, kza, parallel, patchwork, reshape2, rjson, rlang, signal, stats, stringr, tidyr, tidyselect, tools, utils, zoo
Suggests: spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-16 11:32:32 UTC; tefthimi
Author: Themis Efthimiou [aut, cre]
Maintainer: Themis Efthimiou <themiftw20@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-17 08:50:02 UTC

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Thu, 16 Jan 2025

New package smer with initial version 0.0.1
Package: smer
Title: Sparse Marginal Epistasis Test
Version: 0.0.1
URL: https://github.com/lcrawlab/sme, https://lcrawlab.github.io/sme/
BugReports: https://github.com/lcrawlab/sme/issues
Description: The Sparse Marginal Epistasis Test is a computationally efficient genetics method which detects statistical epistasis in complex traits; see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.
License: MIT + file LICENSE
Encoding: UTF-8
LinkingTo: BH, Rcpp, RcppEigen, Rhdf5lib, testthat
Imports: dplyr, genio, logging, mvMAPIT, Rcpp, tidyr
Suggests: GenomicRanges, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0), xml2
SystemRequirements: GNU make
VignetteBuilder: knitr
Depends: R (>= 4.4.0)
LazyData: true
NeedsCompilation: yes
Packaged: 2025-01-16 07:09:10 UTC; jds
Author: Julian Stamp [cre, aut] , Lorin Crawford [aut] , sriramlab [cph] , Blue Brain Project/EPFL [cph]
Maintainer: Julian Stamp <julian.d.stamp@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-16 15:50:01 UTC

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New package SiFINeT with initial version 1.13
Package: SiFINeT
Title: Single Cell Feature Identification with Network Topology
Version: 1.13
Date: 2025-01-01
Author: Qi Gao [aut, cre]
Maintainer: Qi Gao <gqi@med.umich.edu>
Description: Cluster-independent method based on topology structure of gene co-expression network for identifying feature gene sets, extracting cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Without prior cell clustering, SifiNet circumvents potential inaccuracies in clustering that may influence subsequent analyses. This method is introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan, Jichun Xie "SifiNet: a robust and accurate method to identify feature gene sets and annotate cells" (2024) <doi:10.1093/nar/gkae307>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: yes
BuildVignettes: yes
VignetteBuilder: knitr
Depends: R (>= 3.6.0), methods, utils, stats
Imports: Rcpp (>= 1.0.9), quantreg (>= 5.94), igraph (>= 1.3.5), Matrix (>= 1.5-1), ggraph (>= 2.0.6), ggplot2 (>= 3.3.6),
Suggests: rmarkdown (>= 2.20), knitr (>= 1.42)
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2025-01-15 22:31:46 UTC; gqi
Repository: CRAN
Date/Publication: 2025-01-16 15:10:05 UTC

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New package shiny.ollama with initial version 0.1.0
Package: shiny.ollama
Version: 0.1.0
Title: R 'Shiny' Interface for Chatting with Large Language Models Offline on Local with 'ollama'
Description: Chat with large language models on your machine without internet with complete privacy via 'ollama', powered by R shiny interface. For more information on 'ollama', visit <https://ollama.com>.
Maintainer: Indraneel Chakraborty <hello.indraneel@gmail.com>
License: Apache License (>= 2)
URL: https://www.indraneelchakraborty.com/shiny.ollama/, https://github.com/ineelhere/shiny.ollama
BugReports: https://github.com/ineelhere/shiny.ollama/issues
Encoding: UTF-8
Imports: shiny (>= 1.7.0), bslib (>= 0.4.0), httr (>= 1.4.0), jsonlite (>= 1.8.0), markdown, mockery
Depends: R (>= 3.5.0)
Suggests: testthat (>= 3.0.0), pkgdown (>= 2.0.0)
Date: 2025-01-12
NeedsCompilation: no
Packaged: 2025-01-16 04:15:33 UTC; neel0
Author: Indraneel Chakraborty [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-16 15:40:02 UTC

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New package phylosignalDB with initial version 0.2.2
Package: phylosignalDB
Title: Explore Phylogenetic Signals Using Distance-Based Methods
Version: 0.2.2
Description: A unified method, called M statistic, is provided for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) <doi:10.1046/j.1420-9101.2002.00472.x> provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic. Also, there are more distance-based methods under development.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.0)
LazyData: true
Imports: ape (>= 5.7), castor (>= 1.8.3), cluster (>= 2.1.6), doParallel (>= 1.0.17), foreach (>= 1.5.2)
URL: https://github.com/anonymous-eco/phylosignalDB
BugReports: https://github.com/anonymous-eco/phylosignalDB/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-01-16 06:38:55 UTC; YE YUAN
Author: Liang Yao [aut, cre], Ye Yuan [aut]
Maintainer: Liang Yao <dylanyao@126.com>
Repository: CRAN
Date/Publication: 2025-01-16 15:40:05 UTC

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New package drugsens with initial version 0.1.0
Package: drugsens
Title: Automated Analysis of 'QuPath' Output Data and Metadata Extraction
Description: A comprehensive toolkit for analyzing microscopy data output from 'QuPath' software. Provides functionality for automated data processing, metadata extraction, and statistical analysis of imaging results. The methodology implemented in this package is based on Labrosse et al. (2024) <doi:10.1016/j.xpro.2024.103274> "Protocol for quantifying drug sensitivity in 3D patient-derived ovarian cancer models", which describes the complete workflow for drug sensitivity analysis in patient-derived cancer models.
Version: 0.1.0
BugReports: https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues
SystemRequirements: QuPath™ 4.0.0 or higher
URL: https://git.scicore.unibas.ch/ovca-research/drugsens/
Maintainer: Flavio Lombardo <flavio.lombardo@unibas.ch>
License: MIT + file LICENSE
Imports: dplyr, ggplot2, ggpubr, knitr, roxygen2, stats, stringr, tidyr, tidyselect, utils, testthat (>= 3.0.0)
Depends: R (>= 4.2)
Encoding: UTF-8
Suggests:
NeedsCompilation: no
Packaged: 2025-01-15 21:52:50 UTC; flalom
Author: Flavio Lombardo [aut, cre, cph] , Ricardo Coelho [cph], Ovarian Cancer Research [cph], University of Basel and University Hospital Basel [cph]
Repository: CRAN
Date/Publication: 2025-01-16 15:10:02 UTC

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New package twig with initial version 1.0.0.0
Version: 1.0.0.0
Title: For Streamlining Decision and Economic Evaluation Models using Grammar of Modeling
Package: twig
URL: https://www.dashlab.ca/, https://hjalal.github.io/twig/, https://www.dashlab.ca/projects/decision_twig/
BugReports: https://github.com/hjalal/twig/issues
Maintainer: Hawre Jalal <hjalal@uottawa.ca>
Description: Provides tools for building decision and cost-effectiveness analysis models. It enables users to write these models concisely, simulate outcomes—including probabilistic analyses—efficiently using optimized vectorized processes and parallel computing, and produce results. The package employs a Grammar of Modeling approach, inspired by the Grammar of Graphics, to streamline model construction. For an interactive graphical user interface, see 'DecisionTwig' at <https://www.dashlab.ca/projects/decision_twig/>. Comprehensive tutorials and vignettes are available at <https://hjalal.github.io/twig/>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: ggplot2, parallel, foreach, utils, stats, reshape2, abind, doParallel
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-15 12:09:22 UTC; hjalal
Author: Hawre Jalal [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-16 10:50:02 UTC

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New package trace with initial version 0.5.0
Package: trace
Title: Tandem Repeat Analysis by Capillary Electrophoresis
Version: 0.5.0
Description: A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: dplyr, ggplot2, knitr, rmarkdown, shinytest2, testthat (>= 3.0.0)
Imports: graphics, grDevices, lme4, methods, mgcv, plotly, pracma, seqinr, shiny, stats, utils
VignetteBuilder: knitr
Depends: R (>= 2.10)
LazyData: true
URL: https://zachariahmclean.github.io/trace/
NeedsCompilation: no
Packaged: 2025-01-15 19:42:44 UTC; gusella_lab
Author: Zachariah McLean [aut, cre, cph] , Kevin Correia [aut], Andrew Jiang [ctb]
Maintainer: Zachariah McLean <zachariah.louis.mclean@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-16 11:00:02 UTC

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New package stenographer with initial version 1.0.0
Package: stenographer
Title: Flexible and Customisable Logging System
Version: 1.0.0
URL: https://github.com/dereckmezquita/stenographer
BugReports: https://github.com/dereckmezquita/stenographer/issues
Maintainer: Dereck Mezquita <dereck@mezquita.io>
Description: A comprehensive logging framework for R applications that provides hierarchical logging levels, database integration, and contextual logging capabilities. The package supports 'SQLite' storage for persistent logs, provides colour-coded console output for better readability, includes parallel processing support, and implements structured error reporting with 'JSON' formatting.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
Imports: R6, rlang, jsonlite, fs, crayon, DBI
Suggests: testthat (>= 3.0.0), diffviewer, knitr, rmarkdown, box, future, future.apply, RSQLite
NeedsCompilation: no
Packaged: 2025-01-15 14:38:01 UTC; work
Author: Dereck Mezquita [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-16 10:50:06 UTC

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New package rwlifetable with initial version 0.1.0-6
Package: rwlifetable
Title: Estimation of Life Tables Using Rolling Windows
Version: 0.1.0-6
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Description: Estimates life tables, specifically (crude) death rates and (raw and graduated) death probabilities, using rolling windows in one (e.g., age), two (e.g., age and time) or three (e.g., age, time and income) dimensions. The package can also be utilised for summarising statistics and smoothing continuous variables through rolling windows in other domains, such as estimating averages of self-positioning ideology in political science. Acknowledgements: The authors wish to thank Ministerio de Ciencia, Innovación y Universidades (grant PID2021-128228NB-I00) and Generalitat Valenciana (grants HIECPU/2023/2, Conselleria de Hacienda, Economía y Administración Pública, and CIGE/2023/7, Conselleria de Educación, Cultura, Universidades y Empleo) for supporting this research.
License: EPL
Encoding: UTF-8
Imports: stats, splines
NeedsCompilation: no
Packaged: 2025-01-15 16:47:07 UTC; mariaamparo
Author: Jose M. Pavia [aut, cre] , Josep Lledo [aut]
Repository: CRAN
Date/Publication: 2025-01-16 11:00:06 UTC

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New package rbm25 with initial version 0.0.3
Package: rbm25
Title: A Light Wrapper Around the 'BM25' 'Rust' Crate for Okapi BM25 Text Search
Version: 0.0.3
Description: BM25 is a ranking function used by search engines to rank matching documents according to their relevance to a user's search query. This package provides a light wrapper around the 'BM25' 'rust' crate for Okapi BM25 text search. For more information, see Robertson et al. (1994) <https://trec.nist.gov/pubs/trec3/t3_proceedings.html>.
Encoding: UTF-8
URL: https://davzim.github.io/rbm25/, https://github.com/DavZim/rbm25/
BugReports: https://github.com/DavZim/rbm25/issues
SystemRequirements: Cargo (Rust's package manager), rustc >= 1.71.1
Imports: R6
Suggests: testthat (>= 3.0.0)
License: MIT + file LICENSE
NeedsCompilation: yes
Packaged: 2025-01-15 11:55:21 UTC; dazimme
Author: David Zimmermann-Kollenda [aut, cre], Michael Barlow [aut] , Authors of the dependency Rust crates [aut]
Maintainer: David Zimmermann-Kollenda <david_j_zimmermann@hotmail.com>
Repository: CRAN
Date/Publication: 2025-01-16 10:40:02 UTC

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New package parttree with initial version 0.1.0
Package: parttree
Title: Visualize Simple 2-D Decision Tree Partitions
Version: 0.1.0
Date: 2025-10-14
Description: Visualize the partitions of simple decision trees, involving one or two predictors, on the scale of the original data. Provides an intuitive alternative to traditional tree diagrams, by visualizing how a decision tree divides the predictor space in a simple 2D plot alongside the original data. The 'parttree' package supports both classification and regression trees from 'rpart' and 'partykit', as well as trees produced by popular frontend systems like 'tidymodels' and 'mlr3'. Visualization methods are provided for both base R graphics and 'ggplot2'.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://grantmcdermott.com/parttree/
BugReports: https://github.com/grantmcdermott/parttree/issues
Imports: graphics, stats, data.table, partykit, rlang, rpart, tinyplot (>= 0.2.0)
Enhances: ggplot2 (>= 3.4.0)
Suggests: tinytest, tinysnapshot (>= 0.0.3), fontquiver, rsvg, svglite, palmerpenguins, titanic, mlr3, parsnip, workflows, magick, imager, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-15 02:46:38 UTC; gmcd
Author: Grant McDermott [aut, cre] , Achim Zeileis [ctb] , Brian Heseung Kim [ctb] , Julia Silge [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Repository: CRAN
Date/Publication: 2025-01-16 10:30:02 UTC

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New package NPBBBDAefficiency with initial version 0.1.0
Package: NPBBBDAefficiency
Title: A-Efficiency for Nested Partially Balanced Bipartite Block (NPBBB) Designs
Version: 0.1.0
Maintainer: Vinayaka <vinayaka.b3vs@gmail.com>
Description: Nested Partially Balanced Bipartite Block (NPBBB) designs involve two levels of blocking: (i) The block design (ignoring sub-block classification) serves as a partially balanced bipartite block (PBBB) design, and (ii) The sub-block design (ignoring block classification) also serves as a PBBB design. More details on constructions of the PBBB designs and their characterization properties are available in Vinayaka et al.(2023) <doi:10.1080/03610926.2023.2251623>. This package calculates A-efficiency values for both block and sub-block structures, along with all parameters of a given NPBBB design.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-15 16:20:55 UTC; DELL
Author: Vinayaka [aut, cre], B.N. Mandal [aut, ctb], Rajender Parsad [aut, ctb], Vinaykumar L.N. [aut, ctb]
Repository: CRAN
Date/Publication: 2025-01-16 10:50:10 UTC

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New package babyTimeR with initial version 0.1.0
Package: babyTimeR
Title: Parse Output from 'BabyTime' Application
Version: 0.1.0
Author: Dann Hekman [aut, cre]
Maintainer: Dann Hekman <dannhek@gmail.com>
Description: 'BabyTime' is an application for tracking infant and toddler care activities like sleeping, eating, etc. This package will take the outputted .zip files and parse it into a usable list object with cleaned data. It handles malformed and incomplete data gracefully and is designed to parse one directory at a time.
License: MIT + file LICENSE
Depends: dplyr (>= 1.1.4), glue (>= 1.8.0), janitor (>= 2.2.0), lubridate (>= 1.9.3), methods (>= 4.4.1), R (>= 4.4.0), readr (>= 2.1.5), snakecase (>= 0.11.1), stringr (>= 1.5.1)
Imports: utils
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-15 01:22:38 UTC; djh
Repository: CRAN
Date/Publication: 2025-01-16 10:30:05 UTC

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Wed, 15 Jan 2025

New package pmd with initial version 0.2.7
Package: pmd
Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Version: 0.2.7
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
URL: https://yufree.github.io/pmd/
BugReports: https://github.com/yufree/pmd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, shiny, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Imports: RColorBrewer, stats, graphics, utils, igraph, enviGCMS
NeedsCompilation: no
Packaged: 2025-01-15 18:31:33 UTC; yufree
Author: Miao YU [aut, cre]
Maintainer: Miao YU <yufreecas@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 19:40:05 UTC

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New package VAJointSurv with initial version 0.1.1
Package: VAJointSurv
Title: Variational Approximation for Joint Survival and Marker Models
Version: 0.1.1
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Description: Estimates joint marker (longitudinal) and survival (time-to-event) outcomes using variational approximations. The package supports multivariate markers allowing for correlated error terms and multiple types of survival outcomes which may be left-truncated, right-censored, and recurrent. Time-varying fixed and random covariate effects are supported along with non-proportional hazards.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/boennecd/VAJointSurv
BugReports: https://github.com/boennecd/VAJointSurv/issues
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, testthat, psqn (>= 0.3.0)
Imports: Rcpp, splines, utils, stats, SimSurvNMarker, psqn, Matrix, methods, lme4
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), xml2, R.rsp
Depends: R (>= 3.5.0), survival
VignetteBuilder: R.rsp
SystemRequirements: C++17
NeedsCompilation: yes
Packaged: 2025-01-14 13:44:21 UTC; benjaminnon-work
Author: Benjamin Christoffersen [cre, aut] , Mark Clements [aut], Birzhan Akynkozhayev [aut], Antoine Savine [cph]
Repository: CRAN
Date/Publication: 2025-01-15 18:10:09 UTC

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New package shinyscholar with initial version 0.2.2
Package: shinyscholar
Version: 0.2.2
Date: 2025-01-14
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE).
Depends: R (>= 3.5.0), gargoyle, leaflet (>= 2.0.2), shiny (>= 1.8.1)
Imports: curl, devtools, glue, knitr, magrittr, tools, zip
Suggests: bslib, DT (>= 0.5), dplyr (>= 1.0.2), future, httr2, knitcitations, leaflet.extras (>= 1.0.0), markdown, promises, R6, RColorBrewer, renv, rintrojs, rmarkdown, shinyAce, shinyalert, shinybusy, shinyjs, shinytest2, shinyWidgets (>= 0.6.0), terra, testthat, xml2
License: GPL-3
URL: https://simon-smart88.github.io/shinyscholar/
BugReports: https://github.com/simon-smart88/shinyscholar/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-14 15:29:15 UTC; simon
Author: Simon E. H. Smart [aut, cre, cph], Tim Lucas [aut] , Jamie M. Kass [ctb], Gonzalo E. Pinilla-Buitrago [ctb], Andrea Paz [ctb], Bethany A. Johnson [ctb], Valentina Grisales-Betancur [ctb], Dean Attali [ctb], Matthew E. Aiello-Lammens [ctb], Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Repository: CRAN
Date/Publication: 2025-01-15 18:30:02 UTC

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New package RCTRecruit with initial version 0.1.24
Package: RCTRecruit
Title: Non-Parametric Recruitment Prediction for Randomized Clinical Trials
Version: 0.1.24
Description: Accurate prediction of subject recruitment for Randomized Clinical Trials (RCT) remains an ongoing challenge. Many previous prediction models rely on parametric assumptions. We present functions for non-parametric RCT recruitment prediction under several scenarios.
License: MIT + file LICENSE
Depends: R (>= 3.5)
Imports: lubridate, methods, Rcpp
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
URL: https://github.com/imalagaris/RCTRecruit
BugReports: https://github.com/imalagaris/RCTRecruit/issues
Suggests: knitr, magrittr, testthat (>= 3.0.0), withr
NeedsCompilation: yes
Packaged: 2025-01-14 22:29:52 UTC; iomalaga
Author: Ioannis Malagaris [aut, cre, cph] , Alejandro Villasante-Tezanos [aut], Christopher Kurinec [aut], Xiaoying Yu [aut]
Maintainer: Ioannis Malagaris <iomalaga@utmb.edu>
Repository: CRAN
Date/Publication: 2025-01-15 19:00:04 UTC

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New package qmj with initial version 0.2.1
Package: qmj
Title: Quality Scores for the Russell 3000
Version: 0.2.1
Description: Produces quality scores for each of the US companies from the Russell 3000, following the approach described in "Quality Minus Junk" (Asness, Frazzini, & Pedersen, 2013) <http://www.aqr.com/library/working-papers/quality-minus-junk>. The package includes datasets for users who wish to view the most recently uploaded quality scores. It also provides tools to automatically gather relevant financials and stock price information, allowing users to update their data and customize their universe for further analysis.
Imports: quantmod(>= 0.4-3), dplyr, reticulate, rlang
Depends: R (>= 3.5.0)
Suggests: testthat
License: GPL-3
BugReports: https://github.com/anttsou/qmj/issues
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-14 13:52:36 UTC; milz
Author: Anthoney Tsou [aut], Eugene Choe [aut], David Kane [aut], Ryan Kwon [aut], Yanrong Song [aut, cre], Zijie Zhu [aut]
Maintainer: Yanrong Song <yrsong129@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 18:20:02 UTC

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New package PSpower with initial version 0.1.0
Package: PSpower
Title: Sample Size Calculation for Propensity Score Analysis
Version: 0.1.0
Maintainer: Bo Liu <bl226@duke.edu>
Description: Sample size calculations in causal inference with observational data are increasingly desired. This package is a tool to calculate sample size under prespecified power with minimal summary quantities needed.
Depends: ggplot2
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-14 22:33:44 UTC; bo
Author: Bo Liu [aut, cre], Xiaoxiao Zhou [ctb], Fan Li [ctb]
Repository: CRAN
Date/Publication: 2025-01-15 19:00:08 UTC

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New package ProtE with initial version 1.0.1
Package: ProtE
Title: Processing Proteomics Data, Statistical Analysis and Visualization
Version: 1.0.1
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, circlize, vegan, UniProt.ws, stringr, missRanger, vsn, car, openxlsx, tidyr, broom, reshape2, ggpubr, ggplot2, VIM, forcats, grDevices, grid, limma, ComplexHeatmap,
Suggests: BiocManager, rmarkdown, knitr
URL: https://github.com/theomargel/ProtE
BugReports: https://github.com/theomargel/ProtE/issues
Depends: R (>= 2.10)
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-14 17:38:39 UTC; tedma
Author: Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph]
Repository: CRAN
Date/Publication: 2025-01-15 18:40:02 UTC

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New package poobly with initial version 0.1.1
Package: poobly
Title: Poolability Tests in Panel Data
Version: 0.1.1
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Description: Homogeneity tests of the coefficients in panel data. Currently, only the Hsiao test for determining coefficient homogeneity between the panel data individuals is implemented, as described in Hsiao (2022), "Analysis of Panel Data" (<doi:10.1017/9781009057745>).
License: GPL-3
Encoding: UTF-8
URL: https://github.com/cadam00/poobly, https://cadam00.github.io/poobly/
BugReports: https://github.com/cadam00/poobly/issues
Imports: stats, methods, plm
Suggests: Rfast, Rfast2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-01-14 10:47:28 UTC; Administrator
Author: Christos Adam [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-15 18:10:01 UTC

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New package diario with initial version 0.1.0
Package: diario
Title: 'R' Interface to the 'Diariodeobras' Application
Version: 0.1.0
Date: 2025-01-09
Description: Provides a set of functions for securely storing 'API' tokens and interacting with the <https://diariodeobras.net> system. Includes convenient wrappers around the 'httr2' package to perform authenticated requests, retrieve project details, tasks, reports, and more.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tibble, httr2, keyring
URL: <https://github.com/StrategicProjects/diario>
NeedsCompilation: no
Packaged: 2025-01-14 11:58:34 UTC; leite
Author: Andre Leite [aut, cre], Felipe Ferreira [aut], Hugo Vaconcelos [aut], Diogo Bezerra [aut], Roger Azevedo [aut]
Maintainer: Andre Leite <leite@castlab.org>
Repository: CRAN
Date/Publication: 2025-01-15 18:10:05 UTC

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New package froggeR with initial version 0.3.0
Package: froggeR
Title: Enhance 'Quarto' Project Workflows and Standards
Version: 0.3.0
Maintainer: Kyle Grealis <kyleGrealis@icloud.com>
Description: Streamlines 'Quarto' workflows by providing tools for consistent project setup and documentation. Enables portability through reusable metadata, automated project structure creation, and standardized templates. Features include enhanced project initialization, pre-formatted 'Quarto' documents, comprehensive data protection settings, custom styling, and structured documentation generation. Designed to improve efficiency and collaboration in R data science projects by reducing repetitive setup tasks while maintaining consistent formatting across multiple documents. There are many valuable resources providing in-depth explanations of customizing 'Quarto' templates and theme styling by the Posit team: <https://quarto.org/docs/output-formats/html-themes.html#customizing-themes> & <https://quarto.org/docs/output-formats/html-themes-more.html>, and at the Bootstrap community's GitHub at <https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: cli (>= 3.0.0), glue (>= 1.6.0), here (>= 1.0.1), quarto (>= 1.3.0), rappdirs, readr (>= 2.0.0), rstudioapi, stringr (>= 1.5.0), usethis (>= 2.2.0), yaml
Suggests: knitr, mockery, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
URL: https://kylegrealis.github.io/froggeR/
BugReports: https://github.com/kyleGrealis/froggeR/issues
NeedsCompilation: no
Packaged: 2025-01-13 18:06:23 UTC; kyle
Author: Kyle Grealis [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-15 16:30:06 UTC

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New package sfhelper with initial version 0.2.2.0
Package: sfhelper
Title: Repair Functions for 'sf' Package Objects
Version: 0.2.2.0
Description: A group of functions that support the 'sf' package, focused primarily on repairing polygons that break when re-projected.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: RCurl, rjson, mapview, sf, stringr, dplyr, ggplot2
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-01-13 23:32:54 UTC; mr56267
Author: Mark Ravina [aut, cre]
Maintainer: Mark Ravina <mark.ravina@austin.utexas.edu>
Repository: CRAN
Date/Publication: 2025-01-15 10:40:02 UTC

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New package SampleSizeSingleArmSurvival with initial version 0.1.0
Package: SampleSizeSingleArmSurvival
Title: Calculate Sample Size for Single-Arm Survival Studies
Version: 0.1.0
Description: Provides methods to calculate sample size for single-arm survival studies using the arcsine transformation, incorporating uniform accrual and exponential survival assumptions. Includes functionality for detailed numerical integration and simulation. This method is based on Nagashima et al. (2021) <doi:10.1002/pst.2090>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-13 20:00:05 UTC; moko
Author: Mohamed Kamal [aut, cre]
Maintainer: Mohamed Kamal <mohamedkamalhospital@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 10:20:02 UTC

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New package psHarmonize with initial version 0.3.5
Package: psHarmonize
Title: Creates a Harmonized Dataset Based on a Set of Instructions
Version: 0.3.5
Description: Functions which facilitate harmonization of data from multiple different datasets. Data harmonization involves taking data sources with differing values, creating coding instructions to create a harmonized set of values, then making those data modifications. 'psHarmonize' will assist with data modification once the harmonization instructions are written. Coding instructions are written by the user to create a "harmonization sheet". This sheet catalogs variable names, domains (e.g. clinical, behavioral, outcomes), provides R code instructions for mapping or conversion of data, specifies the variable name in the harmonized data set, and tracks notes. The package will then harmonize the source datasets according to the harmonization sheet to create a harmonized dataset. Once harmonization is finished, the package also has functions that will create descriptive statistics using 'RMarkdown'. Data Harmonization guidelines have been described by Fortier I, Raina P, Van den Heuvel ER, et al. ( [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, glue, magrittr, purrr, RColorBrewer, rlang, rmarkdown, stringr, tidyr
Suggests: testthat (>= 3.0.0), knitr
VignetteBuilder: knitr
Depends: R (>= 2.10)
URL: https://github.com/NUDACC/psHarmonize
BugReports: https://github.com/NUDACC/psHarmonize/issues
NeedsCompilation: no
Packaged: 2025-01-13 22:15:29 UTC; jjs7028
Author: John Stephen [aut, cre]
Maintainer: John Stephen <John.Stephen@northwestern.edu>
Repository: CRAN
Date/Publication: 2025-01-15 10:40:05 UTC

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New package fromhere with initial version 0.1.0
Package: fromhere
Title: File Paths Relative to Project Roots
Version: 0.1.0
Description: Provides a set of helper functions for constructing file paths relative to the root of various types of projects, such as R packages, Git repositories, and more. File paths are specified with function arguments, or `$` to navigate into folders to specific files supported by auto-completion.
License: MIT + file LICENSE
Imports: rprojroot, utils
Suggests: here, knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
URL: https://github.com/mitchelloharawild/fromhere
BugReports: https://github.com/mitchelloharawild/fromhere/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-14 08:18:32 UTC; mitchell
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Repository: CRAN
Date/Publication: 2025-01-15 10:50:03 UTC

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New package fftab with initial version 0.1.0
Package: fftab
Title: Tidy Manipulation of Fourier Transformed Data
Version: 0.1.0
Description: The 'fftab' package stores Fourier coefficients in a tibble and allows their manipulation in various ways. Functions are available for converting between complex, rectangular ('re', 'im'), and polar ('mod', 'arg') representations, as well as for extracting components as vectors or matrices. Inputs can include vectors, time series, and arrays of arbitrary dimensions, which are restored to their original form when inverting the transform. Since 'fftab' stores Fourier frequencies as columns in the tibble, many standard operations on spectral data can be easily performed using tidy packages like 'dplyr'.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: ggfortify, patchwork, testthat (>= 3.0.0), zoo
Imports: dplyr, ggplot2, lifecycle, tibble, tidyr
URL: https://github.com/thk686/fftab, https://thk686.github.io/fftab/
BugReports: https://github.com/thk686/fftab/issues
NeedsCompilation: no
Packaged: 2025-01-13 22:31:34 UTC; keittth
Author: Timothy Keitt [aut, cre]
Maintainer: Timothy Keitt <tkeitt@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 10:40:08 UTC

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New package epiCo with initial version 1.0.1
Package: epiCo
Title: Statistical and Viz Tools for Vector-Borne Diseases in Colombia
Version: 1.0.1
Description: Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
License: MIT + file LICENSE
URL: https://epiverse-trace.github.io/epiCo/, https://github.com/epiverse-trace/epiCo
BugReports: https://github.com/epiverse-trace/epiCo/issues
Depends: R (>= 4.0.0)
Imports: dplyr, ggplot2, ggraph, grDevices, igraph, incidence, leaflet, lubridate, magrittr, rlang, scales, spdep, stats, treemapify, utils
Suggests: checkmate, covr, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-08 22:03:21 UTC; juandanielumanacaro
Author: Juan D. Umana [aut, cre, cph] , Juan Montenegro-Torres [aut] , Julian Otero [aut] , Hugo Gruson [ctb]
Maintainer: Juan D. Umana <jd.umana10@uniandes.edu.co>
Repository: CRAN
Date/Publication: 2025-01-15 10:10:01 UTC

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New package rlibkriging with initial version 0.9-1
Package: rlibkriging
Title: Kriging Models using the 'libKriging' Library
Version: 0.9-1
Date: 2025-01-15
Maintainer: Yann Richet <yann.richet@irsn.fr>
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should provide most standard Kriging / Gaussian process regression features (like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages). 'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson, 'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
License: Apache License (>= 2)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.2)
Imports: Rcpp (>= 1.0.12), methods, DiceKriging
Suggests: testthat, RobustGaSP, utils, DiceDesign, foreach
SystemRequirements: GNU make, cmake (>= 3.2.0), gcc, gfortran
URL: https://github.com/libKriging
NeedsCompilation: yes
Packaged: 2025-01-15 08:53:50 UTC; richet
Author: Yann Richet [aut, cre] , Pascal Have [aut], Yves Deville [aut], Conrad Sanderson [ctb], Ciyou Zhu [ctb], Richard Byrd [ctb], Jorge Nocedal [ctb], Jose Luis Morales [ctb], Mike Smith [ctb]
Repository: CRAN
Date/Publication: 2025-01-15 09:40:02 UTC

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New package faux with initial version 1.2.2
Package: faux
Title: Simulation for Factorial Designs
Version: 1.2.2
Date: 2025-01-13
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://debruine.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Depends: R (>= 3.2.4)
Imports: lme4, dplyr (>= 1.1.1), ggplot2 (>= 3.3.0), jsonlite, truncnorm, rlang
License: MIT + file LICENSE
Suggests: testthat (>= 2.1.0), tidyr, knitr, rmarkdown, roxygen2, cowplot, ggExtra, purrr, broom, broom.mixed, psych, lmerTest, kableExtra, glue, openssl, readr, patchwork
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
URL: https://github.com/debruine/faux, https://debruine.github.io/faux/
BugReports: https://github.com/debruine/faux/issues
NeedsCompilation: no
Packaged: 2025-01-14 13:55:02 UTC; debruine
Author: Lisa DeBruine [aut, cre, cph] , Anna Krystalli [ctb] , Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 09:10:01 UTC

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New package arcgisplaces with initial version 0.1.1
Package: arcgisplaces
Title: Search for POIs using ArcGIS 'Places Service'
Version: 0.1.1
Description: The ArcGIS 'Places service' is a ready-to-use location service that can search for businesses and geographic locations around the world. It allows you to find, locate, and discover detailed information about each place. Query for places near a point, within a bounding box, filter based on categories, or provide search text. 'arcgisplaces' integrates with 'sf' for out of the box compatibility with other spatial libraries. Learn more in the 'Places service' API reference <https://developers.arcgis.com/rest/places/>.
License: Apache License (>= 2)
Encoding: UTF-8
Language: en
Imports: arcgisutils (>= 0.3.0), cli, httr2 (>= 1.0.5), rlang, wk
SystemRequirements: Cargo (Rust's package manager), rustc, OpenSSL
Suggests: sf
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: yes
Packaged: 2025-01-13 20:25:59 UTC; josiahparry
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 09:40:07 UTC

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Tue, 14 Jan 2025

New package RPANDA with initial version 2.4
Package: RPANDA
Version: 2.4
Date: 2025-01-14
Title: Phylogenetic ANalyses of DiversificAtion
Depends: R (>= 3.5.0), ape, picante, methods,
Suggests: testthat
Imports: BB, bipartite, cluster, coda, deSolve, fields, fpc, geiger, glassoFast, graphics, grDevices, igraph, Matrix, mvtnorm, mvMORPH (>= 1.1.6), GUniFrac, parallel, ParallelLogger, phangorn, phytools, pracma, pspline, pvclust, raster, RColorBrewer, R.utils, Rmpfr, stats, TESS, utils, vegan
Encoding: UTF-8
Author: Helene Morlon [aut, cre, cph], Eric Lewitus [aut, cph], Fabien Condamine [aut, cph], Marc Manceau [aut, cph], Julien Clavel [aut, cph], Jonathan Drury [aut, cph], Olivier Billaud [aut, cph], Odile Maliet [aut, cph], Leandro Aristide [aut, cph], Benoi [...truncated...]
Maintainer: Helene Morlon <helene.morlon@bio.ens.psl.eu>
Description: Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>, Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>, Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewi [...truncated...]
License: GPL-2
URL: https://github.com/hmorlon/PANDA
Repository: CRAN
NeedsCompilation: yes
Packaged: 2025-01-14 17:11:06 UTC; morlon
Date/Publication: 2025-01-14 23:40:09 UTC

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New package sgapi with initial version 1.0.3
Package: sgapi
Title: Aid Querying 'nomis' and 'Office for National Statistics Open Geography' APIs
Version: 1.0.3
Description: Facilitates extraction of geospatial data from the 'Office for National Statistics Open Geography' and 'nomis' Application Programming Interfaces (APIs). Simplifies process of querying 'nomis' datasets <https://www.nomisweb.co.uk/> and extracting desired datasets in dataframe format. Extracts area shapefiles at chosen resolution from 'Office for National Statistics Open Geography' <https://geoportal.statistics.gov.uk/>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://defra-data-science-centre-of-excellence.github.io/sgapi/, https://github.com/Defra-Data-Science-Centre-of-Excellence/sgapi
BugReports: https://github.com/Defra-Data-Science-Centre-of-Excellence/sgApi/issues
Imports: magrittr, sf, dplyr, httr, readr, xml2, methods
Suggests: testthat (>= 3.0.0)
Depends: R (>= 3.6)
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-14 21:47:50 UTC; Andrew
Author: Andrew Christy [aut, cre], James Macpherson [aut], Hadyn Jenkins [aut], Crown Copyright [cph]
Maintainer: Andrew Christy <sgapi.orhub@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-14 22:30:02 UTC

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New package hhmR with initial version 0.0.1
Package: hhmR
Title: Hierarchical Heatmaps
Version: 0.0.1
Maintainer: Michael Mahony <michael.mahony@cantab.net>
Description: Allows users to create high-quality heatmaps from labelled, hierarchical data. Specifically, for data with a two-level hierarchical structure, it will produce a heatmap where each row and column represents a category at the lower level. These rows and columns are then grouped by the higher-level group each category belongs to, with the names for each category and groups shown in the margins. While other packages (e.g. 'dendextend') allow heatmap rows and columns to be arranged by groups only, 'hhmR' also allows the labelling of the data at both the category and group level.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/sgmmahon/hhmR, https://sgmmahon.github.io/hhmR/
BugReports: https://github.com/sgmmahon/hhmR/issues
Depends: R (>= 3.5.0)
Imports: dplyr, purrr, tidyr, rlang, grid, ggplot2, patchwork, grDevices, magrittr, utils
Language: en-UK
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-13 19:56:44 UTC; MAH113916
Author: Michael Mahony [cre, aut, cph] , Francisco Rowe [aut] , Carmen Cabrera-Arnau [aut]
Repository: CRAN
Date/Publication: 2025-01-14 15:10:01 UTC

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New package pudu with initial version 0.1.0
Package: pudu
Title: C++ Tools for Cleaning Strings
Description: Provides function declarations and inline function definitions that facilitate cleaning strings in C++ code before passing them to R.
Version: 0.1.0
Suggests: cpp11, desc, knitr, mockery, rmarkdown, testthat (>= 3.0.0), withr
Depends: R(>= 3.5.0)
License: Apache License (>= 2)
BugReports: https://github.com/pachadotdev/pudu/issues
URL: https://pacha.dev/pudu/, https://github.com/pachadotdev/pudu
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-13 16:43:15 UTC; pacha
Author: Mauricio Vargas Sepulveda [aut, cre] , Munk School of Global Affairs and Public Policy [fnd]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2025-01-14 15:00:02 UTC

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New package ggstackplot with initial version 0.4
Package: ggstackplot
Title: Create Overlapping Stacked Plots
Version: 0.4
Description: Easily create overlapping grammar of graphics plots for scientific data visualization. This style of plotting is particularly common in climatology and oceanography research communities.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: rlang, cli, methods, lifecycle, tidyselect, dplyr, tidyr, ggplot2, cowplot, RColorBrewer
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vdiffr, scales, pangaear
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-13 15:25:59 UTC; sk
Author: Sebastian Kopf [aut, cre, cph] , Tristan Caro [aut], Jamie McFarlin [aut] , Jon Raberg [aut]
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>
Repository: CRAN
Date/Publication: 2025-01-14 14:40:02 UTC

More information about ggstackplot at CRAN
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New package FLASHMM with initial version 1.0.0
Package: FLASHMM
Title: Fast and Scalable Single Cell Differential Expression Analysis using Mixed-Effects Models
Version: 1.0.0
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm for analysis of single-cell differential expression. The algorithm uses summary-level statistics and requires less computer memory to fit the LMM.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, MASS, Matrix
Suggests: knitr, bookdown, rmarkdown, devtools, SingleCellExperiment, ExperimentHub
VignetteBuilder: knitr
URL: https://github.com/BaderLab/FLASHMM
BugReports: https://github.com/BaderLab/FLASHMM/issues
NeedsCompilation: no
Packaged: 2025-01-13 03:37:58 UTC; changjiangxu
Author: Changjiang Xu [aut, cre], Gary Bader [aut]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Repository: CRAN
Date/Publication: 2025-01-14 13:20:05 UTC

More information about FLASHMM at CRAN
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New package bitstreamio with initial version 0.1.0
Package: bitstreamio
Title: Read and Write Bits from Files, Connections and Raw Vectors
Version: 0.1.0
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
URL: https://github.com/coolbutuseless/bitstreamio
BugReports: https://github.com/coolbutuseless/bitstreamio/issues
Description: Bit-level reading and writing are necessary when dealing with many file formats e.g. compressed data and binary files. Currently, R connections are manipulated at the byte level. This package wraps existing connections and raw vectors so that it is possible to read bits, bit sequences, unaligned bytes and low-bit representations of integers.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-13 09:07:43 UTC; mike
Author: Mike Cheng [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-01-14 13:20:01 UTC

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New package BIS with initial version 0.4
Package: BIS
Title: Programmatic Access to Bank for International Settlements Data
Version: 0.4
Description: Provides an interface to data provided by the Bank for International Settlements <https://www.bis.org>, allowing for programmatic retrieval of a large quantity of (central) banking data.
License: CC0
URL: https://github.com/stefanangrick/BIS
BugReports: https://github.com/stefanangrick/BIS/issues
Suggests: knitr, rmarkdown, ggplot2, zoo
Imports: dplyr, readr, rvest, xml2
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-02 07:38:01 UTC; qwerty
Author: Stefan Angrick [aut, cre], Eric Persson [aut]
Maintainer: Stefan Angrick <contact@stefanangrick.net>
Repository: CRAN
Date/Publication: 2025-01-14 13:20:08 UTC

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New package PLStests with initial version 0.1.0
Package: PLStests
Title: Model Checking for High-Dimensional GLMs via Random Projections
Version: 0.1.0
Maintainer: Wen Chen <tlqdcw@gmail.com>
Description: Provides methods for testing the goodness-of-fit of generalized linear models (GLMs) using random projections. It is specifically designed for high-dimensional scenarios where the number of predictors substantially exceeds the sample size. The statistical methodologies implemented in this package are detailed in the paper by Wen Chen and Falong Tan (2024, <doi:10.48550/arXiv.2412.10721>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: glmnet, harmonicmeanp, MASS, psych,stats
NeedsCompilation: no
Packaged: 2025-01-12 06:12:50 UTC; Aorus
Author: Wen Chen [aut, cre], Jie Liu [aut], Heng Peng [aut], FaLong Tan [aut], Lixing Zhu [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-01-14 13:00:02 UTC

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New package OpenRange with initial version 0.0.1
Package: OpenRange
Title: Code to Access Open Access Species Range Maps
Version: 0.0.1
Description: Allows access to a proof-of-concept database containing Open Access species range models and relevant metadata. Access to the database is via both 'PostgreSQL' connection and API <https://github.com/EnquistLab/Biendata-Frontend>, allowing diverse use-cases.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.2.1), RPostgreSQL
Imports: DBI, sf, httr, jsonlite
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), maps, tidyverse, vcr, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-12 16:30:14 UTC; Brian Maitner
Author: Brian Maitner [aut, cre] , Cory Merow [aut], Brad Boyle [aut], Xiao Feng [aut], Rethvick Sriram Yugendra Babu [aut], Brian Enquist [aut]
Maintainer: Brian Maitner <bmaitner@usf.edu>
Repository: CRAN
Date/Publication: 2025-01-14 13:00:05 UTC

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New package theorytools with initial version 0.1.0
Package: theorytools
Title: FAIR Theory Construction
Version: 0.1.0
Description: An integrated suite of tools for creating, maintaining, and reusing FAIR (Findable, Accessible, Interoperable, Reusable) theories. Designed to support transparent and collaborative theory development, the package enables users to formalize theories, track changes with version control, assess pre-empirical coherence, and derive testable hypotheses. Aligning with open science principles and workflows, 'theorytools' facilitates the systematic improvement of theoretical frameworks and enhances their discoverability and usability.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/cjvanlissa/theorytools
Imports: worcs (>= 0.1.16), gert, gh, cli, jsonlite
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), pkgdown, withr, usethis, fs
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-11 17:39:02 UTC; vanlissa
Author: Caspar J. Van Lissa [aut, cre]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Repository: CRAN
Date/Publication: 2025-01-14 10:20:01 UTC

More information about theorytools at CRAN
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New package pam with initial version 1.0.0
Package: pam
Title: Fast and Efficient Processing of PAM Data
Version: 1.0.0
URL: https://github.com/biotoolbox/pam
BugReports: https://github.com/biotoolbox/pam/issues
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data generated by WALZ hardware. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: data.table, dplyr, ggplot2, minpack.lm, cowplot, gridExtra, ggthemes
NeedsCompilation: no
Packaged: 2025-01-11 19:58:25 UTC; julien
Author: Julien Boehm [cre, aut] , Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Repository: CRAN
Date/Publication: 2025-01-14 10:20:05 UTC

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New package ggmapcn with initial version 0.1.2
Package: ggmapcn
Title: Customizable China Map Visualizations
Version: 0.1.2
Description: A 'ggplot2' extension for visualizing China’s map, offering customizable projections, boundary styles, and buffer zones for thematic maps. Suitable for spatial data analysis and enhancing map visualization with flexible styling options.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0), ggplot2 (>= 3.4.0)
Imports: sf (>= 1.0.0), dplyr (>= 1.1.0), rlang (>= 1.1.3), ggspatial (>= 1.1.8), terra (>= 1.7), tidyterra (>= 0.6.0), curl (>= 6.0.0)
URL: https://rimagination.github.io/ggmapcn/
BugReports: https://github.com/Rimagination/ggmapcn/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-11 16:39:20 UTC; Administrator
Author: Liang Ren [aut, cre]
Maintainer: Liang Ren <rl23@mails.tsinghua.edu.cn>
Repository: CRAN
Date/Publication: 2025-01-14 10:10:01 UTC

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New package spNetwork with initial version 0.4.4.4
Package: spNetwork
Title: Spatial Analysis on Network
Version: 0.4.4.4
Description: Perform spatial analysis on network. Implement several methods for spatial analysis on network: Network Kernel Density estimation, building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation References: Okabe et al (2019) <doi:10.1080/13658810802475491>; Okabe et al (2012, ISBN:978-0470770818);Baddeley et al (2015, ISBN:9781482210200).
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: spdep (>= 1.1.2), igraph (>= 1.2.6), cubature (>= 2.0.4.1), future.apply (>= 1.4.0), methods (>= 1.7.1), ggplot2 (>= 3.3.0), progressr (>= 0.4.0), data.table (>= 1.12.8), Rcpp (>= 1.0.4.6), Rdpack (>= 2.1.1), dbscan (>= 1.1-8), sf (>= 1.0-3), abind (>= 1.4-5), sfheaders (>= 0.4.4), cppRouting (>= 3.1)
Depends: R (>= 3.6)
Suggests: future (>= 1.16.0), testthat (>= 3.0.0), kableExtra (>= 1.1.0), RColorBrewer (>= 1.1-2), classInt (>= 0.4-3), reshape2 (>= 1.4.3), rlang (>= 0.4.6), rgl (>= 0.107.14), tmap (>= 3.3-1), smoothr (>= 0.2.2), concaveman (>= 1.1.0), covr (>= 3.5.1), knitr, rmarkdown
VignetteBuilder: knitr
URL: https://jeremygelb.github.io/spNetwork/
BugReports: https://github.com/JeremyGelb/spNetwork/issues
LinkingTo: Rcpp, RcppProgress, RcppArmadillo, BH
Language: en-CA
SystemRequirements: C++17
NeedsCompilation: yes
Packaged: 2025-01-11 02:47:31 UTC; Gelb
Author: Jeremy Gelb [aut, cre] , Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>
Repository: CRAN
Date/Publication: 2025-01-14 09:50:02 UTC

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New package ProActive with initial version 0.0.2
Package: ProActive
Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Version: 0.0.2
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Description: Automate the detection of gaps and elevations in mapped sequencing read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes and visualizes read coverage patterns in both genomes and metagenomes. Optionally, users may provide gene predictions associated with their genome or metagenome in the form of a .gff file. In this case, 'ProActive' will generate an additional output table containing the gene predictions found within the detected regions of gapped and elevated read coverage.
License: GPL-2
Encoding: UTF-8
LazyData: true
URL: https://github.com/jlmaier12/ProActive, https://jlmaier12.github.io/ProActive/
BugReports: https://github.com/jlmaier12/ProActive/issues
Imports: utils, stats, dplyr, ggplot2, stringr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), kableExtra
VignetteBuilder: knitr
Depends: R (>= 4.2.0)
NeedsCompilation: no
Packaged: 2025-01-10 21:55:08 UTC; jlmaier
Author: Jessie Maier [aut, cre, cph] , Manuel Kleiner [aut, ths]
Repository: CRAN
Date/Publication: 2025-01-14 09:50:10 UTC

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New package enviGCMS with initial version 0.8.0
Package: enviGCMS
Title: GC/LC-MS Data Analysis for Environmental Science
Version: 0.8.0
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
URL: https://github.com/yufree/enviGCMS
BugReports: https://github.com/yufree/enviGCMS/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, testthat, plotly, shiny, rmarkdown, DT, crosstalk
VignetteBuilder: knitr
Depends: R (>= 3.5)
Imports: Rdisop, BiocParallel, grDevices, graphics, stats, utils, animation (>= 2.2.3), RColorBrewer, mixtools, data.table, igraph
NeedsCompilation: no
Packaged: 2025-01-14 02:15:57 UTC; yufree
Author: Miao YU [aut, cre] , Thanh Wang [ctb]
Maintainer: Miao YU <yufreecas@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-14 07:50:02 UTC

More information about enviGCMS at CRAN
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Mon, 13 Jan 2025

New package viafoundry with initial version 1.0.0
Package: viafoundry
Title: R Client for 'Via Foundry' API
Version: 1.0.0
Language: en-US
Description: 'Via Foundry' API provides streamlined tools for interacting with and extracting data from structured responses, particularly for use cases involving hierarchical data from Foundry's API. It includes functions to fetch and parse process-level and file-level metadata, allowing users to efficiently query and manipulate nested data structures. Key features include the ability to list all unique process names, retrieve file metadata for specific or all processes, and dynamically load or download files based on their type. With built-in support for handling various file formats (e.g., tabular and non-tabular files) and seamless integration with API through authentication, this package is designed to enhance workflows involving large-scale data management and analysis. Robust error handling and flexible configuration ensure reliable performance across diverse data environments. Please consult the documentation for the API endpoint for your installation.
License: Apache License 2.0
Encoding: UTF-8
Imports: httr, jsonlite, dplyr, purrr, askpass
URL: https://github.com/ViaScientific/viafoundry-R-SDK
NeedsCompilation: no
Packaged: 2025-01-10 21:57:55 UTC; alper
Author: Alper Kucukural [aut, cre], Via Scientific [aut, cph]
Maintainer: Alper Kucukural <alper@viascientific.com>
Repository: CRAN
Date/Publication: 2025-01-13 18:00:02 UTC

More information about viafoundry at CRAN
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New package urlparse with initial version 0.1.0
Package: urlparse
Title: Fast Simple URL Parser
Version: 0.1.0
Description: A fast and simple 'URL' parser package for 'R'. This package provides functions to parse 'URLs' into their components, such as scheme, user, password, host, port, path, query, and fragment.
License: MIT + file LICENSE
URL: https://github.com/dyfanjones/urlparse, https://dyfanjones.r-universe.dev/urlparse
BugReports: https://github.com/dyfanjones/urlparse/issues
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2025-01-10 13:37:27 UTC; dyfanjones
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 17:30:02 UTC

More information about urlparse at CRAN
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New package spectrolab with initial version 0.0.19
Package: spectrolab
Title: Class and Methods for Spectral Data
Version: 0.0.19
Date: 2025-01-07
Description: Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class spectra that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.
License: GPL-3
URL: https://CRAN.R-project.org/package=spectrolab
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0), stats
Suggests: covr, tinytex, knitr (>= 1.30), rmarkdown (>= 2.5), testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: grDevices, parallel, RColorBrewer (>= 1.0), shiny (>= 1.5.0), shinyjs (>= 1.1)
NeedsCompilation: no
Packaged: 2025-01-10 16:59:40 UTC; meireles
Author: Jose Eduardo Meireles [aut, cre], Anna K. Schweiger [aut], Jeannine Cavender-Bares [aut]
Maintainer: Jose Eduardo Meireles <jemeireles@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 17:50:02 UTC

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New package sequenceR with initial version 1.0.1
Package: sequenceR
Title: A Simple Sequencer for Data Sonification
Version: 1.0.1
Description: A rudimentary sequencer to define, manipulate and mix sound samples. The underlying motivation is to sonify data, as demonstrated in the blog <https://globxblog.github.io/>, the presentation by Renard and Le Bescond (2022, <https://hal.science/hal-03710340v1>) or the poster by Renard et al. (2023, <https://hal.inrae.fr/hal-04388845v1>).
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/benRenard/sequenceR
BugReports: https://github.com/benRenard/sequenceR/issues
Depends: R (>= 3.5.0)
Imports: tuneR
Suggests: knitr, rmarkdown, ggplot2, gganimate, tidyr, dplyr, av
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-10 10:41:06 UTC; brenard
Author: Benjamin Renard [aut, cre, cph] , INRAE [fnd], European Commission [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Repository: CRAN
Date/Publication: 2025-01-13 17:30:05 UTC

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New package rineq with initial version 0.3.0
Package: rineq
Title: Concentration Index and Decomposition for Health Inequalities
Version: 0.3.0
Date: 2025-01-10
Description: Relative, generalized, and Erreygers corrected concentration index; plot Lorenz curves; and decompose health inequalities into contributing factors. The package currently works with (generalized) linear models, survival models, complex survey models, and marginal effects probit models. originally forked by Brecht Devleesschauwer from the 'decomp' package (no longer on CRAN), 'rineq' is now maintained by Kaspar Walter Meili. Compared to the earlier 'rineq' version on 'github' by Brecht Devleesschauwer (<https://github.com/brechtdv/rineq>), the regression tree functionality has been removed. Improvements compared to earlier versions include improved plotting of decomposition and concentration, added functionality to calculate the concentration index with different methods, calculation of robust standard errors, and support for the decomposition analysis using marginal effects probit regression models. The development version is available at <https://github.com/kdevkdev/rineq> [...truncated...]
Depends: R (>= 3.5.0)
Imports: stats, graphics
Suggests: sandwich, lmtest, mfx, survey, survival
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
Language: en-Us
URL: https://github.com/kdevkdev/rineq
BugReports: https://github.com/kdevkdev/rineq/issues
NeedsCompilation: no
Packaged: 2025-01-10 14:11:03 UTC; kaspar
Author: Brecht Devleesschauwer [aut, cph], Saveria Willimes [aut, cph], Carine Van Malderen [aut, cph], Peter Konings [aut, cph], Niko Speybroeck [aut, cph], Kaspar Meili [aut, cre, cph]
Maintainer: Kaspar Meili <meilikaspar@yahoo.de>
Repository: CRAN
Date/Publication: 2025-01-13 17:30:10 UTC

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New package priorityelasticnet with initial version 0.1.0
Package: priorityelasticnet
Title: Comprehensive Analysis of Multi-Omics Data Using an Offset-Based Method
Version: 0.1.0
Description: Priority-ElasticNet extends the Priority-LASSO method (Klau et al. (2018) <doi:10.1186/s12859-018-2344-6>) by incorporating the ElasticNet penalty, allowing for both L1 and L2 regularization. This approach fits successive ElasticNet models for several blocks of (omics) data with different priorities, using the predicted values from each block as an offset for the subsequent block. It also offers robust options to handle block-wise missingness in multi-omics data, improving the flexibility and applicability of the model in the presence of incomplete datasets.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: survival, glmnet, utils, checkmate, shiny, tidyr, dplyr, caret, pROC, PRROC, plotrix, ggplot2, magrittr, tibble, broom, cvms
Suggests: ipflasso, rlang, knitr, rmarkdown, glmSparseNet
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-10 10:30:18 UTC; statl
Author: Laila Qadir Musib [aut, cre], Eunice Carrasquinha [aut], Helena Mourino [aut]
Maintainer: Laila Qadir Musib <statleila98@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 17:30:13 UTC

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New package plug with initial version 0.1.0
Package: plug
Title: Secure and Intuitive Access to 'Plug' Interface
Version: 0.1.0
Date: 2025-01-09
Description: Provides a secure and user-friendly interface to interact with the 'Plug' <https://plugbytpf.com.br> 'API'. It enables developers to store and manage tokens securely using the 'keyring' package, retrieve data from 'API' endpoints with the 'httr2' package, and handle large datasets with chunked data fetching. Designed for simplicity and security, the package facilitates seamless integration with 'Plug' ecosystem.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tibble, httr2, glue, keyring
URL: <https://github.com/StrategicProjects/plug>
NeedsCompilation: no
Packaged: 2025-01-10 16:12:42 UTC; leite
Author: Andre Leite [aut, cre], Felipe Ferreira [aut], Hugo Vaconcelos [aut], Diogo Bezerra [aut], Roger Azevedo [aut]
Maintainer: Andre Leite <leite@castlab.org>
Repository: CRAN
Date/Publication: 2025-01-13 17:50:07 UTC

More information about plug at CRAN
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New package mlr3inferr with initial version 0.1.0
Package: mlr3inferr
Title: Inference on the Generalization Error
Version: 0.1.0
Description: An 'mlr3' extension that provides various resampling-based confidence interval (CI) methods for estimating the generalization error. These CI methods are implemented as 'mlr3' measures, enabling the evaluation of individual algorithms on specific tasks as well as the comparison of different learning algorithms.
License: LGPL-3
URL: https://mlr3inferr.mlr-org.com, https://github.com/mlr-org/mlr3inferr
BugReports: https://github.com/mlr-org/mlr3inferr/issues
Depends: mlr3, R (>= 3.1.0)
Imports: checkmate, data.table, future, lgr, mlr3measures, mlr3misc, paradox, R6, withr
Suggests: rpart, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-10 16:02:33 UTC; sebi
Author: Sebastian Fischer [cre, aut] , Hannah Schulz-Kuempel [aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 17:50:11 UTC

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New package idiffomix with initial version 1.0.0
Package: idiffomix
Title: Integrated Differential Analysis of Multi Omics Data using a Joint Mixture Model
Version: 1.0.0
Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>
Description: A joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: foreach, doParallel, parallel, mclust, stats, utils, edgeR, magrittr, ggplot2, scales, tidyr, dplyr, reshape2, gridExtra, grid, tidyselect, cowplot
Encoding: UTF-8
NeedsCompilation: yes
LazyData: true
LazyDataCompression: xz
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Packaged: 2025-01-10 10:22:28 UTC; koyel
Author: Koyel Majumdar [cre, aut], Isobel Claire Gorley [aut], Thomas Brendan Murphy [aut], Florence Jaffrezic [aut], Andrea Rau [aut]
Repository: CRAN
Date/Publication: 2025-01-13 17:20:02 UTC

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New package fastrerandomize with initial version 0.1
Package: fastrerandomize
Title: Hardware-Accelerated Rerandomization for Improved Balance
Version: 0.1
Description: Provides hardware-accelerated tools for performing rerandomization and randomization testing in experimental research. Using a 'JAX' backend, the package enables exact rerandomization inference even for large experiments with hundreds of billions of possible randomizations. Key functionalities include generating pools of acceptable rerandomizations based on covariate balance, conducting exact randomization tests, and performing pre-analysis evaluations to determine optimal rerandomization acceptance thresholds. The package supports various hardware acceleration frameworks including 'CPU', 'CUDA', and 'METAL', making it versatile across accelerated computing environments. This allows researchers to efficiently implement stringent rerandomization designs and conduct valid inference even with large sample sizes. The package is partly based on Jerzak and Goldstein (2023) <doi:10.48550/arXiv.2310.00861>.
URL: https://github.com/cjerzak/fastrerandomize-software
BugReports: https://github.com/cjerzak/fastrerandomize-software/issues
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: false
Imports: reticulate, assertthat, utils, stats, graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-10 18:19:32 UTC; cjerzak
Author: Fucheng Warren Zhu [aut] , Aniket Sachin Kamat [aut] , Connor Jerzak [aut, cre] , Rebecca Goldstein [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 18:00:05 UTC

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New package FactorHet with initial version 1.0.0
Package: FactorHet
Title: Estimate Heterogeneous Effects in Factorial Experiments Using Grouping and Sparsity
Version: 1.0.0
Date: 2025-01-08
Description: Estimates heterogeneous effects in factorial (and conjoint) models. The methodology employs a Bayesian finite mixture of regularized logistic regressions, where moderators can affect each observation's probability of group membership and a sparsity-inducing prior fuses together levels of each factor while respecting ANOVA-style sum-to-zero constraints. Goplerud, Imai, and Pashley (2024) <doi:10.48550/ARXIV.2201.01357> provide further details.
Depends: R (>= 3.4.0)
License: GPL (>= 2)
Encoding: UTF-8
LinkingTo: Rcpp, RcppEigen (>= 0.3.3.4.0)
Imports: Rcpp (>= 1.0.1), Matrix, ggplot2, ParamHelpers, mlr, mlrMBO, smoof, lbfgs, methods, utils, stats
Suggests: FNN, RSpectra, mclust, ranger, tgp, testthat, covr, tictoc
LazyData: true
URL: https://github.com/mgoplerud/FactorHet
BugReports: https://github.com/mgoplerud/FactorHet/issues
NeedsCompilation: yes
Packaged: 2025-01-10 17:16:01 UTC; mg68977
Author: Max Goplerud [aut, cre], Nicole E. Pashley [aut], Kosuke Imai [aut]
Maintainer: Max Goplerud <mgoplerud@austin.utexas.edu>
Repository: CRAN
Date/Publication: 2025-01-13 18:00:09 UTC

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New package dfeR with initial version 1.0.0
Package: dfeR
Title: Common Department for Education Analysis Tasks
Version: 1.0.0
Description: Preferred methods for common analytical tasks that are undertaken across the Department, including number formatting, project templates and curated reference data.
License: GPL (>= 3)
URL: https://dfe-analytical-services.github.io/dfeR/, https://github.com/dfe-analytical-services/dfeR
BugReports: https://github.com/dfe-analytical-services/dfeR/issues
Depends: R (>= 2.10)
Imports: dplyr, emoji, httr, jsonlite, lifecycle, magrittr, renv, rlang, tidyselect, usethis, utils, withr
Suggests: knitr, readxl, rmarkdown, spelling, stringr, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-10 16:53:04 UTC; CRACE
Author: Cam Race [aut, cre], Department for Education, UK statistics.development@education.gov.uk [cph], Laura Selby [aut], Adam Robinson [aut], Jen Machin [ctb], Jake Tufts [ctb], Rich Bielby [ctb] , Menna Zayed [ctb]
Maintainer: Cam Race <cameron.race@education.gov.uk>
Repository: CRAN
Date/Publication: 2025-01-13 17:50:18 UTC

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New package bnns with initial version 0.1.2
Package: bnns
Title: Bayesian Neural Network with 'Stan'
Version: 0.1.2
Description: Offers a flexible formula-based interface for building and training Bayesian Neural Networks powered by 'Stan'. The package supports modeling complex relationships while providing rigorous uncertainty quantification via posterior distributions. With features like user chosen priors, clear predictions, and support for regression, binary, and multi-class classification, it is well-suited for applications in clinical trials, finance, and other fields requiring robust Bayesian inference and decision-making. References: Neal(1996) <doi:10.1007/978-1-4612-0745-0>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: ggplot2, knitr, mlbench, ranger, rmarkdown, rsample, testthat (>= 3.0.0)
Imports: BH, pROC, RcppEigen, rstan, stats
URL: https://github.com/swarnendu-stat/bnns, https://swarnendu-stat.github.io/bnns/
BugReports: https://github.com/swarnendu-stat/bnns/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-10 13:05:02 UTC; antpc
Author: Swarnendu Chatterjee [aut, cre, cph]
Maintainer: Swarnendu Chatterjee <swarnendu.stat@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-13 17:30:17 UTC

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New package soilassessment with initial version 0.3.0
Package: soilassessment
Title: Soil Health Assessment Models for Assessing Soil Conditions and Suitability
Version: 0.3.0
Description: Soil health assessment builds information to improve decision in soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>], groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>], carbon sequestration, irrigation potential, and status of soil resources.
License: GPL
Depends: R (>= 3.5.0)
Imports: caret, deSolve, e1071, FuzzyAHP, googledrive, Hmisc, methods, nnet, png, randomForest, raster, soiltexture, sp, sf, terra, stats
Suggests: arm, Cubist, aqp, kernlab, nlme, ranger, rpart, plyr, qrnn, quantregForest, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-13 01:22:10 UTC; Cthine
Author: Christian Thine Omuto [aut, cre]
Maintainer: Christian Thine Omuto <thineomuto@yahoo.com>
Repository: CRAN
Date/Publication: 2025-01-13 14:10:01 UTC

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New package quickPWCR with initial version 1.2
Package: quickPWCR
Title: Quickly Construct and Rate Large Binary Pairwised Comparisons
Version: 1.2
Date: 2025-01-12
Description: A collection of functions for constructing large pairwised comparisons and rating them using Elo rating system with supporting parallel processing. The method of random sample pairs is based on Reservoir Sampling proposed by JVitter (1985) <doi:10.1145/3147.3165>.
License: GPL-3
Encoding: UTF-8
Language: en-US
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown
Imports: Rcpp, parallel, pbmcapply, dplyr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2025-01-13 04:16:48 UTC; yangxiaohao
Author: Xiaohao Yang [aut, cre, cph]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Repository: CRAN
Date/Publication: 2025-01-13 14:10:06 UTC

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New package maraca with initial version 0.7.1
Package: maraca
Version: 0.7.1
Title: The Maraca Plot: Visualizing Hierarchical Composite Endpoints
License: Apache License (>= 2)
Description: Supports visual interpretation of hierarchical composite endpoints (HCEs). HCEs are complex constructs used as primary endpoints in clinical trials, combining outcomes of different types into ordinal endpoints, in which each patient contributes the most clinically important event (one and only one) to the analysis. See Karpefors M et al. (2022) <doi:10.1177/17407745221134949>.
URL: https://github.com/AstraZeneca/maraca
BugReports: https://github.com/AstraZeneca/maraca/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), hce (>= 0.5), ggplot2 (>= 3.3)
Imports: dplyr (>= 1.0), tidyr (>= 1.2), checkmate (>= 2.1), patchwork(>= 1.0.0), lifecycle
Suggests: knitr (>= 1.39), here (>= 1.0.1), lintr (>= 3.0.0), withr (>= 2.5.0), testthat (>= 3.1), rmarkdown
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2025-01-13 13:12:55 UTC; hidden
Author: Martin Karpefors [aut] , Samvel B. Gasparyan [aut] , Stefano Borini [ctb], Monika Huhn [aut, cre]
Maintainer: Monika Huhn <monika.huhn@astrazeneca.com>
Repository: CRAN
Date/Publication: 2025-01-13 14:10:09 UTC

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New package dietr with initial version 1.1.6
Package: dietr
Version: 1.1.6
Date: 2025-1-12
Title: Diet Estimated Trophic Levels
Depends: R (>= 4.3)
Imports: rfishbase (>= 5.0)
Description: Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/sborstein/dietr
BugReports: https://github.com/sborstein/dietr/issues
NeedsCompilation: no
Packaged: 2025-01-12 19:24:46 UTC; Sam
Author: Samuel R. Borstein [aut, cre]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Repository: CRAN
Date/Publication: 2025-01-13 14:10:12 UTC

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Sat, 11 Jan 2025

New package openmpt with initial version 0.1.4
Package: openmpt
Title: Open 'ModPlug' Tracker Port
Version: 0.1.4
Description: Tracker music uses audio samples and pattern tables to organise musical compositions. Such music is stored in module files. This package reads, renders and plays module files using the 'libopenmpt' library <https://lib.openmpt.org/>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: av
Suggests: httr2, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0), xml2
LinkingTo: cpp11
SystemRequirements: openmpt: libopenmpt-devel (rpm) or libopenmpt-dev (deb), portaudio-devel (rpm) or portaudio19-dev (deb).
URL: https://pepijn-devries.github.io/openmpt/, https://github.com/pepijn-devries/openmpt, https://lib.openmpt.org/
BugReports: https://github.com/pepijn-devries/openmpt/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-01-08 23:06:24 UTC; vries171
Author: Pepijn de Vries [aut, cre] , Jeroen Ooms [ctb] , Jester [cph, dtc] , OpenMPT Project Developers and Contributors [cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Repository: CRAN
Date/Publication: 2025-01-11 16:00:02 UTC

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Fri, 10 Jan 2025

New package dcsvm with initial version 0.0.1
Package: dcsvm
Title: Density Convoluted Support Vector Machines
Version: 0.0.1
Date: 2025-01-08
Description: Implements an efficient algorithm for solving sparse-penalized support vector machines with kernel density convolution. This package is designed for high-dimensional classification tasks, supporting lasso (L1) and elastic-net penalties for sparse feature selection and providing options for tuning kernel bandwidth and penalty weights. The 'dcsvm' is applicable to fields such as bioinformatics, image analysis, and text classification, where high-dimensional data commonly arise. Learn more about the methodology and algorithm at Wang, Zhou, Gu, and Zou (2023) <doi:10.1109/TIT.2022.3222767>.
Depends: Matrix
Imports: grDevices, graphics, methods, stats
License: GPL-2
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2025-01-10 00:31:20 UTC; boxiang
Author: Boxiang Wang [aut, cre], Le Zhou [aut], Yuwen Gu [aut], Hui Zou [aut]
Maintainer: Boxiang Wang <boxiang-wang@uiowa.edu>
Repository: CRAN
Date/Publication: 2025-01-10 21:20:02 UTC

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New package CMHSU with initial version 0.0.6.9
Package: CMHSU
Title: Mental Health Status, Substance Use Status and their Concurrent Status in North American Healthcare Administrative Databases
Version: 0.0.6.9
Description: Patients' Mental Health (MH) status, Substance Use (SU) status, and concurrent MH/SU status in the American/Canadian Healthcare Administrative Databases can be identified. The detection is based on given parameters of interest by clinicians including the list of plausible ICD MH/SU codes (3/4/5 characters), the required number of visits of hospital for MH/SU , the required number of visits of service physicians for MH/SU, and the maximum time span within MH visits, within SU visits, and, between MH and SU visits. Methods are described in: Khan S <https://pubmed.ncbi.nlm.nih.gov/29044442/>, Keen C, et al. (2021) <doi:10.1111/add.15580>, Lavergne MR, et al. (2022) <doi:10.1186/s12913-022-07759-z>, Casillas, S M, et al. (2022) <doi:10.1016/j.abrep.2022.100464>, CIHI (2022) <https://www.cihi.ca/en>, CDC (2024) <https://www.cdc.gov>, WHO (2019) <https://icd.who.int/en>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: dplyr, magrittr, purrr, tidyr, utils
NeedsCompilation: no
Packaged: 2025-01-10 03:17:57 UTC; chelhee.lee
Author: Mohsen Soltanifar [aut] , Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>
Repository: CRAN
Date/Publication: 2025-01-10 21:20:05 UTC

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New package BerkeleyForestsAnalytics with initial version 2.0.4
Package: BerkeleyForestsAnalytics
Title: Compute and Summarize Core Forest Metrics from Field Data
Version: 2.0.4
Description: A suite of open-source R functions designed to produce standard metrics for forest management and ecology from forest inventory data. The overarching goal is to minimize potential inconsistencies introduced by the algorithms used to compute and summarize core forest metrics. Learn more about the purpose of the package and the specific algorithms used in the package at <https://github.com/kearutherford/BerkeleyForestsAnalytics>.
License: file LICENSE
URL: https://github.com/kearutherford/BerkeleyForestsAnalytics
Depends: R (>= 2.10)
Imports: utils
Suggests: dplyr, knitr, rmarkdown, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-10 00:21:42 UTC; kruth
Author: Kea Rutherford [aut, cre], John Battles [aut], Danny Foster [aut], The Regents of the University of California [cph]
Maintainer: Kea Rutherford <krutherford@berkeley.edu>
Repository: CRAN
Date/Publication: 2025-01-10 21:10:02 UTC

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New package S4DM with initial version 0.0.1
Package: S4DM
Title: Small Sample Size Species Distribution Modeling
Version: 0.0.1
Description: Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sampled taxa, they are united by the fact that they can be utilized with relatively few data points. More details on the currently implemented methodologies can be found in Drake and Richards (2018) <doi:10.1002/ecs2.2373>, Drake (2015) <doi:10.1098/rsif.2015.0086>, and Drake (2014) <doi:10.1890/ES13-00202.1>.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: corpcor, densratio, flexclust, geometry, kernlab, maxnet, mvtnorm, np, pROC, robust, rvinecopulib, sf, terra, dplyr, Rdpack
Suggests: geodata, BIEN, ggplot2, tidyterra, knitr, testthat, rmarkdown
NeedsCompilation: no
Packaged: 2025-01-10 00:20:14 UTC; Brian Maitner
Author: Brian S. Maitner [aut, cre] , Robert L. Richards [aut], Ben S. Carlson [aut], John M. Drake [aut], Cory Merow [aut]
Maintainer: Brian S. Maitner <bmaitner@usf.edu>
Repository: CRAN
Date/Publication: 2025-01-10 21:00:02 UTC

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New package linevis with initial version 1.0.0
Package: linevis
Title: Interactive Time Series Visualizations
Version: 1.0.0
Description: Create interactive time series visualizations. 'linevis' includes an extensive API to manipulate time series after creation, and supports getting data out of the visualization. Based on the 'timevis' package and the 'vis.js' Timeline 'JavaScript' library <https://visjs.github.io/vis-timeline/docs/graph2d/>.
URL: https://gitlab.com/thomaschln/linevis
BugReports: https://gitlab.com/thomaschln/linevis/-/issues
Depends: R (>= 3.1.0)
Imports: crosstalk, htmlwidgets (>= 0.6), jsonlite, magrittr, methods, rmarkdown, shiny
Suggests: knitr, testthat (>= 0.9.1)
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-09 18:46:00 UTC; root
Author: Thomas Charlon [aut, cre] , Dean Attali [aut, cph], Almende B.V. [aut, cph]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Repository: CRAN
Date/Publication: 2025-01-10 20:50:02 UTC

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New package nhanesA with initial version 1.3
Package: nhanesA
Version: 1.3
Date: 2025-01-08
Title: NHANES Data Retrieval
BugReports: https://github.com/cjendres1/nhanes/issues
Depends: R (>= 4.1.0), methods
Imports: stringr, foreign, rvest, xml2, dplyr, plyr
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://cran.r-project.org/package=nhanesA
Suggests: knitr, DBI, odbc, RMariaDB, RPostgres, rmarkdown, survey, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-08 01:28:28 UTC; BadgerDancer
Author: Christopher Endres [aut, cre], Laha Ale [aut] , Robert Gentleman [aut], Deepayan Sarkar [aut]
Maintainer: Christopher Endres <cjendres1@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-10 15:10:02 UTC

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New package geneviewer with initial version 0.1.10
Package: geneviewer
Title: Gene Cluster Visualizations
Version: 0.1.10
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Description: Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Language: en-US
URL: https://github.com/nvelden/geneviewer
BugReports: https://github.com/nvelden/geneviewer/issues
Depends: R (>= 3.5.0)
Imports: htmlwidgets, fontawesome, magrittr, dplyr, tidyr, rlang
Suggests: knitr, rmarkdown, shiny, biomaRt, pwalign, Biostrings, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-01-09 15:43:46 UTC; nielsvandervelden
Author: Niels van der Velden [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-10 14:40:02 UTC

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New package exams.forge.data with initial version 0.1.0
Package: exams.forge.data
Title: Precomputed Dataset Collection Used in 'exams.forge'
Version: 0.1.0
Description: The dataset collection supports Pearson correlation and linear regression analysis, with datasets for n=100,200,400,800,1000, where n is the sum of squared values in x. Each dataset has x values summing to zero, with sample sizes (observations in x) ranging from 2 to 10. Additional data frames include variables with German names and measurement levels, and distribution details with R function names, LaTeX names, discreteness, and package origins.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2025-01-09 14:44:00 UTC; sigbert
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Repository: CRAN
Date/Publication: 2025-01-10 14:40:06 UTC

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New package DHSr with initial version 0.1.0
Package: DHSr
Title: Create Large Scale Repeated Regression Summary Statistics Dataset and Visualization Seamlessly
Version: 0.1.0
Maintainer: Arnab Samanta <arnob.shamanta62@gmail.com>
Description: Mapping, spatial analysis, and statistical modeling of microdata from sources such as the Demographic and Health Surveys <https://www.dhsprogram.com/> and Integrated Public Use Microdata Series <https://www.ipums.org/>. It can also be extended to other datasets. The package supports spatial correlation index construction and visualization, along with empirical Bayes approximation of regression coefficients in a multistage setup. The main functionality is repeated regression — for example, if we have to run regression for n groups, the group ID should be vertically composed into the variable for the parameter `location_var`. It can perform various kinds of regression, such as Generalized Regression Models, logit, probit, and more. Additionally, it can incorporate interaction effects. The key benefit of the package is its ability to store the regression results performed repeatedly on a dataset by the group ID, along with respective p-values and map those estimates.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, ggplot2, rlang, sf, spdep, viridis, nlme, MuMIn, tidyr, stats
Suggests: knitr, spData, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-09 17:34:14 UTC; 91911
Author: Arnab Samanta [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-10 15:00:06 UTC

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New package simulist with initial version 0.4.0
Package: simulist
Title: Simulate Disease Outbreak Line List and Contacts Data
Version: 0.4.0
Description: Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/simulist, https://epiverse-trace.github.io/simulist/
BugReports: https://github.com/epiverse-trace/simulist/issues
Depends: R (>= 3.6.0)
Imports: checkmate, epiparameter (>= 0.4.0), randomNames, rlang, stats
Suggests: dplyr, epicontacts (>= 1.1.3), ggplot2, incidence2 (>= 2.1.0), knitr, rmarkdown, spelling, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2025-01-09 14:04:38 UTC; lshjl15
Author: Joshua W. Lambert [aut, cre, cph] , Carmen Tamayo [aut] , Hugo Gruson [ctb, rev] , Pratik R. Gupte [ctb, rev] , Adam Kucharski [rev] , Chris Hartgerink [rev]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2025-01-10 14:00:02 UTC

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New package HEssRNA with initial version 1.0.1
Package: HEssRNA
Title: Heritability-Based Estimation of Sample Size for RNA-Seq Data
Version: 1.0.1
Description: Provides tools for estimating sample sizes primarily based on heritability, while also considering additional parameters such as statistical power and fold change. The package normalizes heritability values according to trait-specific heritability and classification to enhance accuracy in sample size estimation.
License: GPL-3
Encoding: UTF-8
Suggests: car, testthat (>= 3.0.0)
Imports: tidyr, dplyr, magrittr, stats, utils, DESeq2, ssizeRNA, Rdpack
NeedsCompilation: no
Packaged: 2024-12-24 09:09:39 UTC; hp
Author: Naina Kumari [aut], Jagajjit Sahu [aut], Sarika Jaiswal [aut, cre], Mir Asif Iquebal [aut], Dinesh Kumar [aut]
Maintainer: Sarika Jaiswal <sarika@icar.gov.in>
Repository: CRAN
Date/Publication: 2025-01-10 13:50:01 UTC

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New package gsaot with initial version 0.1.0
Package: gsaot
Title: Compute Global Sensitivity Analysis Indices Using Optimal Transport
Version: 0.1.0
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: boot, ggplot2, patchwork (>= 1.2.0), Rcpp, RcppEigen (>= 0.3.4.0.0), Rdpack (>= 2.4), stats, transport (>= 0.15.0)
URL: https://github.com/pietrocipolla/gsaot, https://pietrocipolla.github.io/gsaot/
BugReports: https://github.com/pietrocipolla/gsaot/issues
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-01-09 14:05:11 UTC; dagileonardo
Author: Leonardo Chiani [aut, cre, cph] , Emanuele Borgonovo [rev], Elmar Plischke [rev], Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Repository: CRAN
Date/Publication: 2025-01-10 14:00:06 UTC

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Thu, 09 Jan 2025

New package RLescalation with initial version 1.0.1
Package: RLescalation
Title: Optimal Dose Escalation Using Deep Reinforcement Learning
Version: 1.0.1
Description: An implementation to compute an optimal dose escalation rule using deep reinforcement learning in phase I oncology trials (Matsuura et al. (2023) <doi:10.1080/10543406.2023.2170402>). The dose escalation rule can directly optimize the percentages of correct selection (PCS) of the maximum tolerated dose (MTD).
URL: https://github.com/MatsuuraKentaro/RLescalation
BugReports: https://github.com/MatsuuraKentaro/RLescalation/issues
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Imports: glue, R6, nleqslv, reticulate, stats, utils
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-01-09 06:02:07 UTC; kmatsuu
Author: Kentaro Matsuura [aut, cre, cph]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-09 18:10:05 UTC

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New package bayesestdft with initial version 1.0.0
Package: bayesestdft
Title: Estimating the Degrees of Freedom of the Student's t-Distribution under a Bayesian Framework
Version: 1.0.0
Description: A Bayesian framework to estimate the Student's t-distribution's degrees of freedom is developed. Markov Chain Monte Carlo sampling routines are developed as in <doi:10.3390/axioms11090462> to sample from the posterior distribution of the degrees of freedom. A random walk Metropolis algorithm is used for sampling when Jeffrey's and Gamma priors are endowed upon the degrees of freedom. In addition, the Metropolis-adjusted Langevin algorithm for sampling is used under the Jeffrey's prior specification. The Log-normal prior over the degrees of freedom is posed as a viable choice with comparable performance in simulations and real-data application, against other prior choices, where an Elliptical Slice Sampler is used to sample from the concerned posterior.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/Roy-SR-007/bayesestdft
BugReports: https://github.com/Roy-SR-007/bayesestdft/issues
Imports: numDeriv, dplyr
Depends: R (>= 4.0.4)
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-09 05:01:34 UTC; somjit
Author: Somjit Roy [aut, cre], Se Yoon Lee [aut, ctb]
Maintainer: Somjit Roy <sroy_123@tamu.edu>
Repository: CRAN
Date/Publication: 2025-01-09 18:10:01 UTC

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New package IVCor with initial version 0.1.0
Package: IVCor
Title: A Robust Integrated Variance Correlation
Version: 0.1.0
Description: A integrated variance correlation is proposed to measure the dependence between a categorical or continuous random variable and a continuous random variable or vector. This package is designed to estimate the new correlation coefficient with parametric and nonparametric approaches. Test of independence for different problems can also be implemented via the new correlation coefficient with this package.
License: GPL-3
Encoding: UTF-8
Imports: splines, quantreg, BwQuant, quantdr, stats
Suggests: knitr, mvtnorm, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-09 02:24:25 UTC; Surface
Author: Wei Xiong [aut], Han Pan [aut, cre], Hengjian Cui [aut]
Maintainer: Han Pan <scott_pan@163.com>
Repository: CRAN
Date/Publication: 2025-01-09 18:00:02 UTC

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New package hydReng with initial version 0.1.0
Package: hydReng
Title: Hydraulic Engineering Tools
Version: 0.1.0
Description: The 'hydReng' package provides a set of functions for hydraulic engineering tasks and natural hazard assessments. It includes basic hydraulics (wetted area, wetted perimeter, flow, flow velocity, flow depth, and maximum flow) for open channels with arbitrary geometry under uniform flow conditions. For structures such as circular pipes, weirs, and gates, the package includes calculations for pressure flow, backwater depth, and overflow over a weir crest. Additionally, it provides formulas for calculating bedload transport. The formulas used can be found in standard literature on hydraulics, such as Bollrich (2019, ISBN:978-3-410-29169-5) or Hager (2011, ISBN:978-3-642-77430-0).
License: GPL-3
Encoding: UTF-8
URL: https://github.com/NiccoloGalatioto/hydReng
BugReports: https://github.com/NiccoloGalatioto/hydReng/issues
Suggests: testthat (>= 3.0.0)
Imports: methods
NeedsCompilation: no
Packaged: 2025-01-08 20:58:10 UTC; NICCOLO
Author: Galatioto Niccolo [cre, aut], Buehlmann Marius [aut], HOLINGER AG [cph, fnd]
Maintainer: Galatioto Niccolo <niccolo.galatioto@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-09 17:40:02 UTC

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New package VARcpDetectOnline with initial version 0.1.0
Package: VARcpDetectOnline
Title: Sequential Change Point Detection for High-Dimensional VAR Models
Version: 0.1.0
Description: Implements the algorithm introduced in Tian, Y., and Safikhani, A. (2024) <doi:10.5705/ss.202024.0182>, "Sequential Change Point Detection in High-dimensional Vector Auto-regressive Models". This package provides tools for detecting change points in the transition matrices of Vector Auto-Regressive (VAR) models, effectively identifying shifts in temporal and cross-correlations within high-dimensional time series data. The package includes functions to generate synthetic VAR data, detect change points in high-dimensional time series, and analyze real-world data. It also demonstrates an application to financial data: the daily log returns of 186 S&P 500 stocks from 2004-02-06 to 2016-03-02.
Encoding: UTF-8
LazyData: true
Imports: MASS, sparsevar
Suggests: ggplot2
License: MIT + file LICENSE
URL: https://github.com/Helloworld9293/VARcpDetectOnline
BugReports: https://github.com/Helloworld9293/VARcpDetectOnline/issues
NeedsCompilation: no
Packaged: 2025-01-08 14:59:15 UTC; AAA
Author: Yuhan Tian [aut, cre], Abolfazl Safikhani [aut]
Maintainer: Yuhan Tian <yuhan.tian@ufl.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-01-09 14:10:02 UTC

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New package QAEnsemble with initial version 1.0.0
Package: QAEnsemble
Title: Ensemble Quadratic and Affine Invariant Markov Chain Monte Carlo
Version: 1.0.0
Description: The Ensemble Quadratic and Affine Invariant Markov chain Monte Carlo algorithms provide an efficient way to perform Bayesian inference in difficult parameter space geometries. The Ensemble Quadratic Monte Carlo algorithm was developed by Militzer (2023) <doi:10.3847/1538-4357/ace1f1>. The Ensemble Affine Invariant algorithm was developed by Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65> and it was implemented in Python by Foreman-Mackey et al (2013) <doi:10.48550/arXiv.1202.3665>. The Quadratic Monte Carlo method was shown to perform better than the Affine Invariant method in the paper by Militzer (2023) <doi:10.3847/1538-4357/ace1f1> and the Quadratic Monte Carlo method is the default method used. The Chen-Shao Highest Posterior Density Estimation algorithm is used for obtaining credible intervals and the potential scale reduction factor diagnostic is used for checking the convergence of the chains.
License: GPL (>= 2)
Encoding: UTF-8
Suggests: coda, diagram, expm, knitr, rmarkdown, svMisc
VignetteBuilder: knitr
Imports: stats
NeedsCompilation: no
Packaged: 2025-01-08 18:47:26 UTC; wroda
Author: Weston Roda [aut, cre] , Karsten Hempel [aut] , Sasha van Katwyk [aut] , Diepreye Ayabina [aut] , Children's Hospital of Eastern Ontario [fnd], Canada's Drug Agency [fnd], Institute of Health Economics [cph]
Maintainer: Weston Roda <wroda@ihe.ca>
Repository: CRAN
Date/Publication: 2025-01-09 14:50:05 UTC

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New package jetty with initial version 0.1.0
Package: jetty
Title: Execute R in a 'Docker' Context
Version: 0.1.0
Description: The goal of 'jetty' is to execute R functions and code snippets in an isolated R subprocess within a 'Docker' container and return the evaluated results to the local R session. 'jetty' can install necessary packages at runtime and seamlessly propagates errors and outputs from the 'Docker' subprocess back to the main session. 'jetty' is primarily designed for sandboxed testing and quick execution of example code.
License: GPL (>= 3)
Encoding: UTF-8
Imports: renv (>= 1.0.0), rlang
Suggests: here, Matrix, ggplot2, testthat (>= 3.0.0)
URL: https://github.com/dmolitor/jetty, http://www.dmolitor.com/jetty/
BugReports: https://github.com/dmolitor/jetty/issues
NeedsCompilation: no
Packaged: 2025-01-08 17:59:08 UTC; dmolitor
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-09 14:50:02 UTC

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New package invivoPKfit with initial version 2.0.0
Package: invivoPKfit
Title: Fits Toxicokinetic Models to In Vivo PK Data Sets
Version: 2.0.0
Date: 2024-12-23
Author: John Wambaugh [aut, cre] , Caroline Ring [aut] , Gilberto Padilla Mercado [aut] , Chris Cook [aut]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Description: Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).
License: GPL-3
Depends: R (>= 3.5.0)
Imports: cli, devtools, dplyr, ggplot2, glue, httk, magrittr, MASS, Matrix, multidplyr (>= 0.1.3), numDeriv, optimx, PK, pracma, purrr, rlang, scales, tibble, tidyr, tidyselect
Suggests: cowplot, knitr, RColorBrewer, rmarkdown, stringr, testthat (>= 3.0.0), tidyverse
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: TRUE
NeedsCompilation: no
Packaged: 2025-01-08 15:27:26 UTC; GPADILLA
Repository: CRAN
Date/Publication: 2025-01-09 14:30:02 UTC

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New package ColombiAPI with initial version 0.1.0
Package: ColombiAPI
Title: Access Colombia's Public Data via 'API-Colombia'
Version: 0.1.0
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Description: Provides a seamless interface to access diverse public data about Colombia through the 'API-Colombia', a RESTful API. The package enables users to explore various aspects of Colombia, including general information, geography, and cultural insights. It includes five API-related functions to retrieve data on topics such as Colombia's general information, airports, departments, regions, and presidents. Additionally, 'ColombiAPI' offers a built-in function to view the datasets available within the package. The package also includes curated datasets covering Bogota air stations, business and holiday dates, public schools, Colombian coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota, making it a comprehensive tool for exploring Colombia's data. For more details on the 'API-Colombia', see <https://api-colombia.com/>.
License: GPL-3
URL: https://github.com/lightbluetitan/colombiapi, https://lightbluetitan.github.io/colombiapi/
BugReports: https://github.com/lightbluetitan/colombiapi/issues
Encoding: UTF-8
LazyData: true
Suggests: ggplot2, testthat (>= 3.0.0), knitr, rmarkdown
Imports: httr, jsonlite, dplyr, magrittr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-08 17:09:40 UTC; renzocrossi
Author: Renzo Caceres Rossi [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-01-09 15:00:02 UTC

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New package collett with initial version 0.1.0
Package: collett
Title: Datasets from "Modelling Survival Data in Medical Research" by Collett
Version: 0.1.0
Maintainer: Mark Clements <mark.clements@ki.se>
Description: Datasets for the book entitled "Modelling Survival Data in Medical Research" by Collett (2023) <doi:10.1201/9781003282525>. The datasets provide extensive examples of time-to-event data.
URL: https://github.com/mclements/collett
BugReports: https://github.com/mclements/collett/issues
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: utils
Suggests: survival
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-08 16:25:24 UTC; marcle
Author: Mark Clements [aut, cre]
Repository: CRAN
Date/Publication: 2025-01-09 14:30:13 UTC

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New package pacta.multi.loanbook with initial version 0.1.1
Package: pacta.multi.loanbook
Title: Run 'PACTA' on Multiple Loan Books Easily
Version: 0.1.1
Description: Run Paris Agreement Capital Transition Assessment ('PACTA') analyses on multiple loan books in a structured way. Provides access to standard 'PACTA' metrics and additional 'PACTA'-related metrics for multiple loan books. Results take the form of 'csv' files and plots and are exported to user-specified project paths.
Encoding: UTF-8
Imports: cli (>= 3.2.0), config, dplyr, ggalluvial, ggplot2, ggrepel, glue, r2dii.analysis (>= 0.3.0), r2dii.data (>= 0.5.0), r2dii.match (>= 0.3.0), r2dii.plot (>= 0.4.0), readr (>= 2.0.0), readxl, rlang, scales, tidyr, yaml, yesno
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Suggests: DiagrammeR, gt, knitr, pkgdown, rmarkdown, usethis, testthat (>= 3.1.9), tibble, withr, writexl
VignetteBuilder: knitr
URL: https://rmi-pacta.github.io/pacta.multi.loanbook/, https://github.com/RMI-PACTA/pacta.multi.loanbook/
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-08 13:47:09 UTC; jkastl
Author: Jacob Kastl [aut, cre, ctr] , CJ Yetman [aut, ctr] , Monika Furdyna [aut, ctr] , RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-09 14:00:01 UTC

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New package ellmer with initial version 0.1.0
Package: ellmer
Title: Chat with Large Language Models
Version: 0.1.0
Description: Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.
License: MIT + file LICENSE
URL: https://ellmer.tidyverse.org, https://github.com/tidyverse/ellmer
BugReports: https://github.com/tidyverse/ellmer/issues
Imports: cli, coro (>= 1.1.0), glue, httr2 (>= 1.0.7), jsonlite, later (>= 1.4.0), promises (>= 1.3.1), R6, rlang (>= 1.1.0), S7 (>= 0.2.0)
Suggests: base64enc, bslib, curl (>= 6.0.1), gitcreds, knitr, magick, openssl, paws.common, rmarkdown, shiny, shinychat (>= 0.1.1), testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-07 23:15:32 UTC; hadleywickham
Author: Hadley Wickham [aut, cre], Joe Cheng [aut], Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Repository: CRAN
Date/Publication: 2025-01-09 13:50:05 UTC

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New package rdss with initial version 1.0.14
Package: rdss
Title: Companion Datasets and Functions for Research Design in the Social Sciences
Version: 1.0.14
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.
Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, broom, purrr, estimatr, randomizr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), rdrobust, DIDmultiplegt, broom.mixed, marginaleffects, grf, CausalQueries, metafor, cjoint, lme4, rstanarm, spdep, DeclareDesign, curl
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2025-01-09 03:31:45 UTC; gblair
Author: Graeme Blair [aut, cre] , Alexander Coppock [aut] , Macartan Humphreys [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-09 12:10:02 UTC

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New package approxOT with initial version 1.2
Package: approxOT
Title: Approximate and Exact Optimal Transport Methods
Version: 1.2
Date: 2025-01-06
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Description: R and C++ functions to perform exact and approximate optimal transport. All C++ methods can be linked to other R packages via their header files.
License: GPL (== 3.0)
Imports: Rcpp (>= 1.0.3), stats
LinkingTo: Rcpp, RcppEigen, RcppCGAL, BH
BugReports: https://github.com/ericdunipace/approxOT/issues
Suggests: testthat (>= 2.1.0), transport
Encoding: UTF-8
SystemRequirements: C++17
URL: https://github.com/ericdunipace/approxOT
NeedsCompilation: yes
Packaged: 2025-01-09 00:44:28 UTC; eifer
Author: Eric Dunipace [aut, cre] , Andrew Johnson [ctb] , Espen Bernton [ctb] , Mathieu Gerber [ctb] , Pierre Jacob [ctb] , Dominic Schuhmacher [ctb] , Nicolas Bonneel [ctb]
Repository: CRAN
Date/Publication: 2025-01-09 12:30:06 UTC

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Wed, 08 Jan 2025

New package vegIndexCalc with initial version 0.1.0
Package: vegIndexCalc
Title: Vegetation Indices (VIs) Calculation for Remote Sensing Analysis
Version: 0.1.0
Maintainer: Bijoy Chanda <bijoychanda08@gmail.com>
Description: It provides a comprehensive toolkit for calculating a suite of common vegetation indices (VIs) derived from remote sensing imagery. VIs are essential tools used to quantify vegetation characteristics, such as biomass, leaf area index (LAI) and photosynthetic activity, which are essential parameters in various ecological, agricultural, and environmental studies. Applications of this package include biomass estimation, crop monitoring, forest management, land use and land cover change analysis and climate change studies. For method details see, Deb,D.,Deb,S.,Chakraborty,D.,Singh,J.P.,Singh,A.K.,Dutta,P.and Choudhury,A.(2020)<doi:10.1080/10106049.2020.1756461>. Utilizing this R package, users can effectively extract and analyze critical information from remote sensing imagery, enhancing their comprehension of vegetation dynamics and their importance in global ecosystems. The package includes the function vegetation_indices().
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-08 08:02:46 UTC; ICAR-CAFRI
Author: Dibyendu Deb [aut, ctb], Arpan Bhowmik [aut, ctb], Bijoy Chanda [aut, cre, ctb], J.P. Singh [aut], Sunil Mandi [aut], Alemwati Pongener [aut]
Repository: CRAN
Date/Publication: 2025-01-08 16:30:01 UTC

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New package rmlnomogram with initial version 0.1.2
Package: rmlnomogram
Title: Construct Explainable Nomogram for a Machine Learning Model
Version: 0.1.2
Description: Construct an explainable nomogram for a machine learning (ML) model to improve availability of an ML prediction model in addition to a computer application, particularly in a situation where a computer, a mobile phone, an internet connection, or the application accessibility are unreliable. This package enables a nomogram creation for any ML prediction models, which is conventionally limited to only a linear/logistic regression model. This nomogram may indicate the explainability value per feature, e.g., the Shapley additive explanation value, for each individual. However, this package only allows a nomogram creation for a model using categorical without or with single numerical predictors. Detailed methodologies and examples are documented in our vignette, available at <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rmlnomogram/blob/master/doc/ml_nomogram_exemplar.html>.
Depends: R (>= 4.4)
Imports: dplyr, purrr, broom, stats, ggplot2, ggpubr, stringr, tidyr, utils
Suggests: tidyverse, knitr, caret, randomForest, iml, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-08 10:07:20 UTC; rstudio
Author: Herdiantri Sufriyana [aut, cre] , Emily Chia-Yu Su [aut]
Maintainer: Herdiantri Sufriyana <herdi@nycu.edu.tw>
Repository: CRAN
Date/Publication: 2025-01-08 16:40:02 UTC

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New package MOODE with initial version 1.0.1
Package: MOODE
Title: Multi-Objective Optimal Design of Experiments
Version: 1.0.1
Description: Provides functionality to generate compound optimal designs for targeting the multiple experimental objectives directly, ensuring that the full set of research questions is answered as economically as possible. Designs can be found using point or coordinate exchange algorithms combining estimation, inference and lack-of-fit criteria that account for model inadequacy. Details and examples are given by Koutra et al. (2024) <doi:10.48550/arXiv.2412.17158>.
License: GPL (>= 3)
URL: https://github.com/vkstats/MOODE
BugReports: https://github.com/vkstats/MOODE/issues
Imports: cli, far, progressr, Rdpack, rlang
Suggests: doFuture, foreach
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-08 05:43:28 UTC; vallia
Author: Vasiliki Koutra [aut, cre, cph] , Olga Egorova [aut, cph], Steven Gilmour [aut, cph], Luzia Trinca [aut, cph]
Maintainer: Vasiliki Koutra <vasiliki.koutra@kcl.ac.uk>
Repository: CRAN
Date/Publication: 2025-01-08 16:10:02 UTC

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New package MADMMplasso with initial version 1.0.0
Package: MADMMplasso
Title: Multi Variate Multi Response ADMM with Interaction Effects
Version: 1.0.0
Description: This system allows one to model a multi-variate, multi-response problem with interaction effects. It combines the usual squared error loss for the multi-response problem with some penalty terms to encourage responses that correlate to form groups and also allow for modeling main and interaction effects that exit within the covariates. The optimization method employed is the Alternating Direction Method of Multipliers (ADMM). The implementation is based on the methodology presented on Quachie Asenso, T., & Zucknick, M. (2023) <doi:10.48550/arXiv.2303.11155>.
Imports: Matrix, MASS, Rcpp, RcppArmadillo, foreach, doParallel, class, graphics, parallel, stats, spatstat.sparse, methods
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0), lintr
License: GPL-3
Encoding: UTF-8
Date: 2025-01-08
Language: en-GB
NeedsCompilation: yes
Packaged: 2025-01-08 11:56:39 UTC; waldir
Author: Theophilus Quachie Asenso [aut], Manuela Zucknick [aut], Waldir Leoncio [aut, cre] , Chi Zhang [aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Repository: CRAN
Date/Publication: 2025-01-08 16:40:06 UTC

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New package drone with initial version 1.0.0
Package: drone
Title: Data for Data Visualisation Geometries Encyclopedia
Version: 1.0.0
Description: This is the companion package to the Data Visualization Geometries Encyclopedia, providing seamless access to the associated data.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 4.4.0)
Imports: utils
NeedsCompilation: no
Packaged: 2025-01-08 07:16:47 UTC; DELL
Author: Thiyanga S. Talagala [aut, cre]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Repository: CRAN
Date/Publication: 2025-01-08 16:20:02 UTC

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New package dRiftDM with initial version 0.2.1
Package: dRiftDM
Title: Estimating (Time-Dependent) Drift Diffusion Models
Version: 0.2.1
License: MIT + file LICENSE
Description: Fit and explore Drift Diffusion Models (DDMs), a common tool in psychology for describing decision processes in simple tasks. It can handle both time-independent and time-dependent DDMs. You either choose prebuilt models or create your own, and the package takes care of model predictions and parameter estimation. Model predictions are derived via the numerical solutions provided by Richter, Ulrich, and Janczyk (2023, <doi:10.1016/j.jmp.2023.102756>).
Suggests: testthat (>= 3.0.0), cowsay, knitr, rmarkdown, DMCfun, truncnorm, vdiffr
Encoding: UTF-8
LazyData: true
Imports: withr, parallel, DEoptim, dfoptim, Rcpp, Rdpack, progress, stats
LinkingTo: Rcpp
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
URL: https://github.com/bucky2177/dRiftDM, https://bucky2177.github.io/dRiftDM/
BugReports: https://github.com/bucky2177/dRiftDM/issues
NeedsCompilation: yes
Packaged: 2025-01-08 08:26:07 UTC; vkoob
Author: Valentin Koob [cre, aut, cph], Thomas Richter [aut, cph], Markus Janczyk [ctb]
Maintainer: Valentin Koob <v.koob@web.de>
Repository: CRAN
Date/Publication: 2025-01-08 16:30:05 UTC

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New package tidyprompt with initial version 0.0.1
Package: tidyprompt
Title: Prompt Large Language Models and Enhance Their Functionality
Version: 0.0.1
Description: Easily construct prompts and associated logic for interacting with large language models (LLMs). 'tidyprompt' introduces the concept of prompt wraps, which are building blocks that you can use to quickly turn a simple prompt into a complex one. Prompt wraps do not just modify the prompt text, but also add extraction and validation functions that will be applied to the response of the LLM. This ensures that the user gets the desired output. 'tidyprompt' can add various features to prompts and their evaluation by LLMs, such as structured output, automatic feedback, retries, reasoning modes, autonomous R function calling, and R code generation and evaluation. It is designed to be compatible with any LLM provider that offers chat completion.
License: GPL (>= 3) | file LICENSE
Encoding: UTF-8
URL: https://github.com/tjarkvandemerwe/tidyprompt, https://tjarkvandemerwe.github.io/tidyprompt/
BugReports: https://github.com/tjarkvandemerwe/tidyprompt/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), here, callr, skimr, jsonvalidate, tidyjson, DBI
VignetteBuilder: knitr
Imports: dplyr, glue, httr2, jsonlite, stringr, utils, cli
NeedsCompilation: no
Packaged: 2025-01-07 21:45:11 UTC; dhrko
Author: Luka Koning [aut, cre, cph], Tjark Van de Merwe [aut, cph], Kennispunt Twente [fnd]
Maintainer: Luka Koning <l.koning@kennispunttwente.nl>
Repository: CRAN
Date/Publication: 2025-01-08 15:30:02 UTC

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New package npiv with initial version 0.1.3
Package: npiv
Title: Nonparametric Instrumental Variables Estimation and Inference
Version: 0.1.3
Date: 2024-12-10
Imports: progress, MASS, Formula, withr
Maintainer: Timothy Christensen <timothy.christensen@yale.edu>
Description: Implements methods introduced in Chen, Christensen, and Kankanala (2024) <doi:10.1093/restud/rdae025> for estimating and constructing uniform confidence bands for nonparametric structural functions using instrumental variables, including data-driven choice of tuning parameters. All methods in this package apply to nonparametric regression as a special case.
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2025-01-07 18:18:07 UTC; tmc49
Author: Jeffrey S. Racine [aut], Timothy Christensen [aut, cre], Patrick Alken [ctb], Rhys Ulerich [ctb], Simon N. Wood [ctb]
Repository: CRAN
Date/Publication: 2025-01-08 15:10:02 UTC

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New package learner with initial version 0.1.0
Package: learner
Title: Latent Space-Based Transfer Learning
Version: 0.1.0
Maintainer: Sean McGrath <sean.mcgrath514@gmail.com>
Description: Implements transfer learning methods for low-rank matrix estimation. These methods leverage similarity in the latent row and column spaces between the source and target populations to improve estimation in the target population. The methods include the LatEnt spAce-based tRaNsfer lEaRning (LEARNER) method and the direct projection LEARNER (D-LEARNER) method described by McGrath et al. (2024) <doi:10.48550/arXiv.2412.20605>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://github.com/stmcg/learner
BugReports: https://github.com/stmcg/learner/issues
Imports: doParallel, foreach, ScreeNOT
Suggests: testthat (>= 3.0.0)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2025-01-07 19:57:41 UTC; Sean
Author: Sean McGrath [aut, cre] , Cenhao Zhu [aut], Rui Duan [aut]
Repository: CRAN
Date/Publication: 2025-01-08 15:10:08 UTC

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New package KOFM with initial version 0.1.1
Package: KOFM
Title: Test the Kronecker Product Structure in Tensor Factor Models
Version: 0.1.1
Date: 2025-01-02
Author: Zetai Cen [aut, cre]
Maintainer: Zetai Cen <z.cen@lse.ac.uk>
Description: To test if a tensor time series following a Tucker-decomposition factor model has a Kronecker product structure. Supplementary functions for tensor reshape and its reversal are also included.
License: GPL-3
Imports: tensorMiss, MEFM, RSpectra, stats, utils
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-02 12:25:05 UTC; pc
Repository: CRAN
Date/Publication: 2025-01-08 15:50:02 UTC

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New package goldilocks with initial version 0.4.0
Package: goldilocks
Title: Goldilocks Adaptive Trial Designs for Time-to-Event Endpoints
Version: 0.4.0
Description: Implements the Goldilocks adaptive trial design for a time to event outcome using a piecewise exponential model and conjugate Gamma prior distributions. The method closely follows the article by Broglio and colleagues <doi:10.1080/10543406.2014.888569>, which allows users to explore the operating characteristics of different trial designs.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/graemeleehickey/goldilocks
BugReports: https://github.com/graemeleehickey/goldilocks/issues
Depends: R (>= 3.6.0), survival
Imports: dplyr, parallel, pbmcapply, PWEALL, Rcpp, rlang, stats
Suggests: covr, testthat (>= 3.0.0), knitr, rmarkdown
LinkingTo: BH, Rcpp
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-01-07 21:54:40 UTC; hickeg3
Author: Graeme L. Hickey [aut, cre] , Ying Wan [aut], Thevaa Chandereng [aut] , Becton, Dickinson and Company [cph], Tim Kacprowski [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-08 15:30:08 UTC

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New package cdid with initial version 0.1.0
Package: cdid
Title: The Chained Difference-in-Differences
Version: 0.1.0
URL: https://github.com/joelcuerrier/cdid
Maintainer: David Benatia <david.benatia@hec.ca>
Description: Extends the 'did' package to improve efficiency and handling of unbalanced panel data. Bellego, Benatia, and Dortet-Bernadet (2024), "The Chained Difference-in-Differences", Journal of Econometrics, <doi:10.1016/j.jeconom.2024.105783>.
License: GPL-2
Encoding: UTF-8
Imports: Matrix, purrr, MASS, did, BMisc, methods, stats, utils
BugReports: https://github.com/joelcuerrier/cdid/issues
VignetteBuilder: knitr
Suggests: rmarkdown, knitr, openxlsx, data.table, jsonlite, stargazer, devtools,
NeedsCompilation: no
Packaged: 2025-01-07 18:07:00 UTC; dvbn
Author: David Benatia [cre, aut], Christophe Bellego [aut], Joel Cuerrier [aut], Vincent Dortet-Bernadet [aut]
Repository: CRAN
Date/Publication: 2025-01-08 15:10:12 UTC

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New package voronoifortune with initial version 1.0
Package: voronoifortune
Version: 1.0
Date: 2025-01-07
Title: Voronoi Tessellation by Fortune Algorithm
Description: Fortune's (1987, <doi:10.1007/BF01840357>) algorithm is a very efficient method to perform Voronoi tessellation and Delaunay triangulation. This package is a port of the original code published in the early 1990's by Steven Fortune.
License: GPL-3
URL: https://github.com/emmanuelparadis/voronoifortune
BugReports: https://github.com/emmanuelparadis/voronoifortune/issues
NeedsCompilation: yes
Packaged: 2025-01-07 17:22:52 UTC; paradis
Author: Emmanuel Paradis [aut, cre, cph] , Steven Fortune [aut, ctb], Plan 9 Foundation [cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Repository: CRAN
Date/Publication: 2025-01-08 15:00:01 UTC

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New package shinybody with initial version 0.1.3
Package: shinybody
Title: An Interactive Anatomography Widget for 'shiny'
Version: 0.1.3
Description: An 'htmlwidget' of the human body that allows you to hide/show and assign colors to 79 different body parts. The 'human' widget is an 'htmlwidget', so it works in Quarto documents, R Markdown documents, or any other HTML medium. It also functions as an input/output widget in a 'shiny' app.
URL: https://github.com/robert-norberg/shinybody
BugReports: https://github.com/robert-norberg/shinybody/issues
Imports: htmlwidgets (>= 0.8), htmltools, crosstalk
Suggests: knitr, rmarkdown, shiny
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2024-12-23 15:55:57 UTC; 4478023
Author: Robert Norberg [aut, cre], Sebastian Zapata-Tamayo [aut, ctb], Mehrun Huda [aut, ctb] , Moffitt Cancer Center [cph]
Maintainer: Robert Norberg <Robert.Norberg@moffitt.org>
Repository: CRAN
Date/Publication: 2025-01-08 14:40:02 UTC

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New package epiparameter with initial version 0.4.0
Package: epiparameter
Title: Classes and Helper Functions for Working with Epidemiological Parameters
Version: 0.4.0
Description: Classes and helper functions for loading, extracting, converting, manipulating, plotting and aggregating epidemiological parameters for infectious diseases. Epidemiological parameters extracted from the literature are loaded from the 'epiparameterDB' R package.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/epiparameter/, https://epiverse-trace.github.io/epiparameter/
BugReports: https://github.com/epiverse-trace/epiparameter/issues
Depends: R (>= 4.1.0)
Imports: cachem, checkmate, cli, distcrete, distributional, epiparameterDB, graphics, lifecycle, pillar, rlang, stats, tools, utils
Suggests: bookdown, DT, ggplot2, knitr, RColorBrewer, rmarkdown, spelling, testthat (>= 3.0.0), vdiffr (>= 1.0.7), visNetwork
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2025-01-07 16:58:31 UTC; lshjl15
Author: Joshua W. Lambert [aut, cre, cph] , Adam Kucharski [aut, cph] , Carmen Tamayo [aut] , Hugo Gruson [ctb, rev] , Sebastian Funk [ctb] , Pratik Gupte [rev] , James M. Azam [rev] , Chris Hartgerink [rev] , Tim Taylor [rev]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2025-01-08 14:50:09 UTC

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New package archeofrag.gui with initial version 0.1.0
Package: archeofrag.gui
Title: Spatial Analysis in Archaeology from Refitting Fragments (GUI)
Version: 0.1.0
Date: 2024-12-18
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Description: A 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets. Features include: exclusive focus on connection relationships (i.e. physical refits), built-in documentation and convenient workflow, plot generation and export, R code generation to re-execute the simulations in R and ensure reproducibility, support for parallel computing to speed up computation. A demonstration version of the app is available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
License: GPL-3
Repository: CRAN
Encoding: UTF-8
Imports: archeofrag, dendextend, doParallel, DT, foreach, ggplot2, grDevices, igraph, shiny, shinythemes,
Suggests: RBGL,
URL: https://github.com/sebastien-plutniak/archeofrag.gui
BugReports: https://github.com/sebastien-plutniak/archeofrag.gui/issues
NeedsCompilation: no
Packaged: 2024-12-18 23:07:18 UTC; seb
Date/Publication: 2025-01-08 14:50:14 UTC

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New package spqdep with initial version 0.1.3.5
Package: spqdep
Title: Testing for Spatial Independence of Cross-Sectional Qualitative Data
Version: 0.1.3.5
Date: 2024-12-17
Description: Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://f8l5h9.github.io/spqdep/
LazyData: true
VignetteBuilder: knitr
Imports: broom, dplyr, ggplot2, gt, gtools, igraph, Matrix, methods, purrr, rsample, sf, sp, spatialreg, spdep, stats, tidyr
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
BugReports: https://github.com/f8l5h9/spqdep/issues
NeedsCompilation: no
Packaged: 2024-12-18 10:30:18 UTC; fernandoair
Author: Fernando Lopez [aut, cre] , Roman Minguez [aut] , Antonio Paez [aut] , Manuel Ruiz [aut]
Maintainer: Fernando Lopez <fernando.lopez@upct.es>
Repository: CRAN
Date/Publication: 2025-01-08 09:00:02 UTC

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Tue, 07 Jan 2025

New package WIPF with initial version 0.1.0-1
Package: WIPF
Title: Weighted Iterative Proportional Fitting
Version: 0.1.0-1
Description: Implementation of the weighted iterative proportional fitting (WIPF) procedure for updating/adjusting a N-dimensional array (currently N<=3) given a weight structure and some target marginals. Acknowledgements: The author wish to thank Ministerio de Ciencia, Innovación y Universidades (grant PID2021-128228NB-I00) and Fundación Mapfre (grant 'Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el cálculo de productos de vida') for supporting this research.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-07 14:22:04 UTC; pavia
Author: Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Repository: CRAN
Date/Publication: 2025-01-07 16:30:05 UTC

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New package utf8ify with initial version 0.1.0
Package: utf8ify
Title: Format Text Using Unicode
Version: 0.1.0
Description: Format text (bold, italic, ...) and numbers using UTF-8. Offers functions to search for emojis and include them in your text.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/rolkra/utf8ify
Depends: R (>= 4.1.0)
Imports:
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-07 15:05:48 UTC; rolkra
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-07 16:50:06 UTC

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New package DNNSIM with initial version 0.1.1
Package: DNNSIM
Title: Single-Index Neural Network for Skewed Heavy-Tailed Data
Version: 0.1.1
Maintainer: Qingyang Liu <rh8liuqy@gmail.com>
Description: Provides a deep neural network model with a monotonic increasing single index function tailored for periodontal disease studies. The residuals are assumed to follow a skewed T distribution, a skewed normal distribution, or a normal distribution. More details can be found at Liu, Huang, and Bai (2024) <doi:10.1016/j.csda.2024.108012>.
License: GPL (>= 3)
Encoding: UTF-8
SystemRequirements: Python (>= 3.8.0); PyTorch (https://pytorch.org/); NumPy (https://numpy.org/); SciPy (https://scipy.org/); sklearn (https://scikit-learn.org/stable/);
Imports: reticulate (>= 1.37.0), stats (>= 4.3.0), Rdpack (>= 2.6)
NeedsCompilation: no
Packaged: 2025-01-07 04:07:56 UTC; Kevin_Liu
Author: Qingyang Liu [aut, cre] , Shijie Wang [aut], Ray Bai [aut] , Dipankar Bandyopadhyay [aut]
Repository: CRAN
Date/Publication: 2025-01-07 16:50:13 UTC

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New package creepyalien with initial version 1.0.0
Package: creepyalien
Title: Puzzle Game for the R Console
Version: 1.0.0
Description: Puzzle game that can be played in the R console. Help the alien to find the ship.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/rolkra/creepyalien
Imports: beepr, cli, glue, stats
NeedsCompilation: no
Packaged: 2025-01-07 14:02:19 UTC; rolkra
Author: Roland Krasser [aut, cre], Peter Prevos [aut]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-07 16:30:01 UTC

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New package Certara.RsNLME.ModelExecutor with initial version 3.0.1
Package: Certara.RsNLME.ModelExecutor
Title: Execute Pharmacometric Models Using 'shiny'
Version: 3.0.1
Description: Execute Nonlinear Mixed Effects (NLME) models for pharmacometrics using a 'shiny' interface. Specify engine parameters and select from different run options, including simple estimation, stepwise covariate search, bootstrapping, simulation, visual predictive check, and more. Models are executed using the 'Certara.RsNLME' package.
Depends: R (>= 4.0)
License: LGPL-3
URL: https://certara.github.io/R-RsNLME-model-executor/
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: Certara.RsNLME, Certara.NLME8, shinyAce, shinymeta, bslib (>= 0.7.0), htmltools, magrittr, dplyr, shiny (>= 1.7.4), shinyFiles, shinyjs, shinyWidgets, stringr, tools, fs, ggplot2, future, promises, reshape, jsonlite, DT
NeedsCompilation: no
Packaged: 2025-01-06 21:35:16 UTC; jcraig
Author: James Craig [aut, cre], Mike Talley [aut], Vitalii Nazarov [aut], Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Repository: CRAN
Date/Publication: 2025-01-07 16:40:01 UTC

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New package cpp11bigwig with initial version 0.1.0
Package: cpp11bigwig
Title: Read bigWig and bigBed Files
Version: 0.1.0
Description: Read bigWig and bigBed files using "libBigWig" <https://github.com/dpryan79/libBigWig>. Provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.
License: MIT + file LICENSE
URL: https://rnabioco.github.io/cpp11bigwig/, https://github.com/rnabioco/cpp11bigwig
BugReports: https://github.com/rnabioco/cpp11bigwig/issues
Imports: GenomicRanges, IRanges, tibble
Suggests: testthat (>= 3.0.0)
LinkingTo: cpp11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-01-07 13:44:13 UTC; jayhesselberth
Author: Jay Hesselberth [aut, cre], RNA Bioscience Initiative [fnd, cph], Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-07 14:50:02 UTC

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New package ritalic with initial version 0.10.1
Package: ritalic
Title: Interface to the ITALIC Database of Lichen Biodiversity
Version: 0.10.1
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>). ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys. More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>. The API documentation is available at <https://italic.units.it/?procedure=api>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/plant-data/ritalic
BugReports: https://github.com/plant-data/ritalic/issues
Depends: R (>= 3.5.3)
Imports: httr, jsonlite, utils
NeedsCompilation: no
Packaged: 2024-12-19 10:36:37 UTC; matteoconti
Author: Matteo Conti [aut, cre] , Luana Francesconi [aut], Alice Musina [aut]
Repository: CRAN
Date/Publication: 2025-01-07 14:00:02 UTC

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New package MuPETFlow with initial version 0.1.0
Package: MuPETFlow
Title: Multiple Ploidy Estimation Tool for all Species Compatible with Flow Cytometry
Version: 0.1.0
Description: A graphical user interface tool to estimate ploidy from DNA cells stained with fluorescent dyes and analyzed by flow cytometry, following the methodology of Gómez-Muñoz and Fischer (2024) <doi:10.1101/2024.01.24.577056>. Features include multiple file uploading and configuration, peak fluorescence intensity detection, histogram visualizations, peak error curation, ploidy and genome size calculations, and easy results export.
License: GPL (>= 3)
Encoding: UTF-8
Date/Publication: 2025-01-07 14:00:11 UTC
Imports: BiocManager, dplyr, DT, flowCore, ggplot2, ggrepel, gridExtra, markdown, shiny, shinythemes, tidyr, zoo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-23 11:17:37 UTC; cintia
Author: Cintia Gomez-Munoz [aut, cre] , Gilles Fischer [aut]
Maintainer: Cintia Gomez-Munoz <cintia.gomez_munoz@sorbonne-universite.fr>
Repository: CRAN

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Mon, 23 Dec 2024

New package sigugr with initial version 1.0.0
Package: sigugr
Title: Workflow for Geographic Data
Version: 1.0.0
Description: Streamlines geographic data transformation, storage and publication, simplifying data preparation and enhancing interoperability across formats and platforms.
License: MIT + file LICENSE
URL: https://josesamos.github.io/sigugr/, https://github.com/josesamos/sigugr
BugReports: https://github.com/josesamos/sigugr/issues
Depends: R (>= 2.10)
Imports: clc, gdalUtilities, httr, jsonlite, rpostgis, sf, snakecase, terra
Suggests: httptest2, knitr, mockery, purrr, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2024-12-20 13:13:21 UTC; jsamos
Author: Jose Samos [aut, cre] , Universidad de Granada [cph]
Maintainer: Jose Samos <jsamos@ugr.es>
Repository: CRAN
Date/Publication: 2024-12-23 11:20:01 UTC

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New package itmsa with initial version 0.1.0
Package: itmsa
Title: Information-Theoretic Measures for Spatial Association
Version: 0.1.0
Description: Leveraging information-theoretic measures like mutual information and v-measure to quantify spatial associations between patterns (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>; Bai, H. et al. (2023) <doi:10.1080/24694452.2023.2223700>).
License: GPL-3
Encoding: UTF-8
URL: https://stscl.github.io/itmsa/, https://github.com/stscl/itmsa
BugReports: https://github.com/stscl/itmsa/issues
Depends: R (>= 4.1.0)
LinkingTo: Rcpp, RcppThread
Imports: dplyr, purrr, sdsfun (>= 0.6.0), sf
Suggests: knitr, Rcpp, RcppThread, readr, rmarkdown, tibble
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-12-22 14:12:03 UTC; dell
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-23 11:30:01 UTC

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New package ForestElementsR with initial version 2.0.1
Package: ForestElementsR
Title: Data Structures and Functions for Working with Forest Data
Version: 2.0.1
Date: 2024-12-20
Description: Provides generic data structures and algorithms for use with forest mensuration data in a consistent framework. The functions and objects included are a collection of broadly applicable tools. More specialized applications should be implemented in separate packages that build on this foundation. Documentation about 'ForestElementsR' is provided by three vignettes included in this package. For an introduction to the field of forest mensuration, refer to the textbooks by Kershaw et al. (2017) <doi:10.1002/9781118902028>, and van Laar and Akca (2007) <doi:10.1007/978-1-4020-5991-9>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: magrittr, ggplot2, tibble, dplyr, purrr, rlang, Rdpack, tidyr, vctrs, stringr, tidyselect (>= 1.2.0), doBy
Depends: R (>= 4.3), sf
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.2.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-20 21:06:25 UTC; peter
Author: Peter Biber [aut, cre, cph] , Astor Torano Caicoya [aut] , Torben Hilmers [ctb]
Maintainer: Peter Biber <p.biber@tum.de>
Repository: CRAN
Date/Publication: 2024-12-23 11:10:07 UTC

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New package dataset with initial version 0.3.4
Package: dataset
Title: Create Data Frames that are Easier to Exchange and Reuse
Version: 0.3.4
Date: 2024-12-20
Language: en-US
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Description: The aim of the 'dataset' package is to make tidy datasets easier to release, exchange and reuse. It organizes and formats data frame 'R' objects into well-referenced, well-described, interoperable datasets into release and reuse ready form.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://dataset.dataobservatory.eu/
BugReports: https://github.com/dataobservatory-eu/dataset/issues/
LazyData: true
Imports: assertthat, cli, haven, ISOcodes, labelled, methods, pillar, rlang, tibble, utils, vctrs (>= 0.5.2)
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Depends: R (>= 3.5)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-20 19:39:04 UTC; antal
Author: Daniel Antal [aut, cre] , Marcelo Perlin [rev]
Repository: CRAN
Date/Publication: 2024-12-23 11:10:02 UTC

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New package TwoTimeScales with initial version 1.0.0
Package: TwoTimeScales
Title: Analysis of Event Data with Two Time Scales
Version: 1.0.0
URL: https://github.com/AngelaCar/TwoTimeScales, https://angelacar.github.io/TwoTimeScales/
Description: Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales and also, if covariates are available, to estimate a proportional hazards model with such a two-dimensional baseline hazard. Functions are provided to prepare the raw data for estimation, to estimate and to plot the two-dimensional smooth hazard. Extension to a competing risks model are implemented. For details about the method please refer to Carollo et al. (2024) <doi:10.1002/sim.10297>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: colorspace, Epi, fields, JOPS, LMMsolver, popEpi, reshape2, spam, ucminf, viridis
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
BugReports: https://github.com/AngelaCar/TwoTimeScales/issues
NeedsCompilation: no
Packaged: 2024-12-20 08:58:34 UTC; Carollo
Author: Angela Carollo [aut, cre, cph] , Paul H.C. Eilers [aut], Jutta Gampe [aut]
Maintainer: Angela Carollo <carollo@demogr.mpg.de>
Repository: CRAN
Date/Publication: 2024-12-23 10:50:10 UTC

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New package metalite.sl with initial version 0.1.0
Package: metalite.sl
Title: Subject-Level Analysis Using 'metalite'
Version: 0.1.0
Description: Analyzes subject-level data in clinical trials using the 'metalite' data structure. The package simplifies the workflow to create production-ready tables, listings, and figures discussed in the subject-level analysis chapters of "R for Clinical Study Reports and Submission" by Zhang et al. (2022) <https://r4csr.org/>.
Depends: R (>= 4.1.0)
License: GPL (>= 3)
Imports: glue, metalite, metalite.ae, forestly, r2rtf, reactable, stringr, rlang, plotly, htmltools, brew, uuid
Suggests: dplyr, knitr, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-20 05:05:16 UTC; fukuhiro
Author: Benjamin Wang [aut, cre], Yujie Zhao [aut], Hiroaki Fukuda [aut], PoYao Niu [aut], Nan Xiao [aut], Jeetener Chauhan [ctb], Li Ma [ctb], Chen Wang [ctb], Merck Sharp & Dohme Corp [cph]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Repository: CRAN
Date/Publication: 2024-12-23 10:50:01 UTC

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New package HSAR with initial version 0.6.0
Package: HSAR
Title: Hierarchical Spatial Autoregressive Model
Version: 0.6.0
Description: A Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm (Dong and Harris (2014) <doi:10.1111/gean.12049>). The creation of this package was supported by the Economic and Social Research Council (ESRC) through the Applied Quantitative Methods Network: Phase II, grant number ES/K006460/1.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://spatlyu.github.io/HSAR/, https://github.com/spatlyu/HSAR
BugReports: https://github.com/spatlyu/HSAR/issues
Depends: R (>= 3.5)
Imports: spdep, spatialreg, stats
Suggests: knitr, Matrix, RColorBrewer, Rcpp, RcppArmadillo, rmarkdown, sdsfun, sf, tidyverse
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2024-12-20 02:26:53 UTC; dell
Author: Guanpeng Dong [aut, cph] , Wenbo Lv [aut, cre] , Richard Harris [aut], Angelos Mimis [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-23 10:30:02 UTC

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New package hdthreshold with initial version 1.0.0
Package: hdthreshold
Title: Inference on Many Jumps in Nonparametric Panel Regression Models
Version: 1.0.0
Description: Provides uniform testing procedures for existence and heterogeneity of threshold effects in high-dimensional nonparametric panel regression models. The package accompanies the paper Chen, Keilbar, Su and Wang (2023) "Inference on many jumps in nonparametric panel regression models". arXiv preprint <doi:10.48550/arXiv.2312.01162>.
Imports: fdrtool, KernSmooth, rdrobust, stats
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-20 16:39:58 UTC; georg
Author: Georg Keilbar [aut, cre, cph], Likai Chen [ctb], Liangjun Su [ctb], Weining Wang [ctb]
Maintainer: Georg Keilbar <georg.keilbar@hu-berlin.de>
Repository: CRAN
Date/Publication: 2024-12-23 10:50:06 UTC

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Sun, 22 Dec 2024

New package CopernicusMarine with initial version 0.2.4
Package: CopernicusMarine
Title: Search Download and Handle Data from Copernicus Marine Service Information
Version: 0.2.4
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Description: Subset and download data from EU Copernicus Marine Service Information: <https://data.marine.copernicus.eu>. Import data on the oceans physical and biogeochemical state from Copernicus into R without the need of external software.
Depends: R (>= 4.1.0)
Imports: crayon, dplyr, httr2, leaflet, purrr, rlang, sf, stringr, tidyr, utils, xml2
Suggests: lifecycle, ncmeta, stars, testthat (>= 3.0.0)
URL: https://github.com/pepijn-devries/CopernicusMarine, https://pepijn-devries.github.io/CopernicusMarine/
BugReports: https://github.com/pepijn-devries/CopernicusMarine/issues
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-22 18:29:20 UTC; vries171
Repository: CRAN
Date/Publication: 2024-12-22 23:20:02 UTC

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Fri, 20 Dec 2024

New package desk with initial version 1.1.2
Package: desk
Title: Didactic Econometrics Starter Kit
Version: 1.1.2
Description: Written to help undergraduate as well as graduate students to get started with R for basic econometrics without the need to import specific functions and datasets from many different sources. Primarily, the package is meant to accompany the German textbook Auer, L.v., Hoffmann, S., Kranz, T. (2024, ISBN: 978-3-662-68263-0) from which the exercises cover all the topics from the textbook Auer, L.v. (2023, ISBN: 978-3-658-42699-6).
URL: https://github.com/OvGU-SH/desk
BugReports: https://github.com/OvGU-SH/desk/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cli, rstudioapi, stats, graphics, grDevices, utils
Suggests: wooldridge
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-12-20 10:11:07 UTC; Name
Author: Soenke Hoffmann [cre, aut], Tobias Kranz [aut]
Maintainer: Soenke Hoffmann <sohoffma@ovgu.de>
Repository: CRAN
Date/Publication: 2024-12-20 12:40:06 UTC

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New package sTSD with initial version 0.1.0
Package: sTSD
Title: Simulate Time Series Diagnostics
Version: 0.1.0
Maintainer: Steven Miller <steve@svmiller.com>
Description: These are tools that allow users to do time series diagnostics, primarily tests of unit root, by way of simulation. While there is nothing necessarily wrong with the received wisdom of critical values generated decades ago, simulation provides its own perks. Not only is simulation broadly informative as to what these various test statistics do and what are their plausible values, simulation provides more flexibility for assessing unit root by way of different thresholds or different hypothesized distributions.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
NeedsCompilation: no
Packaged: 2024-12-19 13:45:13 UTC; steve
Author: Steven Miller [aut, cre]
Repository: CRAN
Date/Publication: 2024-12-20 10:40:02 UTC

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New package multvardiv with initial version 1.0.10
Package: multvardiv
Title: Multivariate Probability Distributions, Statistical Divergence
Version: 1.0.10
Maintainer: Pierre Santagostini <pierre.santagostini@institut-agro.fr>
Description: Multivariate generalized Gaussian distribution, Multivariate Cauchy distribution, Multivariate t distribution. Distance between two distributions (see N. Bouhlel and A. Dziri (2019): <doi:10.1109/LSP.2019.2915000>, N. Bouhlel and D. Rousseau (2022): <doi:10.3390/e24060838>, N. Bouhlel and D. Rousseau (2023): <doi:10.1109/LSP.2023.3324594>). Manipulation of these multivariate probability distributions.
Depends: R (>= 4.4.0)
Imports: rgl, MASS, data.table
License: GPL (>= 3)
URL: https://forgemia.inra.fr/imhorphen/multvardiv
BugReports: https://forgemia.inra.fr/imhorphen/multvardiv/-/issues
Encoding: UTF-8
Suggests: testthat (>= 3.2.1)
NeedsCompilation: no
Packaged: 2024-12-19 16:27:32 UTC; psantagosti
Author: Pierre Santagostini [aut, cre], Nizar Bouhlel [aut]
Repository: CRAN
Date/Publication: 2024-12-20 11:00:02 UTC

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New package ggtaxplot with initial version 0.0.1
Package: ggtaxplot
Title: Create Plots to Visualize Taxonomy
Version: 0.0.1
Maintainer: Clement Coclet <clement.coclet@gmail.com>
Description: Provides a comprehensive suite of functions for processing and visualizing taxonomic data. It includes functionality to clean and transform taxonomic data, categorize it into hierarchical ranks (such as Phylum, Class, Order, Family, and Genus), and calculate the relative abundance of each category. The package also generates a color palette for visual representation of the taxonomic data, allowing users to easily identify and differentiate between various taxonomic groups. Additionally, it features a river plot visualization to effectively display the distribution of individuals across different taxonomic ranks, facilitating insights into taxonomic visualization.
License: GPL-3
Imports: ggplot2, dplyr, tidyr, tidyverse, scales, RColorBrewer, cluster, vegan, ggalluvial, magrittr, rlang
Suggests: knitr, rmarkdown, testthat, devtools
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-19 17:39:58 UTC; ccoclet
Author: Clement Coclet [aut, cre]
Repository: CRAN
Date/Publication: 2024-12-20 11:00:06 UTC

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New package ciphertext with initial version 0.1.0
Package: ciphertext
Title: Classical Cryptography Methods for Words and Phrases
Version: 0.1.0
Description: Classical cryptography methods for words and brief phrases. Substitution, transposition and concealment (null) ciphers are available, like Caesar, Vigenère, Atbash, affine, simple substitution, Playfair, rail fence, Scytale, single column, and Polybius ciphers.
License: GPL-3
URL: https://github.com/Luigi-Annic/ciphertext
BugReports: https://github.com/Luigi-Annic/ciphertext/issues
Encoding: UTF-8
Depends: R (>= 4.3.0)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-12-19 14:37:44 UTC; luigi
Author: Luigi Annicchiarico [cre, aut]
Maintainer: Luigi Annicchiarico <luigi.annic@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-20 10:40:05 UTC

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New package Certara.RsNLME.ModelBuilder with initial version 3.0.1
Package: Certara.RsNLME.ModelBuilder
Title: Pharmacometric Model Building Using 'shiny'
Version: 3.0.1
Description: Develop Nonlinear Mixed Effects (NLME) models for pharmacometrics using a 'shiny' interface. The Pharmacometric Modeling Language (PML) code updates in real time given changes to user inputs. Models can be executed using the 'Certara.RsNLME' package. Additional support to generate the underlying 'Certara.RsNLME' code to recreate the corresponding model in R is provided in the user interface.
Depends: R (>= 4.0)
License: LGPL-3
URL: https://certara.github.io/R-RsNLME-model-builder/
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: Certara.RsNLME, shinymeta, shinyAce, bslib (>= 0.7.0), data.table, DT, ggplot2, ggforce, htmltools, htmlwidgets, magrittr, methods, shiny (>= 1.7.0), shinyjs, shinyWidgets, tools, utils, fs
NeedsCompilation: no
Packaged: 2024-12-19 17:16:42 UTC; jcraig
Author: James Craig [aut, cre], Mike Talley [aut], Shuhua Hu [ctb], Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Repository: CRAN
Date/Publication: 2024-12-20 11:00:10 UTC

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New package bruneimap with initial version 0.3.1
Package: bruneimap
Title: Maps and Spatial Data of Brunei
Version: 0.3.1
Description: Provides spatial data for mapping Brunei, including boundaries for districts, mukims, and kampongs, as well as locations of key infrastructure such as masjids, hospitals, clinics, and schools. The package supports researchers, analysts, and developers working with Brunei’s geographic and demographic data, offering a quick and accessible foundation for creating maps and conducting spatial studies.
License: GPL (>= 3)
URL: https://github.com/Bruneiverse/bruneimap, https://bruneiverse.github.io/bruneimap/
BugReports: https://github.com/Bruneiverse/bruneimap/issues
Depends: R (>= 3.5), sf
Suggests: ggplot2, knitr, rmarkdown, tidyverse
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
Imports: dplyr, lifecycle
NeedsCompilation: no
Packaged: 2024-12-19 12:57:23 UTC; haziqj
Author: Haziq Jamil [aut, cre, cph] , Hafeezul Raziq [ctb], Alvin Bong [ctb], Aniq Najwa Ariffin [ctb], Danish Ikhwan Mohamad Zainin [ctb], Muhammad Rayme Hijazi Jassrie [ctb], Angela Chan [ctb], Irdina Batrisyia Norharddyman [ctb], Nursyafiqah Mohammad Yusu [...truncated...]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-20 10:40:09 UTC

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New package backtestGraphics with initial version 0.1.7
Package: backtestGraphics
Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics interface to visualize backtest results of different financial instruments, such as equities, futures, and credit default swaps. The package does not run backtests on the given data set but displays a graphical explanation of the backtest results. Users can look at backtest graphics for different instruments, investment strategies, and portfolios. Summary statistics of different portfolio holdings are shown in the left panel, and interactive plots of profit and loss (P\&L), net market value (NMV) and gross market value (GMV) are displayed in the right panel.
Version: 0.1.7
Date: 2024-12-18
License: GPL-3
LazyData: true
Depends: R (>= 3.5.0)
Imports: dygraphs, dplyr, scales, xts, shiny
Suggests: testthat
NeedsCompilation: no
Packaged: 2024-12-19 01:48:25 UTC; milz
Repository: CRAN
Date/Publication: 2024-12-20 10:30:02 UTC
Encoding: UTF-8
Author: Yanrong Song [aut, cre], Zijie Zhu [aut], David Kane [aut], Ziqi Lu [aut], Karan Tibrewal [aut], Fan Zhang [aut]
Maintainer: Yanrong Song <yrsong129@gmail.com>

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Thu, 19 Dec 2024

New package subincomeR with initial version 0.2.2
Package: subincomeR
Title: Access to Global Sub-National Income Data
Version: 0.2.2
Description: Provides access to granular sub-national income data from the MCC-PIK Database Of Sub-national Economic Output (DOSE). The package downloads and processes the data from its open repository on 'Zenodo' (<https://zenodo.org/records/13773040>). Functions are provided to fetch data at multiple geographic levels, match coordinates to administrative regions, and access associated geometries.
License: MIT + file LICENSE
URL: https://github.com/pablogguz/subincomeR, https://pablogguz.github.io/subincomeR/
BugReports: https://github.com/pablogguz/subincomeR/issues
Imports: countrycode, curl, dplyr, rlang, sf, tidygeocoder, utils, zip
Suggests: extrafont, fixest, ggplot2, ggtext, knitr, rmarkdown, spelling
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-12-18 19:16:07 UTC; pablo
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Repository: CRAN
Date/Publication: 2024-12-19 20:40:02 UTC

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New package RGS with initial version 1.0
Package: RGS
Title: Recursive Gradient Scanning Algorithm
Version: 1.0
Description: Provides a recursive gradient scanning algorithm for discretizing continuous variables in Logistic and Cox regression models. This algorithm is especially effective in identifying optimal cut-points for variables with U-shaped relationships to 'lnOR' (the natural logarithm of the odds ratio) or 'lnHR' (the natural logarithm of the hazard ratio), thereby enhancing model fit, interpretability, and predictive power. By iteratively scanning and calculating gradient changes, the method accurately pinpoints critical cut-points within nonlinear relationships, transforming continuous variables into categorical ones. This approach improves risk classification and regression analysis performance, increasing interpretability and practical relevance in clinical and risk management settings.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rms, SemiPar, survival
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-12-19 00:44:14 UTC; 14715
Author: Shuo Yang [aut, cre], Yi Fei [aut], Jinxin Zhang [ths]
Maintainer: Shuo Yang <yangsh223@mail2.sysu.edu.cn>
Repository: CRAN
Date/Publication: 2024-12-19 20:50:02 UTC

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New package fmpapi with initial version 0.2.0
Package: fmpapi
Title: Flexible Client for the 'Financial Modeling Prep' API
Version: 0.2.0
Description: Provides a flexible interface to the 'Financial Modeling Prep' API <https://site.financialmodelingprep.com/developer/docs>. The package supports all available endpoints and parameters, enabling R users to interact with a wide range of financial data.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: httr2 (>= 1.0.0), dplyr (>= 1.0.0), cli (>= 1.0.0)
Suggests: spelling, testthat (>= 3.0.0)
URL: https://github.com/tidy-finance/r-fmpapi, https://tidy-finance.github.io/r-fmpapi/
BugReports: https://github.com/tidy-finance/r-fmpapi/issues
Language: en-US
NeedsCompilation: no
Packaged: 2024-12-18 18:37:47 UTC; krise
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Repository: CRAN
Date/Publication: 2024-12-19 20:40:05 UTC

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New package creditr with initial version 0.6.2
Package: creditr
Version: 0.6.2
Date: 2024-12-15
Title: Credit Default Swaps
Depends: R (>= 3.1.0)
Imports: utils, quantmod, devtools, methods, Rcpp (>= 0.10.6), RCurl, XML, zoo, xts
LinkingTo: Rcpp
Suggests: testthat
License: file LICENSE
URL: https://github.com/yanrong-stacy-song/creditr
Description: Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.
LazyData: true
Repository: CRAN
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-12-19 03:11:31 UTC; milz
Author: Yanrong Song [aut, cre], Zijie Zhu [aut], David Kane [aut], Heidi Chen [aut], Yuanchu Dang [aut], Yang Lu [aut], Kanishka Malik [aut], Skylar Smith [aut], International Swaps and Derivatives Association [cph]
Maintainer: Yanrong Song <yrsong129@gmail.com>
Date/Publication: 2024-12-19 21:00:02 UTC

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New package cpp11qpdf with initial version 1.3.5
Package: cpp11qpdf
Title: Split, Combine and Compress PDF Files
Version: 1.3.5
Description: Bindings to 'qpdf': 'qpdf' (<https://qpdf.sourceforge.io/>) is a an open-source PDF rendering library that allows to conduct content-preserving transformations of PDF files such as split, combine, and compress PDF files.
License: Apache License (>= 2)
URL: https://pacha.dev/cpp11qpdf/
BugReports: https://github.com/pachadotdev/cpp11qpdf/issues
SystemRequirements: libjpeg ( deb: libjpeg-dev, rpm: libjpeg-devel, brew: libjpeg )
Imports: curl
LinkingTo: cpp11
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-12-18 19:37:59 UTC; pacha
Author: Mauricio Vargas Sepulveda [aut, cre] , Jeroen Ooms [aut] , Ben Raymond [ctb], Jay Berkenbilt [cph] , Munk School of Global Affairs and Public Policy [fnd]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2024-12-19 20:40:09 UTC

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New package bivariateLeaflet with initial version 0.1.0
Package: bivariateLeaflet
Title: Create Bivariate Choropleth Maps with 'Leaflet'
Version: 0.1.0
Description: Creates bivariate choropleth maps using 'Leaflet'. This package provides tools for visualizing the relationship between two variables through a color matrix representation on an interactive map.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: leaflet, dplyr, htmltools, rlang, sf
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, tidycensus, tidyr
VignetteBuilder: knitr
Depends: R (>= 3.50)
NeedsCompilation: no
Packaged: 2024-12-18 18:50:51 UTC; mduprey
Author: Michael Duprey [aut, cre], Chris Inkpen [ctb]
Maintainer: Michael Duprey <mduprey@rti.org>
Repository: CRAN
Date/Publication: 2024-12-19 20:40:13 UTC

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New package ZIM4rv with initial version 0.1.1
Package: ZIM4rv
Title: Gene‐based Association Tests of Zero‐inflated Count Phenotype for Rare Variants
Version: 0.1.1
Maintainer: Xiaomin Liu <e0717571@u.nus.edu>
Description: Gene‐based association tests to model count data with excessive zeros and rare variants using zero-inflated Poisson/zero-inflated negative Binomial regression framework. This method was originally described by Fan, Sun, and Li in Genetic Epidemiology 46(1):73-86 <doi:10.1002/gepi.22438>.
License: GPL-3
URL: https://github.com/fanx0037/ZIM4rv
Encoding: UTF-8
LazyData: true
Depends: data.table, pscl, CompQuadForm, stats, SKAT, RNOmni, R (>= 3.5.0)
Suggests: testthat (>= 3.0.0)
BugReports: https://github.com/fanx0037/ZIM4rv/issues
NeedsCompilation: no
Packaged: 2024-12-18 13:34:34 UTC; liuxiaomin
Author: Xiaomin Liu [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-12-19 16:10:07 UTC

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New package capesR with initial version 0.1.0
Package: capesR
Title: Access to CAPES Data
Version: 0.1.0
Date: 2024-12-17
Description: Provides simplified access to the data from the Catalog of Theses and Dissertations of the Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES, <https://catalogodeteses.capes.gov.br>) for the years 1987 through 2022. The dataset includes variables such as Higher Education Institution (institution), Area of Concentration (area), Graduate Program Name (program_name), Type of Work (type), Language of Work (language), Author Identification (author), Abstract (abstract), Advisor Identification (advisor), Development Region (region), State (state).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
Imports: arrow, dplyr, magrittr, rlang, stringr, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: <https://github.com/hugoavmedeiros/capesR>
NeedsCompilation: no
Packaged: 2024-12-18 16:37:22 UTC; leite
Author: Hugo Vasconcelos Medeiros [aut, cre], Dalson Figueiredo Filho [aut], Andre Leite [aut]
Maintainer: Hugo Vasconcelos Medeiros <hugo.medeiros@ufpe.br>
Repository: CRAN
Date/Publication: 2024-12-19 16:20:02 UTC

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New package sae.projection with initial version 0.1.0
Package: sae.projection
Title: Small Area Estimation Using Model-Assisted Projection Method
Version: 0.1.0
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/Alfrzlp/sae.projection
BugReports: https://github.com/Alfrzlp/sae.projection/issues
Imports: cli, doParallel, dplyr, methods, parsnip, recipes, rlang, rsample, stats, survey, tune, workflows, yardstick, bonsai, ranger, lightgbm
Depends: R (>= 4.3.0), tidymodels
NeedsCompilation: no
Packaged: 2024-12-18 08:10:00 UTC; alfrz
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-19 15:40:02 UTC

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New package doParabar with initial version 1.0.2
Package: doParabar
Title: 'foreach' Parallel Adapter for 'parabar' Backends
Version: 1.0.2
Description: Provides a 'foreach' parallel adapter for 'parabar' backends. This package offers a minimal implementation of the '%dopar%' operator, enabling users to run 'foreach' loops in parallel, leveraging the parallel and progress-tracking capabilities of the 'parabar' package. Learn more about 'parabar' and 'doParabar' at <https://parabar.mihaiconstantin.com>.
License: MIT + file LICENSE
URL: https://github.com/mihaiconstantin/doParabar, https://parabar.mihaiconstantin.com/articles/foreach
BugReports: https://github.com/mihaiconstantin/doParabar/issues
Imports: parabar, foreach, iterators, utils
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-12-18 10:34:28 UTC; mihai
Author: Mihai Constantin [aut, cre]
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Repository: CRAN
Date/Publication: 2024-12-19 16:00:05 UTC

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New package DEploid.utils with initial version 0.0.1
Package: DEploid.utils
Title: 'DEploid' Data Analysis and Results Interpretation
Version: 0.0.1
Description: 'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>) is designed for deconvoluting mixed genomes with unknown proportions. Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. This package provides R functions to support data analysis and results interpretation.
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.2), scales (>= 0.4.0), magrittr (>= 1.5), combinat
Suggests: knitr, rmarkdown(>= 1.6), circlize, testthat (>= 0.9.0)
LinkingTo: Rcpp
Encoding: UTF-8
Date: 2024-11-18
License: Apache License (>= 2)
NeedsCompilation: yes
Packaged: 2024-12-18 12:02:05 UTC; rstudio
Author: Joe Zhu [aut, cre] , Jacob Almagro-Garcia [aut], Gil McVean [aut], University of Oxford [cph], Yinghan Liu [ctb], CodeCogs Zyba Ltd [com, cph], Deepak Bandyopadhyay [com, cph], Lutz Kettner [com, cph]
Maintainer: Joe Zhu <sha.joe.zhu@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-19 16:00:18 UTC

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New package Cleanet with initial version 1.0.0
Package: Cleanet
Title: Automated Doublet Detection and Classification for Cytometry Data
Version: 1.0.0
Description: Automated method for doublet detection in flow or mass cytometry data, based on simulating doublets and finding events whose protein expression patterns are similar to the simulated doublets.
Imports: Rcpp, RcppHNSW, ggplot2, dplyr, tidyr, readr, reshape2, tibble, magrittr, methods
LinkingTo: Rcpp, RcppArmadillo
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown, vctrs
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-12-18 04:51:03 UTC; matei
Author: Matei Ionita [aut, cre]
Maintainer: Matei Ionita <matei.ionita@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-19 15:30:11 UTC

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New package rgeoda with initial version 0.0.11-1
Package: rgeoda
Title: R Library for Spatial Data Analysis
Version: 0.0.11-1
Date: 2024-12-18
Maintainer: Xun Li <lixun910@gmail.com>
Description: Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis, Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis. The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
URL: https://github.com/geodacenter/rgeoda/, https://geodacenter.github.io/rgeoda/
BugReports: https://github.com/geodacenter/rgeoda/issues/
Depends: R (>= 4.0.0), methods, digest
License: GPL (>= 2)
Imports: sf, Rcpp (>= 1.0.1)
LinkingTo: Rcpp, BH (>= 1.87.0-1)
Encoding: UTF-8
Suggests: wkb, sp
SystemRequirements: C++17
NeedsCompilation: yes
Packaged: 2024-12-18 17:46:04 UTC; xun
Author: Xun Li [aut, cre], Luc Anselin [aut]
Repository: CRAN
Date/Publication: 2024-12-19 08:30:02 UTC

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Wed, 18 Dec 2024

New package pwrFDR with initial version 3.2.2
Package: pwrFDR
Version: 3.2.2
Title: FDR Power
Imports: flextable, ggplot2, methods, mvtnorm, stats, stringr, TableMonster
Description: Computing Average and TPX Power under various BHFDR type sequential procedures. All of these procedures involve control of some summary of the distribution of the FDP, e.g. the proportion of discoveries which are false in a given experiment. The most widely known of these, the BH-FDR procedure, controls the FDR which is the mean of the FDP. A lesser known procedure, due to Lehmann and Romano, controls the FDX, or probability that the FDP exceeds a user provided threshold. This is less conservative than FWE control procedures but much more conservative than the BH-FDR proceudre. This package and the references supporting it introduce a new procedure for controlling the FDX which we call the BH-FDX procedure. This procedure iteratively identifies, given alpha and lower threshold delta, an alpha* less than alpha at which BH-FDR guarantees FDX control. This uses asymptotic approximation and is only slightly more conservative than the BH-FDR procedure. Likewise, we can think of the power i [...truncated...]
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2024-12-18 16:31:02 UTC; izmirlig
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Repository: CRAN
Date/Publication: 2024-12-18 17:00:02 UTC

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New package catalytic with initial version 0.1.0
Package: catalytic
Title: Tools for Applying Catalytic Priors in Statistical Modeling
Version: 0.1.0
Description: To improve estimation accuracy and stability in statistical modeling, catalytic prior distributions are employed, integrating observed data with synthetic data generated from a simpler model's predictive distribution. This approach enhances model robustness, stability, and flexibility in complex data scenarios. The catalytic prior distributions are introduced by 'Huang et al.' (2020, <doi:10.1073/pnas.1920913117>), Li and Huang (2023, <doi:10.48550/arXiv.2312.01411>).
License: MIT + file LICENSE
Encoding: UTF-8
Imports: coda, invgamma, rlang, rstan, stats, truncnorm, MASS, lme4, quadform, survival, methods
Depends: R (>= 3.5.0)
LazyData: true
Suggests: knitr, rmarkdown, testthat, pROC
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-17 08:57:19 UTC; rosewu
Author: Yitong Wu [aut] , Dongming Huang [aut, cre] , Weihao Li [aut], Ministry of Education, Singapore [fnd] .)
Maintainer: Dongming Huang <huang.dongming@nus.edu.sg>
Repository: CRAN
Date/Publication: 2024-12-18 16:10:02 UTC

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New package BAREB with initial version 0.1.2
Package: BAREB
Title: A Bayesian Repulsive Biclustering Model for Periodontal Data
Version: 0.1.2
Description: Simultaneously clusters the Periodontal diseases (PD) patients and their tooth sites after taking the patient- and site-level covariates into consideration. 'BAREB' uses the determinantal point process (DPP) prior to induce diversity among different biclusters to facilitate parsimony and interpretability. Essentially, 'BAREB' is a cluster-wise linear model based on Yuliang (2020) <doi:10.1002/sim.8536>.
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
NeedsCompilation: yes
Depends: R (>= 3.5.0)
Repository: CRAN
Packaged: 2024-12-18 01:27:43 UTC; kevin_liu
Author: Yuliang Li [aut], Yanxun Xu [aut], Dipankar Bandyopadhyay [aut], John Burkardt [ctb], Qingyang Liu [aut, cre]
Maintainer: Qingyang Liu <rh8liuqy@gmail.com>
Date/Publication: 2024-12-18 16:10:08 UTC

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New package tatooheene with initial version 0.19.0
Package: tatooheene
Title: Technology Appraisal Toolbox for Health Economic Evaluations in the Netherlands
Version: 0.19.0
Description: Functions to support economic modelling in R based on the methods of the Dutch guideline for economic evaluations in healthcare <https://www.zorginstituutnederland.nl/publicaties/publicatie/2024/01/16/richtlijn-voor-het-uitvoeren-van-economische-evaluaties-in-de-gezondheidszorg>, CBS data <https://www.cbs.nl/>, and OECD data <https://www.oecd.org/en.html>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5)
LazyData: true
Imports: dplyr (>= 1.1.4), assertthat (>= 0.2.1), tidyr (>= 1.3.0), stats
Suggests: cbsodataR, lubridate, here, testthat
NeedsCompilation: no
Packaged: 2024-12-17 16:45:33 UTC; 85304spe
Author: Frederick Thielen [aut] , Stijn Peeters [aut, cre]
Maintainer: Stijn Peeters <s.b.peeters@eshpm.eur.nl>
Repository: CRAN
Date/Publication: 2024-12-18 15:50:06 UTC

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New package stepSplitReg with initial version 1.0.4
Package: stepSplitReg
Title: Stepwise Split Regularized Regression
Version: 1.0.4
Date: 2024-12-16
Description: Functions to perform stepwise split regularized regression. The approach first uses a stepwise algorithm to split the variables into the models with a goodness of fit criterion, and then regularization is applied to each model. The weights of the models in the ensemble are determined based on a criterion selected by the user.
License: GPL (>= 2)
Biarch: true
Imports: Rcpp (>= 1.0.7), SplitGLM, nnls
Suggests: testthat, mvnfast, vctrs
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-12-17 03:35:48 UTC; anthony
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Repository: CRAN
Date/Publication: 2024-12-18 15:20:02 UTC

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New package splineCox with initial version 0.0.1
Package: splineCox
Title: A Two-Stage Estimation Approach to Cox Regression Using M-Spline Function
Version: 0.0.1
Maintainer: Ren Teranishi <ren.teranishi1227@gmail.com>
Description: Implements a two-stage estimation approach for Cox regression using five-parameter M-spline functions to model the baseline hazard. It allows for flexible hazard shapes and model selection based on log-likelihood criteria.
License: GPL (>= 3)
Encoding: UTF-8
Imports: joint.Cox
Suggests: knitr, rmarkdown, spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2024-12-17 23:10:49 UTC; a223ms012t
Author: Ren Teranishi [aut, cre]
Repository: CRAN
Date/Publication: 2024-12-18 16:00:02 UTC

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New package spanishoddata with initial version 0.1.0
Package: spanishoddata
Title: Get Spanish Origin-Destination Data
Version: 0.1.0
Description: Gain seamless access to origin-destination (OD) data from the Spanish Ministry of Transport, hosted at <https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>. This package simplifies the management of these large datasets by providing tools to download zone boundaries, handle associated origin-destination data, and process it efficiently with the 'duckdb' database interface. Local caching minimizes repeated downloads, streamlining workflows for researchers and analysts. Extensive documentation is available at <https://ropenspain.github.io/spanishoddata/index.html>, offering guides on creating static and dynamic mobility flow visualizations and transforming large datasets into analysis-ready formats.
License: MIT + file LICENSE
URL: https://rOpenSpain.github.io/spanishoddata/, https://github.com/rOpenSpain/spanishoddata
BugReports: https://github.com/rOpenSpain/spanishoddata/issues
Depends: R (>= 3.5.0)
Imports: checkmate, curl (>= 5.0.0), DBI, dplyr, duckdb (>= 0.5.0), fs, glue, here, httr2, lubridate, memuse, parallelly, purrr, readr, rlang, sf, stats, stringr, tibble, xml2
Suggests: flowmapblue, flowmapper (>= 0.1.2), furrr, future, hexSticker, mapSpain, quarto, remotes, scales, testthat (>= 3.0.0), tidyverse
VignetteBuilder: quarto
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-17 11:48:19 UTC; ek
Author: Egor Kotov [aut, cre] , Robin Lovelace [aut] , Eugeni Vidal-Tortosa [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-18 15:40:02 UTC

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New package shinychat with initial version 0.1.1
Package: shinychat
Title: Chat UI Component for 'shiny'
Version: 0.1.1
Description: Provides a scrolling chat interface with multiline input, suitable for creating chatbot apps based on Large Language Models (LLMs). Designed to work particularly well with the 'elmer' R package for calling LLMs.
License: MIT + file LICENSE
URL: https://github.com/jcheng5/shinychat, https://jcheng5.github.io/shinychat/
BugReports: https://github.com/jcheng5/shinychat/issues
Imports: bslib, coro, htmltools, promises (>= 1.3.2), rlang, shiny (>= 1.10.0)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-17 19:02:58 UTC; jcheng
Author: Joe Cheng [aut, cre], Carson Sievert [aut], Posit Software, PBC [cph, fnd]
Maintainer: Joe Cheng <joe@posit.co>
Repository: CRAN
Date/Publication: 2024-12-18 15:50:10 UTC

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New package PSGD with initial version 1.0.4
Package: PSGD
Title: Projected Subset Gradient Descent
Version: 1.0.4
Date: 2024-12-16
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Description: Functions to generate ensembles of generalized linear models using a greedy projected subset gradient descent algorithm. The sparsity and diversity tuning parameters are selected by cross-validation.
License: GPL (>= 2)
Biarch: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp (>= 1.0.7)
Suggests: testthat, mvnfast, vctrs
NeedsCompilation: yes
Packaged: 2024-12-17 03:09:42 UTC; anthony
Author: Anthony Christidis [aut, cre], Stefan Van Aelst [aut], Ruben Zamar [aut]
Repository: CRAN
Date/Publication: 2024-12-18 15:20:06 UTC

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New package adas.utils with initial version 1.0.0
Package: adas.utils
Title: Design of Experiments and Factorial Plans Utilities
Version: 1.0.0
Description: A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses. DoE approach follows the approach in "Design and Analysis of Experiments" by Douglas C. Montgomery (2019, ISBN:978-1-119-49244-3). The package also provides utilities used in the course "Analysis of Data and Statistics" at the University of Trento, Italy.
Depends: R (>= 4.0.0)
License: CC BY 4.0
Encoding: UTF-8
Imports: dplyr, gghalfnorm, ggplot2, glue, grDevices, lubridate, magrittr, purrr, readr, rlang, scales, stats, stringr, tibble, tidyr, utils
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), tidyverse
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-17 12:06:56 UTC; p4010
Author: Paolo Bosetti [aut, cre]
Maintainer: Paolo Bosetti <paolo.bosetti@unitn.it>
Repository: CRAN
Date/Publication: 2024-12-18 15:40:07 UTC

More information about adas.utils at CRAN
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