CRANberries

Sat, 12 Apr 2025

New package ProteinPCA with initial version 0.1.0
Package: ProteinPCA
Title: Principal Component Analysis (PCA) Tool on Protein Expression Data
Version: 0.1.0
Author: Paul Angelo C. Manlapaz [aut, cre]
Maintainer: Paul Angelo C. Manlapaz <pacmanlapaz@gmail.com>
Description: Analysis of protein expression data can be done through Principal Component Analysis (PCA), and this R package is designed to streamline the analysis. This package enables users to perform PCA and it generates biplot and scree plot for advanced graphical visualization. Optionally, it supports grouping/clustering visualization with PCA loadings and confidence ellipses. With this R package, researchers can quickly explore complex protein datasets, interpret variance contributions, and visualize sample clustering through intuitive biplots. For more details, see Jolliffe (2001) <doi:10.1007/b98835>, Gabriel (1971) <doi:10.1093/biomet/58.3.453>, Zhang et al. (2024) <doi:10.1038/s41467-024-53239-9>, and Anandan et al. (2022) <doi:10.1038/s41598-022-07781-5>.
License: GPL-3
Encoding: UTF-8
Imports: stats, ggplot2, gridExtra
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-04-10 13:29:23 UTC; PTRI
Repository: CRAN
Date/Publication: 2025-04-12 08:30:05 UTC

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New package FLAG with initial version 0.1
Package: FLAG
Title: Flexible and Accurate Gaussian Graphical Models
Version: 0.1
Description: In order to achieve accurate estimation without sparsity assumption on the precision matrix, element-wise inference on the precision matrix, and joint estimation of multiple Gaussian graphical models, a novel method is proposed and efficient algorithm is implemented. FLAG() is the main function given a data matrix, and FlagOneEdge() will be used when one pair of random variables are interested where their indices should be given. Flexible and Accurate Methods for Estimation and Inference of Gaussian Graphical Models with Applications, see Qian Y (2023) <doi:10.14711/thesis-991013223054603412>, Qian Y, Hu X, Yang C (2023) <doi:10.48550/arXiv.2306.17584>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, MASS
URL: https://github.com/YangLabHKUST/FLAG
BugReports: https://github.com/YangLabHKUST/FLAG/issues
NeedsCompilation: no
Packaged: 2025-04-10 09:36:49 UTC; asus
Author: Yueqi QIAN [aut, cre]
Maintainer: Yueqi QIAN <yqianai@connect.ust.hk>
Repository: CRAN
Date/Publication: 2025-04-12 08:10:06 UTC

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New package energymethod with initial version 1.0
Package: energymethod
Title: Two-Sample Test of many Functional Means using the Energy Method
Version: 1.0
Date: 2025-04-09
Maintainer: David Colin Decker <d.colin.decker@gmail.com>
Description: Given two samples of size n_1 and n_2 from a data set where each sample consists of K functional observations (channels), each recorded on T grid points, the function energy method implements a hypothesis test of equality of channel-wise mean at each channel using the bootstrapped distribution of maximum energy to control family wise error.
License: GPL-3
Imports: Rcpp (>= 1.0.14)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2025-04-10 12:54:17 UTC; David
Author: David Colin Decker [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-12 08:30:02 UTC

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New package e2tree with initial version 0.1.2
Package: e2tree
Title: Explainable Ensemble Trees
Version: 0.1.2
Description: The Explainable Ensemble Trees 'e2tree' approach has been proposed by Aria et al. (2024) <doi:10.1007/s00180-022-01312-6>. It aims to explain and interpret decision tree ensemble models using a single tree-like structure. 'e2tree' is a new way of explaining an ensemble tree trained through 'randomForest' or 'xgboost' packages.
License: MIT + file LICENSE
URL: https://github.com/massimoaria/e2tree
BugReports: https://github.com/massimoaria/e2tree/issues
Encoding: UTF-8
Imports: dplyr, doParallel, parallel, foreach, future.apply, ggplot2, Matrix, partitions, purrr, tidyr, randomForest, rpart.plot, Rcpp, RSpectra, ape
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2025-04-10 11:11:45 UTC; massimoaria
Author: Massimo Aria [aut, cre, cph] , Agostino Gnasso [aut]
Maintainer: Massimo Aria <aria@unina.it>
Repository: CRAN
Date/Publication: 2025-04-12 08:20:02 UTC

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New package butterfly with initial version 1.1.2
Package: butterfly
Title: Verification for Continually Updating Time Series Data
Version: 1.1.2
Description: Verification of continually updating time series data where we expect new values, but want to ensure previous data remains unchanged. Data previously recorded could change for a number of reasons, such as discovery of an error in model code, a change in methodology or instrument recalibration. Monitoring data sources for these changes is not always possible. Other unnoticed changes could include a jump in time or measurement frequency, due to instrument failure or software updates. Functionality is provided that can be used to check and flag changes to previous data to prevent changes going unnoticed, as well as unexpected jumps in time.
License: MIT + file LICENSE
URL: https://docs.ropensci.org/butterfly/, https://github.com/ropensci/butterfly/
BugReports: https://github.com/ropensci/butterfly/issues
Depends: R (>= 4.1.0)
Imports: cli, dplyr, lifecycle, rlang, waldo
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-04 08:09:41 UTC; thozwa
Author: Thomas Zwagerman [aut, cre] , British Antarctic Survey [cph], Quentin Read [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/676>)
Maintainer: Thomas Zwagerman <thozwa@bas.ac.uk>
Repository: CRAN
Date/Publication: 2025-04-12 08:10:02 UTC

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New package artma with initial version 0.1.19
Package: artma
Title: Automatic Replication Tools for Meta-Analysis
Version: 0.1.19
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Description: Provides a unified and straightforward interface for performing a variety of meta-analysis methods directly from user data. Users can input a data frame, specify key parameters, and effortlessly execute and compare multiple common meta-analytic models. Designed for immediate usability, the package facilitates transparent, reproducible research without manual implementation of each analytical method. Ideal for researchers aiming for efficiency and reproducibility, it streamlines workflows from data preparation to results interpretation.
License: GPL-3
URL: https://github.com/PetrCala/artma
BugReports: https://github.com/PetrCala/artma/issues
Depends: R (>= 4.0.0)
Imports: cli, glue, lifecycle, lintr, logger, metafor, rlang, stringr, withr, yaml
Suggests: box, box.linters, covr, devtools, fs, here, jsonlite, knitr, languageserver, mathjaxr, optparse, pkgbuild, remotes, rex, rmarkdown, roxygen2, rstudioapi, testthat, tidyverse, usethis
VignetteBuilder: knitr
Encoding: UTF-8
SystemRequirements: JAGS >= 4.3.1 (https://mcmc-jags.sourceforge.io/)
NeedsCompilation: no
Packaged: 2025-04-10 11:19:09 UTC; runner
Repository: CRAN
Date/Publication: 2025-04-12 08:20:05 UTC

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Fri, 11 Apr 2025

New package clinDataReview with initial version 1.6.2
Package: clinDataReview
Title: Clinical Data Review Tool
Version: 1.6.2
Date: 2025-04-11
Description: Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Imports: bookdown, clinUtils (>= 0.1.0), crosstalk, data.table, ggplot2, grid, haven, htmltools, htmlwidgets, knitr, jsonlite, jsonvalidate, methods, plotly, plyr, rmarkdown, stats, stringr, utils, tools, yaml, xml2, xfun, base64enc
Suggests: countrycode, inTextSummaryTable (>= 3.1.0), patientProfilesVis (>= 0.12.0), testthat, DT, scales, grDevices
SystemRequirements: pandoc (to create a clinical data review report)
URL: https://github.com/openanalytics/clinDataReview
BugReports: https://github.com/openanalytics/clinDataReview/issues
License: MIT + file LICENSE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-11 19:04:21 UTC; lcougnaud
Author: Laure Cougnaud [aut, cre], Michela Pasetto [aut], Lennart Tuijnder [aut], Adriaan Blommaert [aut], Arne De Roeck [ctb, rev] , Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Repository: CRAN
Date/Publication: 2025-04-11 22:10:02 UTC

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New package choroplethr with initial version 4.0.0
Package: choroplethr
Title: Simplify the Creation of Choropleth Maps
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from 'Google Maps'.
Version: 4.0.0
URL: https://github.com/eastnile/choroplethr
Copyright: Trulia, Inc.
License: BSD_3_clause + file LICENSE
Imports: Hmisc, stringr, ggplot2 (>= 2.0.0), dplyr, R6, WDI, ggmap, RgoogleMaps, tigris (>= 1.0), gridExtra, xml2, rvest, tidyr, tidycensus
Suggests: testthat, choroplethrMaps, choroplethrAdmin1 (>= 1.1.0),
Depends: R (>= 3.5.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-11 16:49:37 UTC; zhaochenhe
Author: Ari Lamstein [aut], Zhaochen He [aut, cre], Brian Johnson [ctb], Trulia, Inc. [cph]
Maintainer: Zhaochen He <zhaochen.he@cnu.edu>
Repository: CRAN
Date/Publication: 2025-04-11 22:10:08 UTC

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New package MethEvolSIM with initial version 0.2.1
Package: MethEvolSIM
Title: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies
Version: 0.2.1
Author: Sara Castillo Vicente [aut, cre], Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Description: DNA methylation is an epigenetic modification involved in genomic stability, gene regulation, development and disease. DNA methylation occurs mainly through the addition of a methyl group to cytosines, for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine). Tissue-specific methylation patterns lead to genomic regions with different characteristic methylation levels. E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of expressed genes tend to be unmethylated. 'MethEvolSIM' is a model-based simulation software for the generation and modification of cytosine methylation patterns along a given tree, which can be a genealogy of cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree. The simulations are based on an extension of the model of Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of the met [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: R6, ape
Depends: R (>= 4.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-11 11:08:50 UTC; castillo
Repository: CRAN
Date/Publication: 2025-04-11 22:00:19 UTC

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New package beam with initial version 2.0.4
Package: beam
Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Version: 2.0.4
Date: 2025-03-14
Author: Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@proton.me>
Depends: R (>= 4.1.0)
Imports: stats, methods, grDevices, graphics, Matrix, fdrtool, igraph, knitr, Rcpp, assertthat
Description: Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data. Leday and Richardson (2019), Biometrics, <doi:10.1111/biom.13064>.
LazyLoad: yes
License: GPL (>= 2.0)
LazyData: TRUE
NeedsCompilation: yes
Repository: CRAN
LinkingTo: Rcpp, RcppArmadillo, BH
Suggests: covr, testthat
URL: https://github.com/gleday/beam
Encoding: UTF-8
Packaged: 2025-04-09 14:53:45 UTC; User
Date/Publication: 2025-04-11 10:10:07 UTC

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Thu, 10 Apr 2025

New package ztils with initial version 1.0.0
Package: ztils
Title: Various Common Statistical Utilities
Version: 1.0.0
Description: Utilities for simplifying common statistical operations including probability density functions, cumulative distribution functions, Kolmogorov-Smirnov tests, principal component analysis plots, and prediction plots.
License: MIT + file LICENSE
URL: https://zachpeagler.github.io/ztils/, https://github.com/zachpeagler/ztils
BugReports: https://github.com/zachpeagler/ztils/issues
Encoding: UTF-8
Depends: R (>= 3.3.0)
Imports: ggplot2, MASS, scico, vegan
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-09 17:22:52 UTC; Zach
Author: Zach Peagler [aut, cre, cph]
Maintainer: Zach Peagler <zachpeagler00@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-10 14:30:01 UTC

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New package tickr with initial version 1.0.2
Package: tickr
Title: Consistent Axis Tick Marks
Version: 1.0.2
Maintainer: Benjamin C. Williams <kleheni@gmail.com>
Description: This is a small package to provide consistent tick marks for plotting 'ggplot2' figures. It provides breaks and labels for 'ggplot2' without requiring 'ggplot2' to be installed.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, magrittr, rlang
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/ben-williams/tickr
NeedsCompilation: no
Packaged: 2025-04-09 17:00:52 UTC; Ben.Williams
Author: Benjamin C. Williams [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-10 14:30:05 UTC

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New package piiR with initial version 0.2.0
Package: piiR
Title: Predictive Information Index ('PII')
Version: 0.2.0
Maintainer: Kevin E. Wells <kevin.e.wells@usm.edu>
Description: A simple implementation of the Predictive Information Index ('PII') using mutual information and entropy from the 'infotheo' package. For related methodology, see Wells (2025) <https://github.com/TheotherDrWells/piiR>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats (>= 3.6.0), infotheo (>= 1.2.0), pROC (>= 1.18.0)
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-04-09 16:42:19 UTC; w10105397
Author: Kevin E. Wells [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-10 14:30:08 UTC

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New package neuroim2 with initial version 0.8.1
Package: neuroim2
Title: Data Structures for Brain Imaging Data
Version: 0.8.1
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Maintainer: Bradley R Buchsbaum <brad.buchsbaum@gmail.com>
Description: A collection of data structures and methods for handling volumetric brain imaging data, with a focus on functional magnetic resonance imaging (fMRI). Provides efficient representations for three-dimensional and four-dimensional neuroimaging data through sparse and dense array implementations, memory-mapped file access for large datasets, and spatial transformation capabilities. Implements methods for image resampling, spatial filtering, region of interest analysis, and connected component labeling. General introduction to fMRI analysis can be found in Poldrack et al. (2024, "Handbook of functional MRI data analysis", <ISBN:9781108795760>).
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr, rmarkdown
Depends: R (>= 4.3.0), Matrix
Imports: purrr, assertthat, mmap, Rcpp, RcppParallel, RNifti, dbscan, stringr, methods, colorplane, bigstatsr, RNiftyReg, future.apply, deflist, crayon, ggplot2, magrittr
Suggests: testthat, covr, knitr, roxygen2, rmarkdown, Gmedian, R.utils, spelling
URL: https://github.com/bbuchsbaum/neuroim2, https://bbuchsbaum.github.io/neuroim2/
BugReports: https://github.com/bbuchsbaum/neuroim2/issues
Language: en-US
NeedsCompilation: yes
Packaged: 2025-04-09 21:31:43 UTC; bbuchsbaum
Author: Bradley R Buchsbaum [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-04-10 14:50:06 UTC

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New package MCSimMod with initial version 0.9
Package: MCSimMod
Title: Working with 'MCSim' Models
Version: 0.9
Description: Tools that facilitate ordinary differential equation (ODE) modeling in 'R'. This package allows one to perform simulations for ODE models that are encoded in the GNU 'MCSim' model specification language (Bois, 2009) <doi:10.1093/bioinformatics/btp162> using ODE solvers from the 'R' package 'deSolve' (Soetaert et al., 2010) <doi:10.18637/jss.v033.i09>.
Depends: methods, tools
Imports: deSolve
URL: https://CRAN.R-project.org/package=MCSimMod, https://github.com/USEPA/MCSimMod
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-04-09 18:56:47 UTC; dkapraun
Author: Dustin F. Kapraun [aut, cre] , Todd J. Zurlinden [aut] , Andrew J. Shapiro [aut] , Ryan D. Friese [aut] , Frederic Y. Bois [ctb] , Free Software Foundation, Inc. [cph]
Maintainer: Dustin F. Kapraun <kapraun.dustin@epa.gov>
Repository: CRAN
Date/Publication: 2025-04-10 14:40:06 UTC

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New package marcox with initial version 1.0.0
Package: marcox
Title: Marginal Hazard Ratio Estimation in Clustered Failure Time Data
Version: 1.0.0
Description: Estimation of marginal hazard ratios in clustered failure time data. It implements the weighted generalized estimating equation approach based on a semiparametric marginal proportional hazards model (See Niu, Y. Peng, Y.(2015). "A new estimating equation approach for marginal hazard ratio estimation"), accounting for within-cluster correlations. 5 different correlation structures are supported. The package is designed for researchers in biostatistics and epidemiology who require accurate and efficient estimation methods for survival analysis in clustered data settings.
Depends: R (>= 4.4.0), Matrix
Imports: Rcpp, RcppEigen, survival, ggplot2, stats
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
LazyData: true
Maintainer: Junyi Chen <2655088079@qq.com>
License: GPL-3
NeedsCompilation: yes
Packaged: 2025-04-09 09:55:26 UTC; NTLDR
Author: Junyi Chen [aut, cre], Siqi Zhou [ctb], Shida Li [ctb], Yi Niu [aut]
Repository: CRAN
Date/Publication: 2025-04-10 14:20:02 UTC

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New package geoprofiler with initial version 0.0.2
Package: geoprofiler
Title: Perpendicular Line Transects for Geosciences
Version: 0.0.2
Description: Toolset to create perpendicular profile graphs and swath profiles. Method are based on coordinate rotation algorithm by Schaeben et al. (2024) <doi:10.1002/mma.9823>.
License: GPL (>= 3)
URL: https://tobiste.github.io/geoprofiler/
BugReports: https://github.com/tobiste/geoprofiler/issues
Depends: R (>= 4.1.0)
Imports: dplyr, sf, tectonicr, terra, units
Suggests: ggplot2, knitr, rmarkdown, spelling, testthat (>= 3.0.0), tidyterra
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-09 16:42:59 UTC; tstephan
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Repository: CRAN
Date/Publication: 2025-04-10 14:30:12 UTC

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New package EZFragility with initial version 1.0.3
Package: EZFragility
Title: Compute Neural Fragility for Ictal iEEG Time Series
Version: 1.0.3
Description: Provides tools to compute the neural fragility matrix from intracranial electrocorticographic (iEEG) recordings, enabling the analysis of brain dynamics during seizures. The package implements the method described by Li et al. (2017) <doi:10.23919/ACC.2017.7963378> and includes functions for data preprocessing (`Epoch`), fragility computation (`calcAdjFrag`), and visualization.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
Imports: stats, methods, ggplot2 (>= 3.4.0), viridis, ggtext, glue, rlang, foreach, progress, ramify, reshape2
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), doSNOW
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-09 17:51:22 UTC; jiewang
Author: Jiefei Wang [aut, cre] , Anne-Cecile Lesage [aut] , Ioannis Malagaris [aut] , Oliver Zhou [ctb], Liliana Camarillo Rodriguez [ctb] , Sean O'Leary [ctb] , Patrick Karas [ctb]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-10 14:40:09 UTC

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New package clootl with initial version 0.1.1
Package: clootl
Title: Fetch and Explore the Cornell Lab of Ornithology Open Tree of Life Avian Phylogeny
Version: 0.1.1
Maintainer: Eliot Miller <clootlmaintainers@gmail.com>
URL: https://github.com/eliotmiller/clootl
BugReports: https://github.com/eliotmiller/clootl/issues
Depends: R (>= 4.3.0), ape
Imports: stats, dplyr, RCurl, jsonlite
LazyData: true
LazyDataCompression: xz
Description: Fetches the Cornell Lab of Ornithology Open Tree of Life (clootl) tree in a specified taxonomy. Optionally prune it to a given set of study taxa. Provide a recommended citation list for the studies that informed the extracted tree. Tree generated as described in McTavish et al. (2024) <doi:10.1101/2024.05.20.595017>.
License: GPL-3
Encoding: UTF-8
Suggests: rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-09 19:28:43 UTC; luna
Author: Eliot Miller [aut, cre], Emily Jane McTavish [aut], Luna L. Sanchez Reyes [ctb, aut]
Repository: CRAN
Date/Publication: 2025-04-10 14:40:02 UTC

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New package PwePred with initial version 1.0.0
Package: PwePred
Title: Event/Timeline Prediction Model Based on Piecewise Exponential
Imports: graphics, grDevices, stats, methods, utils, segmented, foreach, doSNOW, parallel
Depends: survival, fastmatch
Suggests: knitr, RColorBrewer, rmarkdown
Version: 1.0.0
Maintainer: Tianchen Xu <zjph602xutianchen@gmail.com>
Description: Efficient algorithm for estimating piecewise exponential hazard models for right-censored data, and is useful for reliable power calculation, study design, and event/timeline prediction for study monitoring.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Repository: CRAN
Packaged: 2025-04-09 07:04:01 UTC; xut13
Date/Publication: 2025-04-10 10:00:02 UTC
NeedsCompilation: no
Author: Tianchen Xu [aut, cre]

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New package puff with initial version 0.1.0
Package: puff
Title: Simulate and Visualize the Gaussian Puff Forward Atmospheric Model
Version: 0.1.0
Description: Simulate and run the Gaussian puff forward atmospheric model in sensor (specific sensor coordinates) or grid (across the grid of a full oil and gas operations site) modes, following Jia, M., Fish, R., Daniels, W., Sprinkle, B. and Hammerling, D. (2024) <doi:10.26434/chemrxiv-2023-hc95q-v3>. Numerous visualization options, including static and animated, 2D and 3D, and a site map generator based on sensor and source coordinates.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/Hammerling-Research-Group/puff
BugReports: https://github.com/Hammerling-Research-Group/puff/issues
Depends: R (>= 4.1.0)
Imports: ggplot2, dplyr, tidyr, magrittr, htmlwidgets, patchwork, plotly, scales, tidyselect
Suggests: knitr, rmarkdown, devtools, akima, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-09 14:38:08 UTC; philipwaggoner
Author: Teagan Ward [aut], Philip Waggoner [aut, cre], Will Daniels [aut], Meng Jia [aut], Dorit Hammerling [aut, ths]
Maintainer: Philip Waggoner <philip.waggoner@mines.edu>
Repository: CRAN
Date/Publication: 2025-04-10 09:40:02 UTC

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New package isard with initial version 0.1.0
Package: isard
Title: Overflow Data for Quantitative Peace Science Research
Version: 0.1.0
Depends: R (>= 3.5.0)
Description: These are data and functions to support quantitative peace science research. The data are important state-year information on democracy and wealth, which require periodic updates and regular maintenance. The functions permit some exploratory and diagnostic assessment of the kinds of data in demand by the community, but do not impose many dependencies on the user.
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: peacesciencer, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-09 13:01:55 UTC; steve
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Repository: CRAN
Date/Publication: 2025-04-10 09:10:01 UTC

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New package hera with initial version 0.1.1
Package: hera
Title: Companion to the 'xeus-r' 'jupyter' Kernel
Version: 0.1.1
Description: Set of R functions to be coupled with the 'xeus-r' 'jupyter' kernel in order to drive execution of code in notebook input cells, how R objects are to be displayed in output cells, and handle two way communication with the front end through comms.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, evaluate, glue, IRdisplay, jsonlite, R6, repr, rlang, tools, utils
URL: https://github.com/jupyter-xeus/xeus-r
BugReports: https://github.com/jupyter-xeus/xeus-r/issues
NeedsCompilation: no
Packaged: 2025-04-09 12:54:37 UTC; romainfrancois
Author: Romain Francois [aut, cre], QuantStack [cph]
Maintainer: Romain Francois <romain@tada.science>
Repository: CRAN
Date/Publication: 2025-04-10 09:10:05 UTC

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New package correlationr with initial version 0.1.0
Package: correlationr
Title: Conduct Robust Correlations on Non-Normal Data
Version: 0.1.0
Maintainer: Aurora Robert <roberta5@myumanitoba.ca>
Description: Allows you to conduct robust correlations on your non-normal data set. The robust correlations included in the package are median-absolute-deviation and median-based correlations. Li, J.C.H. (2022) <doi:10.5964/meth.8467>.
URL: https://liqas.org/1-correlationr-package/, https://github.com/Aurora-UofM/correlationr
BugReports: https://github.com/Aurora-UofM/correlationr/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5)
LazyData: true
Imports: dplyr, stats
NeedsCompilation: no
Packaged: 2025-04-09 14:18:49 UTC; aurorarobert
Author: Johnson Li [aut] , Aurora Robert [cre, aut]
Repository: CRAN
Date/Publication: 2025-04-10 09:40:05 UTC

More information about correlationr at CRAN
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New package TukeyC with initial version 1.3-43
Package: TukeyC
Title: Conventional Tukey Test
Version: 1.3-43
Date: 2025-04-09
Maintainer: Ivan Bezerra Allaman <ivanalaman@gmail.com>
Depends: R (>= 2.6.0)
Imports: doBy, xtable
Suggests: pbkrtest (>= 0.4-6), lme4
Description: Provides tools to perform multiple comparison analyses, based on the well-known Tukey's "Honestly Significant Difference" (HSD) test. In models involving interactions, 'TukeyC' stands out from other R packages by implementing intuitive and easy-to-use functions. In addition to accommodating traditional R methods such as lm() and aov(), it has also been extended to objects of the lmer() class, that is, mixed models with fixed effects. For more details see Tukey (1949) <doi:10.2307/3001913>.
License: GPL (>= 2)
URL: https://github.com/jcfaria/TukeyC
Encoding: UTF-8
LazyLoad: yes
NeedsCompilation: no
Packaged: 2025-04-09 23:55:41 UTC; iballaman
Author: Jose Claudio Faria [aut], Enio G. Jelihovschi [aut], Ivan Bezerra Allaman [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-10 08:50:08 UTC

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New package ernm with initial version 1.0.0
Package: ernm
Title: Exponential-Family Random Network Models
Version: 1.0.0
Date: 2025-04-08
Description: Estimation of fully and partially observed Exponential-Family Random Network Models (ERNM). Exponential-family Random Graph Models (ERGM) and Gibbs Fields are special cases of ERNMs and can also be estimated with the package. Please cite Fellows and Handcock (2012), "Exponential-family Random Network Models" available at <doi:10.48550/arXiv.1208.0121>.
License: LGPL-2.1
Depends: R (>= 3.5.0), BH, methods, network, Rcpp
Imports: dplyr, ggplot2, graphics, moments, rlang, stats, tidyr, trust
Suggests: spelling, testthat
LinkingTo: BH, Rcpp
Copyright: @ 2014-2025 Ian Fellows
Encoding: UTF-8
Language: en-US
LazyData: true
LazyLoad: yes
RcppModules: ernm
NeedsCompilation: yes
Packaged: 2025-04-09 11:13:22 UTC; dac6
Author: Ian Fellows [aut], Duncan Clark [aut, cre]
Maintainer: Duncan Clark <dac6@williams.edu>
Repository: CRAN
Date/Publication: 2025-04-10 08:50:04 UTC

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New package ARTool with initial version 0.11.2
Package: ARTool
Title: Aligned Rank Transform
Version: 0.11.2
Date: 2025-04-09
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Description: The aligned rank transform for nonparametric factorial ANOVAs as described by Wobbrock, Findlater, Gergle, and Higgins (2011) <doi:10.1145/1978942.1978963>. Also supports aligned rank transform contrasts as described by Elkin, Kay, Higgins, and Wobbrock (2021) <doi:10.1145/3472749.3474784>.
Depends: R (>= 3.2)
Imports: lme4, car (>= 2.0-24), plyr, magrittr, dplyr, emmeans
Suggests: testthat (>= 0.10.0), knitr, rmarkdown, ggplot2, tidyr, pander, lmerTest, cluster, phia, survival, psych, stringi, DescTools, tibble, covr
License: GPL (>= 2)
Language: en-US
BugReports: https://github.com/mjskay/ARTool/issues
URL: https://github.com/mjskay/ARTool/
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-10 05:37:43 UTC; matth
Author: Matthew Kay [aut, cre], Lisa A. Elkin [aut], James J. Higgins [aut], Jacob O. Wobbrock [aut]
Repository: CRAN
Date/Publication: 2025-04-10 08:20:02 UTC

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Wed, 09 Apr 2025

New package stilt with initial version 1.3.1
Package: stilt
Title: Separable Gaussian Process Interpolation (Emulation)
Version: 1.3.1
Date: 2025-04-09
Maintainer: Kelsey Ruckert <datamgmt@scrim.psu.edu>
Description: Functions for simplified emulation of time series computer model output in model parameter space using Gaussian processes. Stilt can be used more generally for Kriging of spatio-temporal fields. There are functions to predict at new parameter settings, to test the emulator using cross-validation (which includes information on 95% confidence interval empirical coverage), and to produce contour plots over 2D slices in model parameter space.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: fields
LazyLoad: no
Packaged: 2025-04-09 14:24:41 UTC; klr324
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2025-04-09 16:40:02 UTC
Author: Roman Olson [aut], Won Chang [aut], Klaus Keller [aut], Murali Haran [aut], Kelsey Ruckert [cre]

More information about stilt at CRAN
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New package slurm with initial version 2025.4.9
Package: slurm
Version: 2025.4.9
License: GPL-3
Title: Running and Parsing Slurm Commands
Description: User-friendly functions which parse output of command line programs used to query Slurm. Morris A. Jette and Tim Wickberg (2023) <doi:10.1007/978-3-031-43943-8_1> describe Slurm in detail.
Imports: data.table (>= 1.11.6), nc (>= 2019.11.22)
SystemRequirements: Slurm command line programs (sacct, squeue)
Suggests: testthat, ggplot2, R.utils
NeedsCompilation: no
Packaged: 2025-04-09 09:25:44 UTC; hoct2726
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Repository: CRAN
Date/Publication: 2025-04-09 10:30:02 UTC

More information about slurm at CRAN
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New package seinfitR with initial version 1.0.1
Package: seinfitR
Title: Modeling the Relationship Between Nematode Densities and Plant Growth
Version: 1.0.1
Description: Implements the Seinhorst model to analyze the relationship between initial nematode densities and plant growth response using nonlinear least squares estimation. The package provides tools for model fitting, prediction, and visualization, facilitating the study of plant-nematode interactions. Model parameters can be estimated or set to predefined values based on Seinhorst (1986) <doi:10.1007/978-1-4613-2251-1_11>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: minpack.lm
Suggests: testthat (>= 3.0.0), readxl, knitr, rmarkdown
URL: https://github.com/dslabcena/seinfitR
BugReports: https://github.com/dslabcena/seinfitR/issues
Depends: R (>= 3.5)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-08 20:12:35 UTC; joaon
Author: Deoclecio Amorim [aut] , Joao Novoletti [aut, cre, cph]
Maintainer: Joao Novoletti <joao.novoletti@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-09 10:10:02 UTC

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New package robcp with initial version 0.3.8
Package: robcp
Title: Robust Change-Point Tests
Version: 0.3.8
Description: Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. Focus is on the detection of abrupt changes in location, but changes in the scale or dependence structure can be detected as well. This package provides tests for change detection in uni- and multivariate time series based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <DOI:10.48550/arXiv.1905.06201>, and tests for change detection in univariate time series based on 2-sample U-statistics or 2-sample U-quantiles as proposed by Dehling et al. (2015) <DOI:10.1007/978-1-4939-3076-0_12> and Dehling, Fried and Wendler (2020) <DOI:10.1093/biomet/asaa004>. Furthermore, the packages provides tests on changes in the scale or the correlation as proposed in Gerstenberger, Vogel and Wendler (2020) <DOI:10.1080/01621459.2019.1629938>, Dehling et al. (2017) <DOI:10.1017/S026646661600044X>, and Wied et al. (2014) [...truncated...]
Depends: R (>= 3.3.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2025-04-09 08:59:05 UTC; goerz
Author: Sheila Goerz [aut, cre], Alexander Duerre [aut], Roland Fried [ctb, ths]
Maintainer: Sheila Goerz <sheila.goerz@tu-dortmund.de>
Imports: methods, Rcpp
LinkingTo: Rcpp
Suggests: testthat, MASS, pracma, mvtnorm, cumstats
Repository: CRAN
Date/Publication: 2025-04-09 10:30:05 UTC

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New package npdsim with initial version 1.0.0
Package: npdsim
Title: Simulate Demand and Attributes for New Products
Version: 1.0.0
Description: Simulate demand and attributes for ready to launch new products during their life cycle, or during their introduction and growth phases. You provide the number of products, attributes, time periods and/or other parameters and 'npdsim' can simulate for you the demand for each product during the considered time periods, and the attributes of each product. The simulation for the demand is based on the idea that each product has a shape and a level, where the level is the cumulative demand over the considered time periods, and the shape is the normalized demand across those time periods.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/mohammedhichame/npdsim
BugReports: https://github.com/mohammedhichame/npdsim/issues
Imports: dplyr (>= 1.1.4), tidyr (>= 1.3.1)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-08 22:41:23 UTC; Hichame
Author: Mohammed Hichame BENBITOUR [aut, cre, cph]
Maintainer: Mohammed Hichame BENBITOUR <res.mhichame@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-09 10:20:02 UTC

More information about npdsim at CRAN
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New package GBOP2 with initial version 0.1.2
Package: GBOP2
Title: Generalized Bayesian Optimal Phase II Design (G-BOP2)
Version: 0.1.2
Depends: R (>= 4.1.0)
Maintainer: Wanni Lei <wanni.lei17@gmail.com>
Description: Provides functions for implementing the Generalized Bayesian Optimal Phase II (G-BOP2) design using various Particle Swarm Optimization (PSO) algorithms, including: - PSO-Default, based on Kennedy and Eberhart (1995) <doi:10.1109/ICNN.1995.488968>, "Particle Swarm Optimization"; - PSO-Quantum, based on Sun, Xu, and Feng (2004) <doi:10.1109/ICCIS.2004.1460396>, "A Global Search Strategy of Quantum-Behaved Particle Swarm Optimization"; - PSO-Dexp, based on Stehlík et al. (2024) <doi:10.1016/j.asoc.2024.111913>, "A Double Exponential Particle Swarm Optimization with Non-Uniform Variates as Stochastic Tuning and Guaranteed Convergence to a Global Optimum with Sample Applications to Finding Optimal Exact Designs in Biostatistics"; - and PSO-GO.
Imports: tidyr, R6, Rcpp, doParallel, foreach, dplyr, stats, globpso, parallel, utils, RcppArmadillo
Suggests: knitr, rmarkdown, roxygen2, testthat (>= 3.0.0), R.rsp
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
VignetteBuilder: R.rsp
License: GPL-2
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-04-08 23:46:44 UTC; wanni
Author: Xinying Fang [aut], Wanni Lei [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-09 10:20:05 UTC

More information about GBOP2 at CRAN
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New package flexoki with initial version 0.0.1
Package: flexoki
Title: Inky Color Schemes
Version: 0.0.1
Description: Provides color palettes designed to be reminiscent of text on paper. The color schemes were taken from <https://stephango.com/flexoki>. Includes discrete, continuous, and binned scales that are not necessarily color-blind friendly. Simple scale and theme functions are available for use with 'ggplot2'.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, palette, scales
URL: https://github.com/christopherkenny/flexoki, https://christophertkenny.com/flexoki/
BugReports: https://github.com/christopherkenny/flexoki/issues
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-04-08 21:13:07 UTC; chris
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2025-04-09 10:10:06 UTC

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New package AdsorpR with initial version 0.1.0
Package: AdsorpR
Title: Adsorption Isotherm Models
Version: 0.1.0
Maintainer: Jajati Mandal <J.Mandal2@salford.ac.uk>
Description: Model adsorption behavior using classical isotherms, including Langmuir, Freundlich, Brunauer–Emmett–Teller (BET), and Temkin models. The package supports parameter estimation through both linearized and non-linear fitting techniques and generates high-quality plots for model diagnostics. It is intended for environmental scientists, chemists, and researchers working on adsorption phenomena in soils, water treatment, and material sciences. Functions are compatible with base 'R' and 'ggplot2' for visualization.
License: GPL
Encoding: UTF-8
Imports: ggplot2, stats
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-09 09:28:29 UTC; jajatimandal
Author: Jajati Mandal [cre], Sandipan Samanta [aut]
Repository: CRAN
Date/Publication: 2025-04-09 10:30:09 UTC

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New package yfscreen with initial version 0.1.1
Package: yfscreen
Title: Yahoo Finance 'screener' API
Version: 0.1.1
Description: Simple and efficient access to Yahoo Finance's 'screener' API <https://finance.yahoo.com/research-hub/screener/> for querying and retrieval of financial data. The core functionality abstracts the complexities of interacting with Yahoo Finance APIs, such as session management, crumb and cookie handling, query construction, pagination, and JSON payload generation. This abstraction allows users to focus on filtering and retrieving data rather than managing API details. Use cases include screening across a range of security types including equities, mutual funds, ETFs, indices, and futures. The package supports advanced query capabilities, including logical operators, nested filters, and customizable payloads. It automatically handles pagination to ensure efficient retrieval of large datasets by fetching results in batches of up to 250 entries per request. Filters can be dynamically defined to accommodate a wide range of screening needs. The implementation leverages standard HTTP lib [...truncated...]
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/jasonjfoster/screen
BugReports: https://github.com/jasonjfoster/screen/issues
Depends: R (>= 3.5.0)
Imports: curl, jsonlite
Suggests: covr, testthat
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-08 19:12:38 UTC; jason
Author: Jason Foster [aut, cre]
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-09 10:00:02 UTC

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New package piglet with initial version 1.0.7
Package: piglet
Title: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes
Version: 1.0.7
Description: Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires. The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes. The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.
License: CC BY 4.0
Encoding: UTF-8
Depends: R (>= 3.5.0)
LinkingTo: Rcpp
Imports: dplyr (>= 1.0.9), Biostrings (>= 2.62.0), DECIPHER (>= 2.22.0), alakazam (>= 1.2.0), dendextend (>= 1.9.0), data.table (>= 1.12.2), tigger (>= 1.0.0), methods (>= 3.4.4), rlang (>= 0.4.0), zen4R (>= 0.7), RColorBrewer (>= 1.1.2), ggplot2 (>= 3.3.6), circlize (>= 0.4.15), R6 (>= 2.5.1), jsonlite (>= 1.8.3), Rcpp (>= 0.11.0), magrittr, ComplexHeatmap
Suggests: knitr, rmarkdown, stats, graphics, grDevices, htmltools, stringi, bookdown
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-04-08 19:14:57 UTC; ayelet
Author: Ayelet Peres [aut, cre], William Lees [aut], Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <peresay@biu.ac.il>
Repository: CRAN
Date/Publication: 2025-04-09 10:00:05 UTC

More information about piglet at CRAN
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New package nimblewomble with initial version 0.1.0
Package: nimblewomble
Title: Bayesian Wombling using 'nimble'
Version: 0.1.0
Description: A software package to perform Wombling, or boundary analysis, using the 'nimble' Bayesian hierarchical modeling environment. Wombling is used widely to track regions of rapid change within the spatial reference domain. Specific functions in the package implement Gaussian process models for point-referenced spatial data followed by predictive inference on rates of change over curves using line integrals. We demonstrate model based Bayesian inference using posterior distributions featuring simple analytic forms while offering uncertainty quantification over curves. For more details on wombling please see, Banerjee and Gelfand (2006) <doi:10.1198/016214506000000041> and Halder, Banerjee and Dey (2024) <doi:10.1080/01621459.2023.2177166>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: nimble, ggplot2, MBA, metR, ggspatial, sf, terra, sp, coda, methods
NeedsCompilation: no
Packaged: 2025-04-08 20:02:31 UTC; aritrah-dsph
Author: Aritra Halder [aut, cre], Sudipto Banerjee [aut]
Maintainer: Aritra Halder <aritra.halder@drexel.edu>
Repository: CRAN
Date/Publication: 2025-04-09 10:00:10 UTC

More information about nimblewomble at CRAN
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New package vvbitwarden with initial version 0.1.0
Package: vvbitwarden
Title: Interacts with 'Bitwarden Secrets Manager'
Version: 0.1.0
Description: Provides functions to securely retrieve secrets from a 'Bitwarden Secrets Manager' vault using the 'Bitwarden CLI', enabling secret and configuration management within R packages and workflows. For more information visit <https://bitwarden.com/products/secrets-manager/>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), withr
Imports: jsonlite, processx
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-08 09:58:55 UTC; esr316
Author: Hajo Bons [aut, cre], Tomer Iwan [aut]
Maintainer: Hajo Bons <h.b.bons@vu.nl>
Repository: CRAN
Date/Publication: 2025-04-09 08:10:02 UTC

More information about vvbitwarden at CRAN
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New package valh with initial version 0.1.0
Package: valh
Title: Interface Between R and the OpenStreetMap-Based Routing Service Valhalla
Version: 0.1.0
Description: An interface between R and the 'Valhalla' API. 'Valhalla' is a routing service based on 'OpenStreetMap' data. See <https://valhalla.github.io/valhalla/> for more information. This package enables the computation of routes, trips, isochrones and travel distances matrices (travel time and kilometer distance).
License: GPL (>= 3)
Imports: jsonlite, googlePolylines, curl, utils, sf
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, tinytest
URL: https://github.com/riatelab/valh
BugReports: https://github.com/riatelab/valh/issues
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-08 14:16:19 UTC; tim
Author: Timothee Giraud [cre, aut] , Matthieu Viry [aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Repository: CRAN
Date/Publication: 2025-04-09 08:20:02 UTC

More information about valh at CRAN
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Tue, 08 Apr 2025

New package postcard with initial version 1.0.0
Package: postcard
Title: Estimating Marginal Effects with Prognostic Covariate Adjustment
Version: 1.0.0
Description: Conduct power analyses and inference of marginal effects. Uses plug-in estimation and influence functions to perform robust inference, optionally leveraging historical data to increase precision with prognostic covariate adjustment. The methods are described in Højbjerre-Frandsen et al. (2025) <doi:10.48550/arXiv.2503.22284>.
License: MIT + file LICENSE
URL: https://novonordisk-opensource.github.io/postcard/, https://github.com/NovoNordisk-OpenSource/postcard
BugReports: https://github.com/NovoNordisk-OpenSource/postcard/issues
Imports: cli, Deriv, dplyr, earth, generics, magrittr, options, parsnip, rlang, rsample, stats, stringr, tidyselect, tune, utils, workflowsets, xgboost, yardstick
Suggests: gggrid, ggplot2, knitr, LiblineaR, MASS, ranger, rmarkdown, testthat (>= 3.0.0), withr
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-07 22:22:27 UTC; Swagmeister
Author: Mathias Lerbech Jeppesen [aut, cre], Emilie Hojbjerre-Frandsen [aut], Novo Nordisk A/S [cph]
Maintainer: Mathias Lerbech Jeppesen <mathiasljeppesen@outlook.com>
Repository: CRAN
Date/Publication: 2025-04-08 15:40:02 UTC

More information about postcard at CRAN
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New package PhotoGEA with initial version 1.3.1
Package: PhotoGEA
Version: 1.3.1
Date: 2025-04-07
Title: Photosynthetic Gas Exchange Analysis
Description: Read, process, fit, and analyze photosynthetic gas exchange measurements. Documentation is provided by several vignettes; also see Lochocki, Salesse-Smith, & McGrath (2025) <doi:10.1111/pce.15501>.
Depends: R (>= 3.6.0)
Imports: openxlsx, lattice, dfoptim, DEoptim
Suggests: knitr, rmarkdown, plantecophys, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/eloch216/PhotoGEA, https://eloch216.github.io/PhotoGEA/
NeedsCompilation: no
Packaged: 2025-04-08 01:38:27 UTC; eloch
Author: Edward B. Lochocki [cre, aut] , Coralie E. Salesse-Smith [aut] , Justin M. McGrath [aut] , PhotoGEA authors [cph]
Maintainer: Edward B. Lochocki <eloch@illinois.edu>
Repository: CRAN
Date/Publication: 2025-04-08 15:40:10 UTC

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New package lme4GS with initial version 0.1
Package: lme4GS
Title: 'lme4' for Genomic Selection
Version: 0.1
Date: 2025-04-06
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Depends: R (>= 3.6.3), lme4, methods, Matrix
Suggests: BGLR
Description: Flexible functions that use 'lme4' as computational engine for fitting models used in Genomic Selection (GS). GS is a technology used for genetic improvement, and it has many advantages over phenotype-based selection. There are several statistical models that adequately approach the statistical challenges in GS, such as in linear mixed models (LMMs). The 'lme4' is the standard package for fitting linear and generalized LMMs in the R-package, but its use for genetic analysis is limited because it does not allow the correlation between individuals or groups of individuals to be defined. The 'lme4GS' package is focused on fitting LMMs with covariance structures defined by the user, bandwidth selection, and genomic prediction. The new package is focused on genomic prediction of the models used in GS and can fit LMMs using different variance-covariance matrices. Several examples of GS models are presented using this package as well as the analysis using real data. For more details see Caama [...truncated...]
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-04-07 18:10:32 UTC; pperez
Author: Diana Yanira Caamal Pat [aut], Paulino Perez Rodriguez [aut, cre], Erick Javier Suarez Sanchez [ctb]
Repository: CRAN
Date/Publication: 2025-04-08 15:30:02 UTC

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New package immundata with initial version 0.0.1
Package: immundata
Title: A Unified Data Layer for Single-Cell, Spatial and Bulk Immunomics
Version: 0.0.1
Description: Provides a unified data layer for single-cell, spatial and bulk T-cell and B-cell immune receptor repertoire data, integrating diverse data formats such as AIRR and raw sequencing files. Includes utilities for receptor aggregation, metadata normalization, and clonotype filtering.
License: Apache License (>= 2)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: cli, R6, checkmate, dplyr, duckplyr, glue, lifecycle, readr, rlang
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-07 23:22:15 UTC; vdn
Author: Vadim I. Nazarov [aut, cre]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Repository: CRAN
Date/Publication: 2025-04-08 15:40:07 UTC

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New package DLMRMV with initial version 0.1.0
Package: DLMRMV
Version: 0.1.0
Title: Distributed Linear Regression Models with Response Missing Variables
Depends: R (>= 4.4.0)
Description: As a distributed imputation strategy, the Distributed full information Multiple Imputation method is developed to impute missing response variables in distributed linear regression. The philosophy of the package is described in 'Guo' (2025) <doi:10.1038/s41598-025-93333-6>.
License: Apache License (== 2.0)
Encoding: UTF-8
Imports: stats
Packaged: 2025-04-07 10:25:14 UTC; Administrator
Date/Publication: 2025-04-08 15:10:01 UTC
NeedsCompilation: no
Author: Guangbao Guo [aut, cre] , Limin Song [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Repository: CRAN

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New package childeswordfreq with initial version 0.1.0
Package: childeswordfreq
Title: Word Frequency Extraction and Summarization
Version: 0.1.0
Description: Provides tools to extract word frequencies from the CHILDES (Child Language Data Exchange System) corpus. The main function allows users to input a list of words and receive speaker-role-specific frequency counts and a summary of the dataset. The output includes Excel-formatted tables of word counts and metadata summaries such as number of speakers, transcripts, children, and token counts. Useful for researchers studying early language acquisition, corpus linguistics, and speaker role variation. The CHILDES database is maintained at <https://childes.talkbank.org/>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: childesr, readr, dplyr, tidyr, writexl, rlang, magrittr, stats
URL: https://github.com/n-albudoor/childeswordfreq
BugReports: https://github.com/n-albudoor/childeswordfreq/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-01 15:53:07 UTC; albudoor.1
Author: Nahar Albudoor [aut, cre]
Maintainer: Nahar Albudoor <n.albudoor@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-08 15:20:02 UTC

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New package coda.plot with initial version 0.1.8
Package: coda.plot
Title: Plots for Compositional Data
Version: 0.1.8
Date: 2025-04-03
Description: Provides a collection of easy-to-use functions for creating visualizations of compositional data using 'ggplot2'. Includes support for common plotting techniques in compositional data analysis.
Depends: R (>= 3.5), coda.base (>= 0.5)
License: GPL
Encoding: UTF-8
Imports: ggplot2 (>= 3.5.0), ggtern (>= 3.5.0)
NeedsCompilation: no
Packaged: 2025-04-07 05:08:50 UTC; marc
Author: Marc Comas-Cufi [aut, cre]
Maintainer: Marc Comas-Cufi <mcomas@imae.udg.edu>
Repository: CRAN
Date/Publication: 2025-04-08 09:10:02 UTC

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New package spect with initial version 1.0
Package: spect
Version: 1.0
Date: 2025-04-06
Title: Survival Prediction Ensemble Classification Tool
Author: Stephen Abrams [aut, cre]
Maintainer: Stephen Abrams <stephen.abrams@gmail.com>
Depends: R (>= 4.0), futile.logger, dplyr
Imports: doParallel, ggplot2, survminer, riskRegression, caret, caretEnsemble, survival, rlang
Description: A tool for survival analysis using a discrete time approach with ensemble binary classification. 'spect' provides a simple interface consistent with commonly used R data analysis packages, such as 'caret', a variety of parameter options to help facilitate search automation, a high degree of transparency to the end-user - all intermediate data sets and parameters are made available for further analysis and useful, out-of-the-box visualizations of model performance. Methods for transforming survival data into discrete-time are adapted from the 'autosurv' package by Suresh et al., (2022) <doi:10.1186/s12874-022-01679-6>.
License: GPL-3
URL: https://github.com/dawdawdo/spect
BugReports: https://github.com/dawdawdo/spect/issues
Suggests: knitr, rmarkdown, randomForest, kernlab, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-07 00:26:07 UTC; steph
Repository: CRAN
Date/Publication: 2025-04-08 09:00:02 UTC

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New package sdlrm with initial version 0.1.2
Package: sdlrm
Title: Modified Skew Discrete Laplace Regression for Integer-Valued and Paired Discrete Data
Version: 0.1.2
Description: Implementation of the modified skew discrete Laplace (SDL) regression model. The package provides a set of functions for a complete analysis of integer-valued data, where the dependent variable is assumed to follow a modified SDL distribution. This regression model is useful for the analysis of integer-valued data and experimental studies in which paired discrete observations are collected.
URL: https://github.com/rdmatheus/sdlrm
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: Formula (>= 1.2.3), Rfast
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2025-04-02 17:41:12 UTC; rodri
Author: Rodrigo Medeiros [aut, cre]
Maintainer: Rodrigo Medeiros <rodrigo.matheus@ufrn.br>
Repository: CRAN
Date/Publication: 2025-04-08 08:20:02 UTC

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New package ctsmTMB with initial version 1.0.0
Package: ctsmTMB
Title: Continuous Time Stochastic Modelling using Template Model Builder
Version: 1.0.0
Date: 2025-03-20
Copyright: See the file COPYRIGHTS
Description: Perform state and parameter inference, and forecasting, in stochastic state-space systems using the 'ctsmTMB' class. This class, built with the 'R6' package, provides a user-friendly interface for defining and handling state-space models. Inference is based on maximum likelihood estimation, with derivatives efficiently computed through automatic differentiation enabled by the 'TMB'/'RTMB' packages (Kristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The available inference methods include Kalman filters, in addition to a Laplace approximation-based smoothing method. For further details of these methods refer to the documentation of the 'CTSMR' package <https://ctsm.info/ctsmr-reference.pdf> and Thygesen (2025) <doi:10.48550/arXiv.2503.21358>. Forecasting capabilities include moment predictions and stochastic path simulations, both implemented in 'C++' using 'Rcpp' (Eddelbuettel et al., 2018) <doi:10.1080/00031305.2017.1375990> for computational efficiency.
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/phillipbvetter/ctsmTMB
BugReports: https://github.com/phillipbvetter/ctsmTMB/issues
SystemRequirements: GNU GSL
Depends: R (>= 4.0.0)
Imports: TMB, RTMB (>= 1.7), R6, Deriv, stringr, Rcpp, RcppEigen, RcppXPtrUtils, RcppZiggurat, Matrix, deSolve, ggplot2, ggfortify, patchwork
LinkingTo: Rcpp, RcppEigen, RcppZiggurat
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, RTMBode
Additional_repositories: https://kaskr.r-universe.dev
LazyData: true
NeedsCompilation: yes
Packaged: 2025-04-06 10:58:08 UTC; pbrve
Author: Phillip Vetter [aut, cre, cph], Jan Moeller [ctb], Uffe Thygesen [ctb], Peder Bacher [ctb], Henrik Madsen [ctb]
Maintainer: Phillip Vetter <pbrve@dtu.dk>
Repository: CRAN
Date/Publication: 2025-04-08 08:40:02 UTC

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New package basepenguins with initial version 0.1.0
Package: basepenguins
Title: Convert Files that Use 'palmerpenguins' to Work with 'datasets'
Version: 0.1.0
Description: From 'R' 4.5.0, the 'datasets' package includes the penguins and penguins_raw data sets popularised in the 'palmerpenguins' package. 'basepenguins' takes files that use the 'palmerpenguins' package and converts them to work with the versions from 'datasets' ('R' >= 4.5.0). It does this by removing calls to library(palmerpenguins) and making the necessary changes to column names. Additionally, it provides helper functions to define new files paths for saving the output and a directory of example files to experiment with.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/EllaKaye/basepenguins, https://ellakaye.github.io/basepenguins/
BugReports: https://github.com/EllaKaye/basepenguins/issues
Depends: R (>= 4.2.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-05 16:36:14 UTC; u2175871
Author: Ella Kaye [aut, cre, cph] , Heather Turner [aut] , Achim Zeileis [ctb]
Maintainer: Ella Kaye <ella.kaye@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-08 08:40:06 UTC

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New package multinet with initial version 4.2.2
Package: multinet
Title: Analysis and Mining of Multilayer Social Networks
Version: 4.2.2
Date: 2025-04-07
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Description: Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
License: Apache License (== 2.0)
Depends: igraph (>= 1.2), Rcpp (>= 1.0), methods, RColorBrewer
LinkingTo: Rcpp
RcppModules: multinet
NeedsCompilation: yes
Repository: CRAN
Note: a previous version of the library (main version number: 3) was developed as part of the European Union's Horizon 2020 research and innovation programme under grant agreement No. 727040 (Virt-EU). The package uses functions from eclat <https://borgelt.net/eclat.html>, for association rule mining, Infomap <https://www.mapequation.org>, for the Infomap community detection method (please refer to their web site for up-to-date code), and Howard Hinnant's date and time library <https://github.com/HowardHinnant/date>. The code from these libraries has been included in our source package.
Packaged: 2025-04-07 17:45:46 UTC; matteomagnani
Author: Matteo Magnani [aut, cre], Luca Rossi [aut] , Davide Vega [aut] , Obaida Hanteer [ctb]
Date/Publication: 2025-04-08 07:20:06 UTC

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Mon, 07 Apr 2025

New package visor with initial version 0.1.0
Package: visor
Title: Geospatial Tools for Visibility Analysis
Version: 0.1.0
Description: Provides tools for visibility analysis in geospatial data. It offers functionality to perform isovist calculations, using arbitrary geometries as both viewpoints and occluders.
License: Apache License (>= 2)
URL: https://cityriverspaces.github.io/visor/, https://github.com/CityRiverSpaces/visor
BugReports: https://github.com/CityRiverSpaces/visor/issues
Imports: sf, sfheaders
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 4.1.0)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-03 20:10:49 UTC; claudiuforgaci
Author: Claudiu Forgaci [aut, cre, cph] , Francesco Nattino [aut] , Netherlands eScience Center [fnd]
Maintainer: Claudiu Forgaci <c.forgaci@tudelft.nl>
Repository: CRAN
Date/Publication: 2025-04-07 16:10:01 UTC

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New package StatTools with initial version 0.1.1
Package: StatTools
Title: All-in-One Chi Distribution CI
Version: 0.1.1
Maintainer: David Reese <reesedavid132@gmail.com>
Description: Computes confidence intervals for variance using the Chi-Square distribution, without requiring raw data. Wikipedia (2025) <https://en.wikipedia.org/wiki/Chi-squared_distribution>. 'All-in-One Chi Distribution CI' provides functions to calculate confidence intervals for the population variance based on a chi-squared distribution, utilizing a sample variance and sample size. It offers only a simple all-in-one method for quick calculations to find the CI for Chi Distribution.
License: MIT + file LICENSE
Imports: stats
Suggests: testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-03 20:28:16 UTC; David
Author: David Reese [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-07 16:20:13 UTC

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New package sdtm.terminology with initial version 2025-3-25
Package: sdtm.terminology
Title: CDISC SDTM Controlled Terminology
Version: 2025-3-25
Description: Clinical Data Interchange Standards Consortium (CDISC) Standard Data Tabulation Model (SDTM) controlled terminology, 2025-03-25. Source: <https://evs.nci.nih.gov/ftp1/CDISC/SDTM/>.
License: Apache License (>= 2)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr, tibble
URL: https://github.com/patterninstitute/sdtm.terminology, https://www.pattern.institute/sdtm.terminology/
BugReports: https://github.com/patterninstitute/sdtm.terminology/issues
NeedsCompilation: no
Packaged: 2025-04-04 13:21:25 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2025-04-07 16:30:01 UTC

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New package pplot with initial version 0.9
Package: pplot
Title: Chronological and Ordered p-Plots for Empirical Data
Version: 0.9
Date: 2025-04-04
Author: Roland Pfister [aut, cre], Christian Frings [aut]
Maintainer: Roland Pfister <mail@roland-pfister.net>
Suggests: MBESS
Description: Generates chronological and ordered p-plots for data vectors or vectors of p-values. The p-plot visualizes the evolution of the p-value of a significance test across the sampled data. It allows for assessing the consistency of the observed effects, for detecting the presence of potential moderator variables, and for estimating the influence of outlier values on the observed results. For non-significant findings, it can diagnose patterns indicative of underpowered study designs. The p-plot can thus either back the binary accept-vs-reject decision of common null-hypothesis significance tests, or it can qualify this decision and stimulate additional empirical work to arrive at more robust and replicable statistical inferences.
License: GPL
NeedsCompilation: no
Packaged: 2025-04-04 11:30:12 UTC; pfisterr
Repository: CRAN
Date/Publication: 2025-04-07 16:30:06 UTC

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New package pangoling with initial version 1.0.3
Package: pangoling
Title: Access to Large Language Model Predictions
Version: 1.0.3
Description: Provides access to word predictability estimates using large language models (LLMs) based on 'transformer' architectures via integration with the 'Hugging Face' ecosystem <https://huggingface.co/>. The package interfaces with pre-trained neural networks and supports both causal/auto-regressive LLMs (e.g., 'GPT-2') and masked/bidirectional LLMs (e.g., 'BERT') to compute the probability of words, phrases, or tokens given their linguistic context. For details on GPT-2 and causal models, see Radford et al. (2019) <https://storage.prod.researchhub.com/uploads/papers/2020/06/01/language-models.pdf>, for details on BERT and masked models, see Devlin et al. (2019) <doi:10.48550/arXiv.1810.04805>. By enabling a straightforward estimation of word predictability, the package facilitates research in psycholinguistics, computational linguistics, and natural language processing (NLP).
License: MIT + file LICENSE
URL: https://docs.ropensci.org/pangoling/, https://github.com/ropensci/pangoling
BugReports: https://github.com/ropensci/pangoling/issues
Depends: R (>= 4.1.0)
Imports: cachem, data.table, memoise, reticulate, rstudioapi, stats, tidyselect, tidytable (>= 0.7.2), utils
Suggests: brms, knitr, parallel, rmarkdown, spelling, testthat (>= 3.0.0), tictoc, covr
Encoding: UTF-8
Language: en-US
LazyData: true
StagedInstall: yes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-04 17:48:15 UTC; bruno
Author: Bruno Nicenboim [aut, cre] , Chris Emmerly [ctb], Giovanni Cassani [ctb], Lisa Levinson [rev], Utku Turk [rev]
Maintainer: Bruno Nicenboim <b.nicenboim@tilburguniversity.edu>
Repository: CRAN
Date/Publication: 2025-04-07 17:00:02 UTC

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New package HTGM2D with initial version 1.0
Package: HTGM2D
Version: 1.0
Date: 2025-04-03
Title: Two Dimensional High Throughput 'GoMiner'
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Author: Barry Zeeberg [aut, cre]
Depends: R (>= 4.2.0)
Imports: minimalistGODB, GoMiner, HTGM, grDevices, stats, gplots, jaccard
LazyData: true
LazyDataCompression: xz
Description: The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. Microarray studies are usually analyzed with BP, whereas proteomics researchers often prefer CC. To capture the benefit of both of those ontologies, I developed a two-dimensional version of 'High-Throughput GoMiner' ('HTGM2D'). I generate a 2D heat map whose axes are any two of BP, MF, or CC, and the value within a picture element of the heat map reflects the Jaccard metric p-value for the number of genes in common for the corresponding pair.
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-03 19:55:55 UTC; barryzeeberg
Repository: CRAN
Date/Publication: 2025-04-07 16:10:08 UTC

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New package groupedHyperframe.random with initial version 0.1.0
Package: groupedHyperframe.random
Title: Simulated Grouped Hyper Data Frame
Version: 0.1.0
Date: 2025-04-03
Description: An intuitive interface to simulate (1) superimposed (marked) point patterns with vectorized parameterization of random point pattern and distribution of marks; and (2) grouped hyper data frame based on population parameters and subject-specific random effects.
Encoding: UTF-8
License: GPL-2
Depends: R (>= 4.4), spatstat.random, groupedHyperframe
Language: en-US
Imports: cli, spatstat.geom, MASS
Suggests: knitr, rmarkdown, spatstat.data
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-03 20:25:10 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre] , Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-07 16:20:05 UTC

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New package DasGuptR with initial version 2.1.0
Package: DasGuptR
Title: Das Gupta Standardisation and Decomposition
Version: 2.1.0
Maintainer: Josiah King <josiah.king@ed.ac.uk>
Description: Implementation of Das Gupta's standardisation and decomposition of population rates, as set out "Standardization and decomposition of rates: A user’s manual", Das Gupta (1993) <https://www2.census.gov/library/publications/1993/demographics/p23-186.pdf>. The goal of these methods is to calculate adjusted rates based on compositional 'factors' and quantify the contribution of each factor to the difference in crude rates between populations. The package offers functionality to handle various scenarios for any number of factors and populations, where said factors can be comprised of vectors across sub-populations (including cross-classified population breakdowns), and with the option to specify user-defined rate functions.
License: GPL (>= 3)
URL: https://github.com/josiahpjking/DasGuptR
BugReports: https://github.com/josiahpjking/DasGuptR/issues
Depends: R (>= 4.1.0)
Encoding: UTF-8
LazyData: true
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2025-04-03 18:52:45 UTC; jking34
Author: Josiah King [aut, cre], Ben Matthews [aut]
Repository: CRAN
Date/Publication: 2025-04-07 16:10:12 UTC

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New package clockSim with initial version 0.1.1
Package: clockSim
Title: Streamlined Simulation of Circadian Gene Networks
Version: 0.1.1
Description: A user-friendly workflow for simulating circadian clock gene networks. Despite decades of advances in modeling circadian clock dynamics, the lack of accessible tools for reproducible simulation workflows hinders the integration of computational modeling with experimental studies. 'clockSim' addresses this gap by providing models and helper functions with step-by-step vignettes. This package opens up system-level exploration of the circadian clock to wet-lab experimentalists, and future development will include additional clock architectures and other gene circuit models. Currently implemented models are based on Leloup and Goldbeter (1998) <doi:10.1177/074873098128999934>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: bench, dde, dplyr, ggplot2, lomb, matrixStats, odin, rlang, tidyr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/yeyuan98/clockSim
BugReports: https://github.com/yeyuan98/clockSim/issues
NeedsCompilation: yes
Packaged: 2025-04-03 21:44:27 UTC; yuany
Author: Ye Yuan [aut, cre, cph]
Maintainer: Ye Yuan <yeyu@umich.edu>
Repository: CRAN
Date/Publication: 2025-04-07 16:20:09 UTC

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New package activityCounts with initial version 0.2.1
Package: activityCounts
Title: Generate ActiLife Counts
Version: 0.2.1
Description: ActiLife software generates activity counts from data collected by Actigraph accelerometers <https://s3.amazonaws.com/actigraphcorp.com/wp-content/uploads/2017/11/26205758/ActiGraph-White-Paper_What-is-a-Count_.pdf>. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using ActiLife counts. Unfortunately, ActiLife counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands and it is developed based on the study done by Brond and others (2017) <doi:10.1249/MSS.0000000000001344>.
URL: https://github.com/walkabillylab/activityCounts, https://github.com/jbrond/ActigraphCounts
BugReports: https://github.com/walkabillylab/activityCounts/issues
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, ggplot2, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: seewave, signal, tibble, lubridate, magrittr
NeedsCompilation: no
Packaged: 2025-04-03 18:47:01 UTC; dlf545
Author: Ruben Brondeel [aut], Javad Rahimipour Anaraki [aut], Daniel Fuller [aut, cph, cre], SeyedJavad KhataeiPour [aut], Beap Lab [cph]
Maintainer: Daniel Fuller <daniel.fuller@usask.ca>
Repository: CRAN
Date/Publication: 2025-04-07 16:10:05 UTC

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New package tvcure with initial version 0.6.6
Package: tvcure
Title: Additive Cure Survival Model with Time-Varying Covariates
Version: 0.6.6
Maintainer: Philippe Lambert <p.lambert@uliege.be>
BugReports: https://github.com/plambertULiege/tvcure/issues
Description: Fit of a double additive cure survival model with time-varying covariates. The additive terms in the long- and short-term survival submodels, modelling the cure probability and the event timing for susceptible units, are estimated using Laplace P-splines. For more details, see Lambert and Kreyenfeld (2025) <doi:10.1093/jrsssa/qnaf035>.
License: GPL-3
URL: <https://github.com/plambertULiege/tvcure>
Encoding: UTF-8
Imports: cubicBsplines, Rfast, MASS, Matrix, mgcv
NeedsCompilation: no
Packaged: 2025-04-03 18:11:51 UTC; plambert
Author: Philippe Lambert [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-07 16:00:01 UTC

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New package QR.break with initial version 1.0.1
Package: QR.break
Title: Structural Breaks in Quantile Regression
Version: 1.0.1
Maintainer: Zhongjun Qu <qu@bu.edu>
Description: Methods for detecting structural breaks, determining the number of breaks, and estimating break locations in linear quantile regression, using one or multiple quantiles, based on Qu (2008) and Oka and Qu (2011). Applicable to both time series and repeated cross-sectional data. The main function is rq.break(). References for detailed theoretical and empirical explanations: (1) Qu, Z. (2008). Testing for Structural Change in Regression Quantiles. Journal of Econometrics, 146(1), 170-184 <doi:10.1016/j.jeconom.2008.08.006> (2) Oka, T., and Qu, Z. (2011). Estimating Structural Changes in Regression Quantiles. Journal of Econometrics, 162(2), 248-267 <doi:10.1016/j.jeconom.2011.01.005>.
License: GPL (>= 3)
Depends: R (>= 4.3.0)
Encoding: UTF-8
NeedsCompilation: no
Imports: quantreg
Suggests: SparseM
LazyData: true
Packaged: 2025-03-26 18:57:05 UTC; qu
Author: Zhongjun Qu [aut, cre], Tatsushi Oka [aut], Samuel Messer [ctb]
Repository: CRAN
Date/Publication: 2025-04-07 15:10:02 UTC

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New package CardioCurveR with initial version 1.0.0
Package: CardioCurveR
Title: Nonlinear Modeling of R-R Interval Dynamics
Version: 1.0.0
Description: Automated and robust framework for analyzing R-R interval (RRi) signals using advanced nonlinear modeling and preprocessing techniques. The package implements a dual-logistic model to capture the rapid drop and subsequent recovery of RRi during exercise, as described by Castillo-Aguilar et al. (2025) <doi:10.1038/s41598-025-93654-6>. In addition, 'CardioCurveR' includes tools for filtering RRi signals using zero-phase Butterworth low-pass filtering and for cleaning ectopic beats via adaptive outlier replacement using local regression and robust statistics. These integrated methods preserve the dynamic features of RRi signals and facilitate accurate cardiovascular monitoring and clinical research.
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Imports: signal (>= 1.8.1), ggplot2 (>= 3.5.1), gridExtra (>= 2.3), data.table (>= 1.16.4)
URL: https://github.com/matcasti/CardioCurveR, https://matcasti.github.io/CardioCurveR/
BugReports: https://github.com/matcasti/CardioCurveR/issues
Depends: R (>= 3.5)
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-03 16:47:24 UTC; matias
Author: Matias Castillo-Aguilar [aut, cre, cph]
Maintainer: Matias Castillo-Aguilar <m99castillo@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-07 16:00:09 UTC

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New package brulee with initial version 0.5.0
Package: brulee
Title: High-Level Modeling Functions with 'torch'
Version: 0.5.0
Description: Provides high-level modeling functions to define and train models using the 'torch' R package. Models include linear, logistic, and multinomial regression as well as multilayer perceptrons.
License: MIT + file LICENSE
URL: https://github.com/tidymodels/brulee, https://brulee.tidymodels.org/
BugReports: https://github.com/tidymodels/brulee/issues
Imports: cli, coro (>= 1.0.1), dplyr, generics, ggplot2, glue, hardhat, rlang (>= 1.1.1), stats, tibble, torch (>= 0.13.0), utils
Suggests: covr, modeldata, purrr, recipes, spelling, testthat, yardstick
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-04-07 12:00:34 UTC; max
Author: Max Kuhn [aut, cre] , Daniel Falbel [aut], Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Repository: CRAN
Date/Publication: 2025-04-07 13:50:02 UTC

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New package RcppPlanc with initial version 2.0.3
Package: RcppPlanc
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Version: 2.0.3
Date: 2025-03-26
Description: 'Rcpp' bindings for 'PLANC', a highly parallel and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library. Wraps algorithms described in Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and Eswar et. al (2021) <doi:10.1145/3432185>. Implements algorithms described in Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>, Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Encoding: UTF-8
Imports: methods, Rcpp, Matrix, hdf5r.Extra
Suggests: knitr, withr, rmarkdown, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
License: GPL (>= 2)
SystemRequirements: C++17, cmake >= 3.21.0, hdf5, git, v8, patch, gnumake, hwloc, GNU make
Depends: R (>= 3.5)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-04-04 18:24:29 UTC; andrew
Author: Andrew Robbins [aut, cre] , Yichen Wang [aut], Joshua Welch [cph] , Ramakrishnan Kannan [cph] , UT-Batelle [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Repository: CRAN
Date/Publication: 2025-04-07 12:30:06 UTC

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Sat, 05 Apr 2025

New package GOxploreR with initial version 1.2.8
Package: GOxploreR
Title: Structural Exploration of the Gene Ontology (GO) Knowledge Base
Version: 1.2.8
Maintainer: Kalifa Manjang <kalifamanjang1@gmail.com>
Description: It provides an effective, efficient, and fast way to explore the Gene Ontology (GO). Given a set of genes, the package contains functions to assess the GO and obtain the terms associated with the genes and the levels of the GO terms. The package provides functions for the three different GO ontology. We discussed the methods explicitly in the following article <doi:10.1038/s41598-020-73326-3>.
License: GPL-2
Encoding: UTF-8
Imports: igraph, network, dplyr, biomaRt, annotate, graphics, ggplot2
Depends: R (>= 2.10), GO.db, gontr, ggraph
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-04 20:05:38 UTC; manka
Repository: CRAN
Date/Publication: 2025-04-05 14:20:11 UTC
Author: Kalifa Manjang [aut, cre], Frank Emmert-Streib [aut], Shailesh Tripathi [aut], Olli Yli-Harja [aut], Matthias Dehmer [aut]

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New package osdatahub with initial version 0.3.0
Package: osdatahub
Title: Easier Interaction with the Ordnance Survey Data Hub
Version: 0.3.0
Description: Ordnance Survey ('OS') is the national mapping agency for Great Britain and produces a large variety of mapping and geospatial products. Much of OS's data is available via the OS Data Hub <https://osdatahub.os.uk/>, a platform that hosts both free and premium data products. 'osdatahub' provides a user-friendly way to access, query, and download these data.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: httptest, knitr, rmarkdown, sf, testthat (>= 3.0.0)
Depends: R (>= 2.10)
Imports: geojsonsf, geos, httr, jsonlite
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-04 17:10:43 UTC; wjochem
Author: Chris Jochem [cre, aut], Ordnance Survey Ltd [cph, fnd]
Maintainer: Chris Jochem <chris.jochem@os.uk>
Repository: CRAN
Date/Publication: 2025-04-05 11:20:06 UTC

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Thu, 03 Apr 2025

New package RStanTVA with initial version 0.2.0
Package: RStanTVA
Title: TVA Models in 'Stan' using 'R' and 'StanTVA'
Version: 0.2.0
Description: 'Stan' implementation of the Theory of Visual Attention (TVA; Bundesen, 1990; <doi:10.1037/0033-295X.97.4.523>) and numerous convenience functions for generating, compiling, fitting, and analyzing TVA models.
License: GPL (>= 3)
Encoding: UTF-8
BugReports: https://github.com/mmrabe/RStanTVA/issues
URL: https://github.com/mmrabe/RStanTVA
Date: 2025-03-25
Depends: rstan, R (>= 3.6)
Imports: dplyr, readr, tidyr, methods, utils, tibble, stats, cli, lme4, brms, rlang
Suggests: cmdstanr
Additional_repositories: https://stan-dev.r-universe.dev
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-03 08:29:51 UTC; stp364
Author: Maximilian M. Rabe [aut, cre] , Soeren Kyllingsbaek [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Repository: CRAN
Date/Publication: 2025-04-03 16:10:05 UTC

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New package RobinCar2 with initial version 0.1.1
Package: RobinCar2
Title: ROBust INference for Covariate Adjustment in Randomized Clinical Trials
Version: 0.1.1
Date: 2025-03-30
Description: Performs robust estimation and inference when using covariate adjustment and/or covariate-adaptive randomization in randomized controlled trials. This package is trimmed to reduce the dependencies and validated to be used across industry. See "FDA's final guidance on covariate adjustment"<https://www.regulations.gov/docket/FDA-2019-D-0934>, Tsiatis (2008) <doi:10.1002/sim.3113>, Bugni et al. (2018) <doi:10.1080/01621459.2017.1375934>, Ye, Shao, Yi, and Zhao (2023)<doi:10.1080/01621459.2022.2049278>, Ye, Shao, and Yi (2022)<doi:10.1093/biomet/asab015>, Rosenblum and van der Laan (2010)<doi:10.2202/1557-4679.1138>, Wang et al. (2021)<doi:10.1080/01621459.2021.1981338>, Ye, Bannick, Yi, and Shao (2023)<doi:10.1080/24754269.2023.2205802>, and Bannick, Shao, Liu, Du, Yi, and Ye (2024)<doi:10.48550/arXiv.2306.10213>.
License: Apache License 2.0
URL: https://github.com/openpharma/RobinCar2/
BugReports: https://github.com/openpharma/RobinCar2/issues
Depends: R (>= 3.6)
Imports: checkmate, numDeriv, MASS, sandwich, stats, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-03 09:08:19 UTC; root
Author: Liming Li [aut, cre] , Marlena Bannick [aut] , Dong Xi [aut], Ting Ye [aut], Yanyao Yi [aut], Gregory Chen [ctb], Gilead Sciences, Inc. [cph, fnd], F. Hoffmann-La Roche AG [cph, fnd], Merck Sharp & Dohme, Inc. [cph, fnd], AstraZeneca plc [cph, fnd], [...truncated...]
Maintainer: Liming Li <liming.li1@astrazeneca.com>
Repository: CRAN
Date/Publication: 2025-04-03 16:10:02 UTC

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New package DamageDetective with initial version 1.0.0
Package: DamageDetective
Title: Detecting Damaged Cells in Single-Cell RNA Sequencing Data
Version: 1.0.0
Description: Detects and filters damaged cells in single-cell RNA sequencing (scRNA-seq) data using a novel approach inspired by 'DoubletFinder'. Damage is detected by measuring the extent to which cells deviate from artificially damaged profiles of themselves, simulated through the probabilistic escape of cytoplasmic RNA. As output, a damage score ranging from 0 to 1 is given for each cell providing an intuitive scale for filtering that is standardised across cell types, samples, and experiments.
License: AGPL (>= 3)
Encoding: UTF-8
Language: en-US
LazyData: false
Depends: R (>= 4.4.0)
Imports: cowplot, dplyr, ggplot2, ggpubr, Matrix, patchwork, scales, RcppHNSW, rlang, tidyr, withr
Suggests: Seurat, knitr, rmarkdown, spelling
VignetteBuilder: knitr
URL: https://alicenjoyhenning.github.io/DamageDetective/, https://github.com/alicenjoyhenning/DamageDetective
BugReports: https://github.com/alicenjoyhenning/DamageDetective/issues
NeedsCompilation: no
Packaged: 2025-04-03 10:53:38 UTC; alicen
Author: Alicen Henning [aut, cre, cph]
Maintainer: Alicen Henning <alicen.jhb@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-03 16:20:02 UTC

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New package tabs with initial version 0.1.0
Package: tabs
Title: Temporal Altitudinal Biogeographic Shifts
Version: 0.1.0
Description: A standardized workflow to reconstruct spatial configurations of altitude-bounded biogeographic systems over time. For example, 'tabs' can model how island archipelagos expand or contract with changing sea levels or how alpine biomes shift in response to tree line movements. It provides functionality to account for various geophysical processes such as crustal deformation and other tectonic changes, allowing for a more accurate representation of biogeographic system dynamics. For more information see De Groeve et al. (2025) <doi:10.3897/arphapreprints.e151900>.
License: GPL (>= 3)
URL: https://uva_ibed_piac.gitlab.io/tabs/
BugReports: https://gitlab.com/uva_ibed_piac/tabs/-/issues
Depends: R (>= 2.10)
Imports: ape, dplyr, htmltools, htmlwidgets, httr, jsonlite, geojsonio, leaflet, leaftime, leaflet.extras, mapedit, qs2, rlang, sf, stringi, terra, gpkg, RSQLite
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-02 14:34:03 UTC; jedgroev
Author: Johannes De Groeve [aut, cre] , Sietze Norder [aut] , Eline Sterre Rentier [aut] , Suzette Flantua [ctb] , Kenneth Rijsdijk [ctb]
Maintainer: Johannes De Groeve <j.degroeve@uva.nl>
Repository: CRAN
Date/Publication: 2025-04-03 15:30:02 UTC

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New package NHSRwaitinglist with initial version 0.1.0
Package: NHSRwaitinglist
Title: Waiting List Metrics Using Queuing Theory
Version: 0.1.0
Maintainer: Chris Mainey <c.mainey1@nhs.net>
Description: Waiting list management using queuing theory to analyse, predict and manage queues, based on the approach described in Fong et al. (2022) <doi:10.1101/2022.08.23.22279117>. Aimed at UK National Health Service (NHS) applications, waiting list summary statistics, target-value calculations, waiting list simulation, and scheduling functions are included.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://nhs-r-community.github.io/NHSRwaitinglist/
Imports: cli, dplyr, rlang, utils, stats, randomNames, methods
Suggests: ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
LazyData: true
NeedsCompilation: no
Packaged: 2025-04-02 15:06:58 UTC; ChrisMainey(Birmingh
Author: Neil Walton [aut] , Jacqueline Grout [ctb], Zoe Turner [ctb] , Matt Dray [aut], Paul Fenton [ctb], Peter Shakeshaft [ctb], Tom Smith [aut], Chris Mainey [cre, aut] , NHS-R community [cph]
Repository: CRAN
Date/Publication: 2025-04-03 15:50:02 UTC

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New package ggpicrust2 with initial version 2.0.0
Package: ggpicrust2
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Version: 2.0.0
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
BugReports: https://github.com/cafferychen777/ggpicrust2/issues
URL: https://github.com/cafferychen777/ggpicrust2, https://cafferyang.com/ggpicrust2/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: aplot, dplyr, ggplot2, grid, ggh4x, readr, tibble, tidyr, ggprism, patchwork, ggplotify, magrittr, progress, stats, methods, grDevices, utils
Depends: R (>= 3.5.0)
Suggests: Biobase, KEGGREST, ComplexHeatmap, BiocGenerics, knitr, rmarkdown, testthat (>= 3.0.0), ALDEx2, DESeq2, edgeR, GGally, limma, Maaslin2, metagenomeSeq, MicrobiomeStat, SummarizedExperiment, circlize, lefser
NeedsCompilation: no
Packaged: 2025-04-03 05:53:23 UTC; apple
Author: Chen Yang [aut, cre], Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-03 16:00:05 UTC

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New package friendlynumber with initial version 1.0.0
Package: friendlynumber
Title: Translate Numbers into Number Words
Version: 1.0.0
Description: Converts vectors of numbers into character vectors of numerals, including cardinals (one, two, three) and ordinals (first, second, third). Supports negative numbers, fractions, and arbitrary-precision integer and high-precision floating-point vectors provided by the 'bignum' package.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/EthanSansom/friendlynumber, https://ethansansom.github.io/friendlynumber/
BugReports: https://github.com/EthanSansom/friendlynumber/issues
Suggests: bignum, testthat (>= 3.0.0), withr
NeedsCompilation: no
Packaged: 2025-04-02 10:35:30 UTC; ethansansom
Author: Ethan Sansom [aut, cre, cph]
Maintainer: Ethan Sansom <ethan.sansom29@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-03 15:10:05 UTC

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New package FARS with initial version 0.1.0
Package: FARS
Title: Factor-Augmented Regression Scenarios
Version: 0.1.0
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and block-specific factors using a flexible multilevel factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) estimate factor-augmented quantile regressions; (iv) recover full predictive densities from these quantile forecasts; and (v) estimate the density when the factors are stressed.
Depends: R (>= 3.5.0)
Imports: ggplot2, plotly, sn, nloptr, ellipse, SyScSelection, quantreg, tidyr, dplyr, forcats, MASS, reshape2,
Suggests: devtools, knitr, rmarkdown, openxlsx, readxl, zoo
VignetteBuilder: knitr
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-02 09:44:45 UTC; gianpietro
Author: Gian Pietro Bellocca [aut, cre], Ignacio Garron [aut], Vladimir Rodriguez-Caballero [aut], Esther Ruiz [aut]
Repository: CRAN
Date/Publication: 2025-04-03 15:10:10 UTC

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New package CytoProfile with initial version 0.1.2
Package: CytoProfile
Title: Cytokine Profiling Analysis Tool
Version: 0.1.2
Description: Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.
Encoding: UTF-8
URL: https://github.com/saraswatsh/CytoProfile, https://saraswatsh.github.io/CytoProfile/
Depends: R (>= 4.3)
Imports: mixOmics, dplyr, tidyr, pROC, plot3D, caret, xgboost, randomForest, gplots, e1071, ggplot2, ggrepel, gridExtra, reshape2, prodlim
Suggests: spelling, BiocManager, testthat, knitr, rmarkdown, devtools, Ckmeans.1d.dp
NeedsCompilation: no
License: GPL (>= 2)
LazyData: true
VignetteBuilder: knitr
BugReports: https://github.com/saraswatsh/CytoProfile/issues
Language: en-US
Packaged: 2025-04-02 20:29:41 UTC; shubh
Author: Shubh Saraswat [cre, aut, cph] , Xiaohua Douglas Zhang [aut]
Maintainer: Shubh Saraswat <shubh.saraswat00@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-03 15:50:06 UTC

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New package TractorTsbox with initial version 0.1.1
Package: TractorTsbox
Title: Wrangle and Modify Ts Object with Classic Frequencies and Exact Dates
Version: 0.1.1
Description: The ts objects in R are managed using a very specific date format (in the form c(2022, 9) for September 2022 or c(2021, 2) for the second quarter of 2021, depending on the frequency, for example). We focus solely on monthly and quarterly series to manage the dates of ts objects. The general idea is to offer a set of functions to manage this date format without it being too restrictive or too imprecise depending on the rounding. This is a compromise between simplicity, precision and use of the basic 'stats' functions for creating and managing time series (ts(), window()). Les objets ts en R sont gérés par un format de date très particulier (sous la forme c(2022, 9) pour septembre 2022 ou c(2021, 2) pour le deuxième trimestre 2021 selon la fréquence par exemple). On se concentre uniquement sur les séries mensuelles et trimestrielles pour gérer les dates des objets ts. Lidée générale est de proposer un ensemble de fonctions pour gérer ce format de date sans que ce soit trop contraignant o [...truncated...]
License: GPL (>= 3)
URL: https://github.com/TractorTom/TractorTsbox, https://tractortom.github.io/TractorTsbox/
BugReports: https://github.com/TractorTom/TractorTsbox/issues
Encoding: UTF-8
Imports: stats, checkmate
Depends: R (>= 3.6)
LazyData: true
Suggests: testthat (>= 3.0.0), renv, fuzzr, pkgdown, devtools, usethis, covr, withr, altdoc
NeedsCompilation: no
Packaged: 2025-04-02 08:15:26 UTC; UTZK0M
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tangbarth@hotmail.fr>
Repository: CRAN
Date/Publication: 2025-04-03 15:00:05 UTC

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New package spatemR with initial version 1.0.0
Package: spatemR
Title: Generalized Spatial Autoregresive Models for Mean and Variance
Version: 1.0.0
Description: Modeling spatial dependencies in dependent variables, extending traditional spatial regression approaches. It allows for the joint modeling of both the mean and the variance of the dependent variable, incorporating semiparametric effects in both models. Based on generalized additive models (GAM), the package enables the inclusion of non-parametric terms while maintaining the classical theoretical framework of spatial regression. Additionally, it implements the Generalized Spatial Autoregression (GSAR) model, which extends classical methods like logistic Spatial Autoregresive Models (SAR), probit Spatial Autoregresive Models (SAR), and Poisson Spatial Autoregresive Models (SAR), offering greater flexibility in modeling spatial dependencies and significantly improving computational efficiency and the statistical properties of the estimators. Related work includes: a) J.D. Toloza-Delgado, Melo O.O., Cruz N.A. (2024). "Joint spatial modeling of mean and non-homogeneous variance combining s [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: methods, stats, gamlss (>= 5.3-1), gamlss.dist
Suggests: testthat (>= 3.0.0), sp, spdep
NeedsCompilation: no
Packaged: 2025-04-02 09:04:07 UTC; UIB
Author: Nelson Alirio Cruz Gutierrez [aut, cre, cph], Oscar Orlando Melo [aut], Jurgen Toloza-Delgado [aut]
Maintainer: Nelson Alirio Cruz Gutierrez <nelson-alirio.cruz@uib.es>
Repository: CRAN
Date/Publication: 2025-04-03 15:00:02 UTC

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New package forestdata with initial version 0.3.0
Package: forestdata
Title: Download Forestry Data
Version: 0.3.0
Description: Functions for downloading forestry and land use data for use in spatial analysis. This packages offers a user-friendly solution to quickly obtain datasets such as forest height, forest types, tree species under various climate change scenarios, or land use data among others.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: sf, stringr, tibble, tidyr, dplyr, purrr, terra, stringi, archive, foreign, lifecycle, cli, glue
Depends: R (>= 4.1.0)
Suggests: aws.s3, RODBC, odbc, giscoR, testthat (>= 3.0.0), rmarkdown, ggplot2, tidyterra
URL: https://cidree.github.io/forestdata/
NeedsCompilation: no
Packaged: 2025-04-02 22:26:45 UTC; User
Author: Adrian Cidre Gonzalez [aut, cre]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-03 07:40:02 UTC

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Wed, 02 Apr 2025

New package multiDoE with initial version 0.9.4
Package: multiDoE
Title: Multi-Criteria Design of Experiments for Optimal Design
Version: 0.9.4
Maintainer: Andrea Melloncelli <andrea.melloncelli@vanlog.it>
Description: Multi-criteria design of experiments algorithm that simultaneously optimizes up to six different criteria ('I', 'Id', 'D', 'Ds', 'A' and 'As'). The algorithm finds the optimal Pareto front and, if requested, selects a possible symmetrical design on it. The symmetrical design is selected based on two techniques: minimum distance with the Utopia point or the 'TOPSIS' approach.
License: CC BY 4.0
URL: https://github.com/andreamelloncelli/multiDoE
Depends: R (>= 3.5.0)
Imports: ggplot2, magrittr, plotly, pracma
Suggests: devtools, here, knitr, logr, markdown, rgl, rmarkdown, testthat (>= 3.0.0), usethis
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-02 17:06:07 UTC; mello
Author: Francesca Cucchi [aut], Andrea Melloncelli [aut, cre], Francesco Sambo [aut], Kalliopi Mylona [aut], Matteo Borrotti [aut]
Repository: CRAN
Date/Publication: 2025-04-02 21:50:06 UTC

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New package SwPcIndex with initial version 0.1.0
Package: SwPcIndex
Title: Computation of Survey Weighted PC Based Composite Index
Version: 0.1.0
Depends: R(>= 2.10)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Description: An index is created using a mathematical model that transforms multi-dimensional variables into a single value. These variables are often correlated, and while PCA-based indices can address the issue of multicollinearity, they typically do not account for survey weights, which can lead to inaccurate rankings of survey units such as households, districts, or states. To resolve this, the current package facilitates the development of a principal component analysis-based composite index by incorporating survey weights for each sample observation. This ensures the generation of a survey-weighted principal component-based normalized composite index. Additionally, the package provides a normalized principal component-based composite index and ranks the sample observations based on the values of the composite indices. For method details see, Skinner, C. J., Holmes, D. J. and Smith, T. M. F. (1986) <DOI:10.1080/01621459.1986.10478336>, Singh, D., Basak, P., Kumar, R. and Ahmad, T. (2023) [...truncated...]
License: GPL (>= 2.0)
Encoding: UTF-8
Imports: stats
NeedsCompilation: no
Author: Pradip Basak [aut, cph, cre], Deepak Singh [aut, cph], Raju Kumar [aut, cph], Tauqueer Ahmad [aut, cph]
Maintainer: Pradip Basak <pradip@ubkv.ac.in>
Packaged: 2025-04-01 18:04:36 UTC; Dr. Pradeep
Repository: CRAN
Date/Publication: 2025-04-02 17:40:12 UTC

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New package stochcorr with initial version 0.0.1
Package: stochcorr
Title: Stochastic Correlation Modelling via Circular Diffusion
Version: 0.0.1
Description: Performs simulation and inference of diffusion processes on circle. Stochastic correlation models based on circular diffusion models are provided. For details see Majumdar, S. and Laha, A.K. (2024) "Diffusion on the circle and a stochastic correlation model" <doi:10.48550/arXiv.2412.06343>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, nloptr, progress, foreach, doSNOW, snow
Suggests: ggplot2
Author: Sourav Majumdar [aut, cre]
Maintainer: Sourav Majumdar <souravm@iitk.ac.in>
NeedsCompilation: yes
Packaged: 2025-04-01 05:53:14 UTC; sourav
Repository: CRAN
Date/Publication: 2025-04-02 17:20:01 UTC

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New package SecretsProvider with initial version 1.0.0
Package: SecretsProvider
Title: Save and Retrieve Name-Value Pairs to and from a File
Version: 1.0.0
Date: 2025-03-07
Maintainer: Koen Greuell <vlic@lifewatch.eu>
Description: Facilitates secret management by storing credentials in a dedicated file, keeping them out of your code base. The secrets are stored without encryption. This package is compatible with secrets stored by the 'SecretsProvider' 'Python' package <https://pypi.org/project/SecretsProvider/>.
License: Apache License (== 2.0)
Suggests: testthat (>= 3.0.0), getPass
NeedsCompilation: no
Packaged: 2025-04-01 12:15:59 UTC; koen-greuell
Author: Koen Greuell [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-02 17:20:05 UTC

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New package RKaggle with initial version 0.1.0
Package: RKaggle
Title: 'Kaggle' Dataset Downloader 'API'
Version: 0.1.0
Description: Easily download datasets from Kaggle <https://www.kaggle.com/> directly into your R environment using 'RKaggle'. Streamline your data analysis workflows by importing datasets effortlessly and focusing on insights rather than manual data handling. Perfect for data enthusiasts and professionals looking to integrate Kaggle datasets into their R projects with minimal hassle.
License: MIT + file LICENSE
URL: https://github.com/benyamindsmith/RKaggle
BugReports: https://github.com/benyamindsmith/RKaggle/issues
Encoding: UTF-8
Imports: httr, readr, withr, jsonlite, arrow, readODS, tibble, readxl
Depends: R (>= 4.1.0)
Suggests: conflicted
NeedsCompilation: no
Packaged: 2025-04-01 20:24:14 UTC; ben29
Author: Benjamin Smith [aut, cre]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2025-04-02 17:50:07 UTC

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New package maxEff with initial version 0.1.1
Package: maxEff
Title: Additional Predictor with Maximum Effect Size
Version: 0.1.1
Date: 2025-04-01
Description: Methods of selecting one from many numeric predictors for a regression model, to ensure that the additional predictor has the maximum effect size.
Encoding: UTF-8
License: GPL-2
Depends: R (>= 4.4),
Language: en-US
Imports: caret, parallel, rpart, spatstat.geom
Suggests: knitr, groupedHyperframe, survival, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-01 17:18:23 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre] , Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-02 17:40:01 UTC

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New package HTGM with initial version 1.0
Package: HTGM
Version: 1.0
Date: 2025-03-26
Title: High Throughput 'GoMiner'
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Author: Barry Zeeberg [aut, cre]
Depends: R (>= 4.2.0)
Imports: minimalistGODB, GoMiner, grDevices, stats, gplots
LazyData: true
LazyDataCompression: xz
Description: Two papers published in the early 2000's (Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) and (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005) <doi:10.1186/1471-2105-6-168>) implement 'GoMiner' and 'High Throughput GoMiner' ('HTGM') to map lists of genes to the Gene Ontology (GO) <https://geneontology.org>. Until recently, these were hosted on a server at The National Cancer Institute (NCI). In order to continue providing these services to the bio-medical community, I have developed stand-alone versions. The current package 'HTGM' builds upon my recent package 'GoMiner'. The output of 'GoMiner' is a heatmap showing the relationship of a single list of genes and the significant categories into which they map. 'High Throughput GoMiner' ('HTGM') integrates the results of the individual 'GoMiner' analyses. The output of 'HTGM' is a heatmap showing the relationship of the significant categories derived from each gene list. The heatmap [...truncated...]
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-04-01 13:36:39 UTC; barryzeeberg
Repository: CRAN
Date/Publication: 2025-04-02 17:40:18 UTC

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New package castgen with initial version 1.0.2
Package: castgen
Title: Estimate Sample Size for Population Genomic Studies
Version: 1.0.2
Description: Estimate sample sizes needed to capture target levels of genetic diversity from a population (multivariate allele frequencies) for applications like germplasm conservation and breeding efforts. Compares bootstrap samples to a full population using linear regression, employing the R-squared value to represent the proportion of diversity captured. Iteratively increases sample size until a user-defined target R-squared is met. Offers a parallelized R implementation of a previously developed 'python' method. All ploidy levels are supported. For more details, see Sandercock et al. (2024) <doi:10.1073/pnas.2403505121>.
License: Apache License (>= 2)
URL: https://github.com/alex-sandercock/castgen
BugReports: https://github.com/alex-sandercock/castgen/issues
Imports: doParallel (>= 1.0.17), dplyr (>= 1.1.2), foreach (>= 1.5.2), parallel (>= 4.0.0), Rdpack (>= 0.7), stats, utils, vcfR (>= 1.15.0)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-04-01 19:42:07 UTC; ams866
Author: Alexander M. Sandercock [aut, cre]
Maintainer: Alexander M. Sandercock <ams866@cornell.edu>
Repository: CRAN
Date/Publication: 2025-04-02 17:40:05 UTC

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New package bidsr with initial version 0.1.0
Package: bidsr
Title: A Brain Imaging Data Structure ('BIDS') Parser
Version: 0.1.0
URL: https://dipterix.org/bidsr/, https://github.com/dipterix/bidsr/
BugReports: https://github.com/dipterix/bidsr/issues
Description: Parse and read the files that comply with the brain imaging data structure, or 'BIDS' format, see the publication from Gorgolewski, K., Auer, T., Calhoun, V. et al. (2016) <doi:10.1038/sdata.2016.44>. Provides query functions to extract and check the 'BIDS' entity information (such as subject, session, task, etc.) from the file paths and suffixes according to the specification. The package is developed and used in the reproducible analysis and visualization of intracranial electroencephalography, or 'RAVE', see Magnotti, J. F., Wang, Z., and Beauchamp, M. S. (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("bidsr")' for details and attributions.
Copyright: This software includes material (schema files from directory 'inst/bids-schema') from the 'BIDS' specification, which is licensed under a Creative Commons Attribution 4.0 International License; see a copy of the license under 'inst/bids-schema/LICENSE.txt', and website <https://bids.neuroimaging.io> for details.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Imports: checkmate, data.table, fastmap, fs, jsonlite, nanotime, S7 (>= 0.2.0), utils, uuid
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-01 14:48:04 UTC; dipterix
Author: Zhengjia Wang [aut, cre] , Trustees of the University of Pennsylvania [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-02 17:40:08 UTC

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New package D4TAlink.light with initial version 2.1.18
Package: D4TAlink.light
Title: GDP - Workflow Management
Version: 2.1.18
Date: 2025-03-28
Author: Gregoire Thomas [aut, cre]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Description: Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with ALCOA+ principles as proposed by the U.S. FDA, and with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.
Depends: R (>= 4.0.0), jsonlite, openssl
Imports: officedown, utils, rmarkdown, Biobase, openxlsx,reticulate,feather, getPass
Suggests: knitr, roxygen2 (>= 3.1.0), WriteXLS,XLConnect,xlsx, testthat
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://bitbucket.org/SQ4/d4talink.light
ByteCompile: true
Repository: CRAN
BugReports: https://bitbucket.org/SQ4/d4talink.light/issues
NeedsCompilation: no
Packaged: 2025-03-28 17:12:28 UTC; GregoireThomas
Date/Publication: 2025-04-02 15:50:10 UTC

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New package InterpolateR with initial version 1.2-0
Package: InterpolateR
Title: A Comprehensive Toolkit for Fast and Efficient Spatial Interpolation
Version: 1.2-0
Maintainer: Jonnathan Landi <jonnathan.landi@outlook.com>
Description: Spatial interpolation toolkit designed for environmental and geospatial applications. It includes a range of methods, from traditional techniques to advanced machine learning approaches, ensuring accurate and efficient estimation of values in unobserved locations.
License: GPL (>= 3)
Depends: R (>= 4.4.0)
Imports: terra, randomForest, data.table, pbapply, qmap, hydroGOF
URL: https://github.com/Jonnathan-Landi/InterpolateR
BugReports: https://github.com/Jonnathan-Landi/InterpolateR/issues
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-04-01 01:08:55 UTC; Jonna
Author: Jonnathan Landi [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-04-02 09:10:02 UTC

More information about InterpolateR at CRAN
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New package weathR with initial version 0.1.0
Package: weathR
Title: Interact with the U.S. National Weather Service API
Version: 0.1.0
Description: Enables interaction with the National Weather Service application programming web-interface for fetching of real-time and forecast meteorological data. Users can provide latitude and longitude, Automated Surface Observing System identifier, or Automated Weather Observing System identifier to fetch recent weather observations and recent forecasts for the given location or station. Additionally, auxiliary functions exist to identify stations nearest to a point, convert wind direction from character to degrees, and fetch active warnings. Results are returned as simple feature objects whenever possible.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, httr2, janitor, jsonlite, lubridate, lutz, magrittr, purrr, sf, tibble
Suggests: gt, snakecase, tmap
URL: https://github.com/JeffreyFowler/weathR
BugReports: https://github.com/JeffreyFowler/weathR/issues
NeedsCompilation: no
Packaged: 2025-03-31 23:18:40 UTC; Jeffr
Author: Jeffrey Fowler [aut, cre, cph]
Maintainer: Jeffrey Fowler <JeffreyF6120@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-02 09:00:02 UTC

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New package mbg with initial version 1.0.0
Package: mbg
Title: Model-Based Geostatistics
Version: 1.0.0
Description: Modern model-based geostatistics for point-referenced data. This package provides a simple interface to run spatial machine learning models and geostatistical models that estimate a continuous (raster) surface from point-referenced outcomes and, optionally, a set of raster covariates. The package also includes functions to summarize raster outcomes by (polygon) region while preserving uncertainty.
License: MIT + file LICENSE
Depends: R (>= 4.1.0)
Imports: assertthat, caret, data.table, glue, Matrix, matrixStats, purrr, R6, sf, terra, tictoc
Suggests: INLA, knitr, rmarkdown, ggplot2, scales
Additional_repositories: https://inla.r-inla-download.org/R/stable/
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://henryspatialanalysis.github.io/mbg/
BugReports: https://github.com/henryspatialanalysis/mbg/issues
NeedsCompilation: no
Packaged: 2025-03-31 22:44:30 UTC; nathenry
Author: Nathaniel Henry [aut, cre] , Benjamin Mayala [aut]
Maintainer: Nathaniel Henry <nat@henryspatialanalysis.com>
Repository: CRAN
Date/Publication: 2025-04-02 09:00:06 UTC

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New package ieTest with initial version 2.0
Package: ieTest
Title: Indirect Effects Testing Methods in Mediation Analysis
Version: 2.0
Date: 2025-03-31
Maintainer: John Kidd <jkidd@uvu.edu>
Description: Used in testing if the indirect effect from linear regression mediation analysis is equal to 0. Includes established methods such as the Sobel Test, Joint Significant test (maxP), and tests based off the distribution of the Product or Normal Random Variables. Additionally, this package adds more powerful tests based on Intersection-Union theory. These tests are the S-Test, the ps-test, and the ascending squares test. These new methods are uniformly more powerful than maxP, which is more powerful than Sobel and less anti-conservative than the Product of Normal Random Variables. These methods are explored by Kidd and Lin, (2024) <doi:10.1007/s12561-023-09386-6> and Kidd et al., (2025) <doi:10.1007/s10260-024-00777-7>.
License: GPL (>= 2)
Depends: R (>= 3.3.0), grDevices, graphics, methods, stats, utils
Imports: Rcpp (>= 1.0.3), RcppArmadillo, RcppDist, twosamples, MASS
LinkingTo: Rcpp, RcppArmadillo, RcppDist
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2025-03-31 21:48:21 UTC; 10975067
Author: John Kidd [aut, cre]
Repository: CRAN
Date/Publication: 2025-04-02 09:00:11 UTC

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Tue, 01 Apr 2025

New package semboottools with initial version 0.1.0
Package: semboottools
Title: Bootstrapping Helpers for Structural Equation Modelling
Version: 0.1.0
Description: A collection of helper functions for forming bootstrapping confidence intervals and examining bootstrap estimates in structural equation modelling. Currently supports models fitted by the 'lavaan' package by Rosseel (2012) <doi:10.18637/jss.v048.i02>.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: boot, lavaan, psych, lavaan.printer
URL: https://Yangzhen1999.github.io/semboottools/
BugReports: https://github.com/Yangzhen1999/semboottools/issues
NeedsCompilation: no
Packaged: 2025-03-30 14:06:57 UTC; Administrator
Author: Wendie Yang [aut, cre] , Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:40:06 UTC

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New package RRgeo with initial version 0.0.3
Package: RRgeo
Title: Species Distribution Modelling for Rare Species
Version: 0.0.3
Description: Performs species distribution modeling for rare species with unprecedented accuracy (Mondanaro et al., 2023 <doi:10.1111/2041-210X.14066>) and finds the area of origin of species and past contact between them taking climatic variability in full consideration (Mondanaro et al., 2025 <doi:10.1111/2041-210X.14478>).
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.6.0)
Imports: ape, methods,pbapply,Rphylopars,RRphylo,dismo (>= 1.3),gtools, terra, adehabitatMA, ecospat (>= 3.2.1), foreach, doParallel, PresenceAbsence, parallel, ade4, sp, sf,scales, ks, leastcostpath, doSNOW, biomod2 (>= 4.2),utils
Suggests: ggplot2, cowplot, openxlsx, Bchron, curl, rnaturalearth (>= 1.0.1), rnaturalearthhires, spatstat.geom, spatstat.explore, knitr, httr, jsonlite
Additional_repositories: http://packages.ropensci.org
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-31 09:06:22 UTC; Utente
Author: Alessandro Mondanaro [aut], Mirko Di Febbraro [aut], Silvia Castiglione [aut, cre], Carmela Serio [aut], Marina Melchionna [aut], Giorgia Girardi [aut], Pasquale Raia [aut]
Maintainer: Silvia Castiglione <silvia.castiglione@unina.it>
Repository: CRAN
Date/Publication: 2025-04-01 16:20:10 UTC

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New package LogisticEnsembles with initial version 0.5.0
Package: LogisticEnsembles
Title: Automatically Runs 36 Logistic Models (Individual and Ensembles)
Version: 0.5.0
Description: Automatically returns 36 logistic models including 23 individual models and 13 ensembles of models of logistic data. The package also returns 10 plots, 5 tables, and a summary report. The package automatically builds all 36 models, reports all results, and provides graphics to show how the models performed. This can be used for a wide range of data sets. The package includes medical data (the Pima Indians data set), and information about the performance of Lebron James. The package can be used to analyze many other examples, such as stock market data. The package automatically returns many values for each model, such as True Positive Rate, True Negative Rate, False Positive Rate, False Negative Rate, Positive Predictive Value, Negative Predictive Value, F1 Score, Area Under the Curve. The package also returns 36 Receiver Operating Characteristic (ROC) curves for each of the 36 models.
License: MIT + file LICENSE
Depends: adabag, arm, brnn, C50, car, corrplot, Cubist, doParallel, dplyr, e1071, gam, gbm, ggplot2, ggplotify, graphics, gridExtra, gt, ipred, klaR, MachineShop, magrittr, MASS, mda, parallel, pls, pROC, purrr, R (>= 2.10), randomForest, ranger, reactable, reactablefmtr, readr, rpart, scales, stats, tidyr, tree, utils, xgboost
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/InfiniteCuriosity/LogisticEnsembles
BugReports: https://github.com/InfiniteCuriosity/LogisticEnsembles/issues
NeedsCompilation: no
Packaged: 2025-03-30 23:39:17 UTC; russellconte
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:10:01 UTC

More information about LogisticEnsembles at CRAN
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New package GENEAcore with initial version 1.0.0
Package: GENEAcore
Title: Pre-Processing of 'GENEActiv' Data
Version: 1.0.0
Date: 2025-03-24
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events. For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
License: GPL (>= 2)
Encoding: UTF-8
Imports: changepoint, signal, methods
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), GENEAread (>= 2.0.10), GENEAclassify
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-31 12:36:35 UTC; JiaYingChua
Author: Joss Langford [aut], Ian Long [aut], Jia Ying Chua [aut, cre], Activinsights Ltd [cph]
Repository: CRAN
Date/Publication: 2025-04-01 16:30:10 UTC

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New package ForecastingEnsembles with initial version 0.5.0
Package: ForecastingEnsembles
Title: Time Series Forecasting Using 23 Individual Models
Version: 0.5.0
Description: Runs multiple individual time series models, and combines them into an ensembles of time series models. This is mainly used to predict the results of the monthly labor market report from the United States Bureau of Labor Statistics for virtually any part of the economy reported by the Bureau of Labor Statistics, but it can be easily modified to work with other types of time series data. For example, the package was used to predict the winning men's and women's time for the 2024 London Marathon.
License: MIT + file LICENSE
Depends: doParallel, dplyr, fable, fabletools, fable.prophet, feasts, fracdiff, ggplot2, gt, magrittr, parallel, readr, stats, tibble, tidyr, tsibble, urca, utils, R (>= 2.10)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/InfiniteCuriosity/ForecastingEnsembles
BugReports: https://github.com/InfiniteCuriosity/ForecastingEnsembles/issues
NeedsCompilation: no
Packaged: 2025-03-31 00:06:49 UTC; russellconte
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:20:14 UTC

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New package emend with initial version 0.1.0
Package: emend
Title: Cleaning Text Data with an AI Assistant
Version: 0.1.0
Description: Provides functions to clean and standardize messy data, including textual categories and free-text addresses, using Large Language Models. The package corrects typos, expands abbreviations, and maps inconsistent entries to standardized values. Ideal for Bioinformatics, business, and general data cleaning tasks.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, jsonlite, rlang, ellmer
Depends: R (>= 4.1.0)
LazyData: true
Suggests: rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/anuopensci/emend, https://anuopensci.github.io/emend/
BugReports: https://github.com/anuopensci/emend/issues
NeedsCompilation: no
Packaged: 2025-03-31 00:07:48 UTC; u1133824
Author: Emi Tanaka [aut, cph] , Jiajia Li [aut, cre]
Maintainer: Jiajia Li <lijia970324@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:20:02 UTC

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New package ClassificationEnsembles with initial version 0.5.0
Package: ClassificationEnsembles
Title: Automatically Builds 20 Classification Models
Version: 0.5.0
Description: Automatically builds 20 classification models from data. The package returns 26 plots, 5 tables and a summary report. The package automatically builds 12 individual classification models, including error (RMSE) and predictions. That data is used to create an ensemble, which is then modeled using 8 methods. The process is repeated as many times as the user requests. The mean of the results are presented in a summary table. The package returns the confusion matrices for all 20 models, tables of the correlation of the numeric data, the results of the variance inflation process, the head of the ensemble and the head of the data frame.
License: MIT + file LICENSE
Depends: C50, car, caret, corrplot, doParallel, dplyr, e1071, ggplot2, gt, ipred, MachineShop, magrittr, parallel, pls, purrr, R (>= 2.10), randomForest, ranger, reactable, reactablefmtr, scales, tidyr, tree
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/InfiniteCuriosity/ClassificationEnsembles
BugReports: https://github.com/InfiniteCuriosity/ClassificationEnsembles/issues
NeedsCompilation: no
Packaged: 2025-03-30 22:25:56 UTC; russellconte
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:10:05 UTC

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New package calcite with initial version 0.1.0
Package: calcite
Title: Bindings to the Calcite Design System 'JavaScript' Component Library
Version: 0.1.0
Description: Provides access to the 'Calcite Design System' 'javascript' components via integration with the 'htmltools' and 'shiny' packages. Pre-built and interactive components can be used to generate either static html or interactive web applications. Learn more about the 'Calcite Design System' at <https://developers.arcgis.com/calcite-design-system/>.
License: Apache License (>= 2)
Imports: htmltools, rlang, shiny
Encoding: UTF-8
Language: en
NeedsCompilation: no
Packaged: 2025-03-31 14:58:09 UTC; josiahparry
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:40:10 UTC

More information about calcite at CRAN
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New package biometrics with initial version 1.0.1
Package: biometrics
Version: 1.0.1
Date: 2025-03-27
Title: Functions and Datasets for Forest Biometrics and Modelling
Description: A system of functions and data aiming to apply quantitative analyses to forest ecology, silviculture and decision-support systems. Besides, the package helps to carry out data management, exploratory analysis, and model assessment.
License: GPL-3
URL: https://eljatib.com
Depends: R (>= 3.5.0)
Imports: lattice, ggplot2, stats, graphics, datana
Suggests: foreign, gdata, car, agricolae, multcomp
Encoding: UTF-8
Language: en-US
BuildResaveData: best
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2025-03-31 05:50:30 UTC; christian
Author: Christian Salas-Eljatib [aut, cre] , Pino Nicolas [ctb] , Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-01 16:20:05 UTC

More information about biometrics at CRAN
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New package NumericEnsembles with initial version 0.5.0
Package: NumericEnsembles
Title: Automatically Runs 23 Individual and 17 Ensembles of Models
Version: 0.5.0
Depends: Cubist, Metrics, arm, brnn, broom, car, caret, corrplot, doParallel, dplyr, e1071, earth, gam, gbm, ggplot2, glmnet, graphics, grDevices, gridExtra, ipred, leaps, nnet, parallel, pls, purrr, randomForest, reactable, reactablefmtr, readr, rpart, stats, tidyr, tree, utils, xgboost, R (>= 4.1.0)
Description: Automatically runs 23 individual models and 17 ensembles on numeric data. The package automatically returns complete results on all 40 models, 25 charts, multiple tables. The user simply provides the data, and answers a few questions (for example, how many times would you like to resample the data). From there the package randomly splits the data into train, test and validation sets, builds models on the training data, makes predictions on the test and validation sets, measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions using the 40 pre trained models on totally new (untrained) data if the user selects that feature. This feature alone represents a very effective solution to the issue of reproducibility of models in data science. [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: http://www.NumericEnsembles.com, https://github.com/InfiniteCuriosity/NumericEnsembles
BugReports: https://github.com/InfiniteCuriosity/NumericEnsembles/issues
NeedsCompilation: no
Packaged: 2025-03-30 20:05:59 UTC; russellconte
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Repository: CRAN
Date/Publication: 2025-04-01 15:50:13 UTC

More information about NumericEnsembles at CRAN
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New package nonstat with initial version 0.0.6
Package: nonstat
Title: Detecting Nonstationarity in Time Series
Version: 0.0.6
Maintainer: Martin Hecht <martin.hecht@hsu-hh.de>
Description: Provides a nonvisual procedure for screening time series for nonstationarity in the context of intensive longitudinal designs, such as ecological momentary assessments. The method combines two diagnostics: one for detecting trends (based on the split R-hat statistic from Bayesian convergence diagnostics) and one for detecting changes in variance (a novel extension inspired by Levene's test). This approach allows researchers to efficiently and reproducibly detect violations of the stationarity assumption, especially when visual inspection of many individual time series is impractical. The procedure is suitable for use in all areas of research where time series analysis is central. For a detailed description of the method and its validation through simulations and empirical application, see Zitzmann, S., Lindner, C., Lohmann, J. F., & Hecht, M. (2024) "A Novel Nonvisual Procedure for Screening for Nonstationarity in Time Series as Obtained from Intensive Longitudinal Designs" <htt [...truncated...]
License: GPL-3
Depends: R (>= 3.5.0)
NeedsCompilation: no
Encoding: UTF-8
Language: en-US
Packaged: 2025-03-30 20:01:40 UTC; martin
Author: Martin Hecht [aut, cre], Steffen Zitzmann [aut]
Repository: CRAN
Date/Publication: 2025-04-01 15:50:02 UTC

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New package archeoViz with initial version 1.4.0
Package: archeoViz
Title: Visualisation, Exploration, and Web Communication of Archaeological Spatial Data
Version: 1.4.0
Date: 2025-04-01
Author: Sebastien Plutniak [aut, cre] , Renata Araujo [ctb] , Laura Coltofean [ctb] , Nicolas Delsol [ctb] , Sara Giardino [ctb] , Julian Laabs [ctb]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Description: An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
License: GPL-3
Repository: CRAN
Encoding: UTF-8
Imports: ggplot2, plotly, mgcv, geometry, reshape2, svglite, htmlwidgets, shiny, shinythemes, knitr,
Suggests: covr, SEAHORS, rmarkdown, markdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://archeoviz.hypotheses.org, https://github.com/sebastien-plutniak/archeoviz
BugReports: https://github.com/sebastien-plutniak/archeoviz/issues
NeedsCompilation: no
Packaged: 2025-04-01 11:51:25 UTC; seb
Date/Publication: 2025-04-01 13:10:09 UTC

More information about archeoViz at CRAN
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New package shapr with initial version 1.0.3
Package: shapr
Version: 1.0.3
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in many situations it is crucial to understand and explain why a model made a specific prediction. Shapley values is the only method for such prediction explanation framework with a solid theoretical foundation. Previously known methods for estimating the Shapley values do, however, assume feature independence. This package implements methods which accounts for any feature dependence, and thereby produces more accurate estimates of the true Shapley values. An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
URL: https://norskregnesentral.github.io/shapr/, https://github.com/NorskRegnesentral/shapr/
BugReports: https://github.com/NorskRegnesentral/shapr/issues
License: MIT + file LICENSE
Encoding: UTF-8
ByteCompile: true
Language: en-US
Depends: R (>= 3.5.0)
Imports: stats, data.table (>= 1.15.0), Rcpp (>= 0.12.15), Matrix, future.apply, methods
Suggests: ranger, xgboost, mgcv, testthat (>= 3.0.0), knitr, rmarkdown, roxygen2, ggplot2, gbm, party, partykit, waldo, progressr, future, ggbeeswarm, vdiffr, forecast, torch, GGally, coro, parsnip, recipes, workflows, tune, dials, yardstick, hardhat, rsample, rlang, cli
LinkingTo: RcppArmadillo, Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-03-26 13:36:18 UTC; jullum
Author: Martin Jullum [cre, aut] , Lars Henry Berge Olsen [aut] , Annabelle Redelmeier [aut], Jon Lachmann [aut] , Nikolai Sellereite [aut] , Anders Loeland [ctb], Jens Christian Wahl [ctb], Camilla Lingjaerde [ctb], Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Repository: CRAN
Date/Publication: 2025-03-26 17:10:02 UTC

More information about shapr at CRAN
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New package rim with initial version 0.8.0
Package: rim
Title: Interface to 'Maxima', Enabling Symbolic Computation
Version: 0.8.0
Date: 2025-04-01
Description: An interface to the powerful and fairly complete computer algebra system 'Maxima'. It can be used to start and control 'Maxima' from within R by entering 'Maxima' commands. Results from 'Maxima' can be parsed and evaluated in R. It facilitates outputting results from 'Maxima' in 'LaTeX' and 'MathML'. 2D and 3D plots can be displayed directly. This package also registers a 'knitr'-engine enabling 'Maxima' code chunks to be written in 'RMarkdown' documents.
URL: https://rcst.github.io/rim/
BugReports: https://github.com/rcst/rim/issues
SystemRequirements: Maxima (https://sourceforge.net/projects/maxima/, tested with versions 5.42.0 - 5.46.0), needs to be on PATH
License: GPL (>= 3)
Imports: methods, Rcpp, R6, knitr, GlobalOptions
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0), rmarkdown
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-04-01 06:54:32 UTC; eric
Author: Eric Stemmler [aut, cre], Kseniia Shumelchyk [aut], Hans W. Borchers [aut]
Maintainer: Eric Stemmler <stemmler.eric@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-01 08:50:02 UTC

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New package CytOpT with initial version 0.9.8
Package: CytOpT
Title: Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation
Version: 0.9.8
Date: 2025-03-31
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
SystemRequirements: Python (>= 3.7)
Description: Supervised learning from a source distribution (with known segmentation into cell sub-populations) to fit a target distribution with unknown segmentation. It relies regularized optimal transport to directly estimate the different cell population proportions from a biological sample characterized with flow cytometry measurements. It is based on the regularized Wasserstein metric to compare cytometry measurements from different samples, thus accounting for possible mis-alignment of a given cell population across sample (due to technical variability from the technology of measurements). Supervised learning technique based on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a mixture model Details are presented in Freulon P, Bigot J and Hejblum BP (2023) <doi:10.1214/22-AOAS1660>.
License: GPL (>= 2)
Repository: CRAN
URL: https://sistm.github.io/CytOpT-R/, https://github.com/sistm/CytOpT-R/
Depends: R (>= 3.6)
LazyData: true
Encoding: UTF-8
Imports: ggplot2 (>= 3.0.0), MetBrewer, patchwork, reshape2, reticulate, stats, testthat (>= 3.0.0)
Suggests: rmarkdown, knitr, covr
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-31 22:14:53 UTC; boris
Author: Boris Hejblum [aut, cre], Paul Freulon [aut], Kalidou Ba [aut, trl]
Date/Publication: 2025-04-01 06:50:07 UTC

More information about CytOpT at CRAN
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Mon, 31 Mar 2025

New package tsaux with initial version 1.0.0
Package: tsaux
Title: Time Series Forecasting Auxiliary Functions
Version: 1.0.0
Maintainer: Alexios Galanos <alexios@4dscape.com>
Description: A suite of auxiliary functions that enhance time series estimation and forecasting, including a robust anomaly detection routine based on Chen and Liu (1993) <doi:10.2307/2290724> (imported and wrapped from the 'tsoutliers' package), utilities for managing calendar and time conversions, performance metrics to assess both point forecasts and distributional predictions, advanced simulation by allowing the generation of time series components—such as trend, seasonal, ARMA, irregular, and anomalies—in a modular fashion based on the innovations form of the state space model and a number of transformation methods including Box-Cox, Logit, 'Softplus-Logit' and Sigmoid.
Depends: R (>= 4.1.0), tsmethods
Imports: methods, zoo, xts, lubridate, car, Rdpack, scoringRules, stlplus, tsoutliers, forecast, data.table
License: GPL-2
Encoding: UTF-8
BugReports: https://github.com/tsmodels/tsaux/issues
URL: https://github.com/tsmodels/tsaux
Suggests: knitr, kableExtra, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-29 19:39:16 UTC; alexios
Author: Alexios Galanos [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-03-31 17:30:01 UTC

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New package subselect with initial version 0.16.0
Package: subselect
Version: 0.16.0
Date: 2025-03-29
Title: Selecting Variable Subsets
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut, cre], Jorge Cadima [aut], Manuel Minhoto [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, <doi:10.1016/j.csda.2003.11.001>). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, <doi:10.1006/jmva.2000.1920>). There is a package vignette "subselect", which includes additional references.
Depends: R (>= 3.5.0)
Imports: MASS, ISwR, corpcor
License: GPL (>= 2)
Repository: CRAN
LazyData: TRUE
NeedsCompilation: yes
Packaged: 2025-03-29 11:54:00 UTC; antonio
Date/Publication: 2025-03-31 17:10:01 UTC

More information about subselect at CRAN
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New package MVOPR with initial version 2.0.0
Package: MVOPR
Title: Multi-View Orthogonal Projection Regression for Multi-Modality Integration
Version: 2.0.0
Description: Implements the 'MVOPR' (Multi-View Orthogonal Projection Regression) method for robust variable selection and integration of multi-modality data.
License: GPL-2 | GPL-3
Encoding: UTF-8
Imports: ncvreg, rrpack
Suggests: testthat (>= 3.0.0)
URL: https://arxiv.org/abs/2503.16807
NeedsCompilation: no
Packaged: 2025-03-29 21:26:46 UTC; 10979
Author: Zongrui Dai [aut, cre] , Gen Li [aut]
Maintainer: Zongrui Dai <daizr@umich.edu>
Repository: CRAN
Date/Publication: 2025-03-31 17:30:10 UTC

More information about MVOPR at CRAN
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New package LikertEZ with initial version 0.1.0
Package: LikertEZ
Title: Easy Analysis and Visualization of Likert Scale Data
Version: 0.1.0
Description: Provides functions for summarizing, visualizing, and analyzing Likert-scale survey data. Includes support for computing descriptive statistics, Relative Importance Index (RII), reliability analysis (Cronbach's Alpha), and response distribution plots.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, stats, utils
NeedsCompilation: no
Packaged: 2025-03-29 18:14:56 UTC; ALIENWARE
Author: Mohammad Mollazehi [aut, cre]
Maintainer: Mohammad Mollazehi <mmolazehi@lu.edu.qa>
Repository: CRAN
Date/Publication: 2025-03-31 17:30:13 UTC

More information about LikertEZ at CRAN
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New package delimtools with initial version 0.2.0
Package: delimtools
Title: Helper Functions for Species Delimitation Analysis
Version: 0.2.0
Date: 2025-03-10
Description: Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods. For full functionality, please install suggested software at <https://legallab.github.io/delimtools/articles/install.html>.
License: MIT + file LICENSE
Depends: R (>= 4.2.0)
Imports: cli, dplyr, glue, ggtree, methods, purrr, rlang, stringr, tidyr, tidyselect
Suggests: ape, bGMYC (>= 1.0.2), forcats, furrr, future, ggfun, ggplot2, gtools, knitr, patchwork, randomcoloR, readr, RColorBrewer, scales, splits (>= 1.0.20), spider, tibble, tidytree, vctrs, withr, rmarkdown
Additional_repositories: https://r-forge.r-project.org/, https://pedrosenna.github.io/drat/
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-30 05:00:59 UTC; pedro
Maintainer: Pedro Bittencourt <pedro.sennabittencourt@gmail.com>
URL: https://github.com/legalLab/delimtools, https://legallab.github.io/delimtools/
BugReports: https://github.com/legalLab/delimtools/issues
VignetteBuilder: knitr
Author: Pedro Bittencourt [aut, cre, cph] , Rupert Collins [aut, ctb, cph] , Tomas Hrbek [aut, ctb]
Repository: CRAN
Date/Publication: 2025-03-31 18:00:02 UTC

More information about delimtools at CRAN
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New package sixtyfour with initial version 0.2.0
Package: sixtyfour
Title: Humane Interface to Amazon Web Services
Version: 0.2.0
Description: An opinionated interface to Amazon Web Services <https://aws.amazon.com>, with functions for interacting with 'IAM' (Identity and Access Management), 'S3' (Simple Storage Service), 'RDS' (Relational Data Service), Redshift, and Billing. Lower level functions ('aws_' prefix) are for do it yourself workflows, while higher level functions ('six_' prefix) automate common tasks.
URL: https://github.com/getwilds/sixtyfour, https://getwilds.org/sixtyfour/
BugReports: https://github.com/getwilds/sixtyfour/issues
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 4.1.0)
Imports: dplyr, paws (>= 0.9.0), paws.common (>= 0.8.1), purrr, rlang, tibble, fs, s3fs (>= 0.1.5), cli, glue, memoise, uuid, jsonlite, curl, tidyr, clipr, withr, ipaddress
Suggests: knitr, rmarkdown, roxyglobals, DBI, RPostgres, RMariaDB, ggplot2, lubridate, testthat (>= 3.0.0), vcr (>= 0.6.0), webmockr
NeedsCompilation: no
Packaged: 2025-03-28 21:39:39 UTC; schambe3
Author: Sean Kross [aut], Scott Chamberlain [aut, cre] , Fred Hutchinson Cancer Center [fnd]
Maintainer: Scott Chamberlain <sachamber@fredhutch.org>
Repository: CRAN
Date/Publication: 2025-03-31 16:40:02 UTC

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New package serofoi with initial version 1.0.3
Package: serofoi
Title: Bayesian Estimation of the Force of Infection from Serological Data
Version: 1.0.3
Description: Estimating the force of infection from time varying, age varying, or constant serocatalytic models from population based seroprevalence studies using a Bayesian framework, including data simulation functions enabling the generation of serological surveys based on this models. This tool also provides a flexible prior specification syntax for the force of infection and the seroreversion rate, as well as methods to assess model convergence and comparison criteria along with useful visualisation functions.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/serofoi, https://epiverse-trace.github.io/serofoi/
BugReports: https://github.com/epiverse-trace/serofoi/issues
Depends: R (>= 4.1.0)
Imports: bayesplot, checkmate, config, cowplot, dplyr, ggplot2, glue, graphics, loo, expm, methods, purrr, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.3.1), stats, tibble, tidyr
Suggests: knitr, rlang, rmarkdown, scales, spelling, testthat (>= 3.0.0)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
VignetteBuilder: knitr
Biarch: true
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: yes
SystemRequirements: GNU make
Packaged: 2025-03-27 14:51:29 UTC; torresn
Author: Zulma M. Cucunuba [aut, cre] , Nicolas T. Dominguez [aut] , Ben Lambert [aut], Pierre Nouvellet [aut], Geraldine Gomez [ctb] , Jaime A. Pavlich-Mariscal [ctb] , Hugo Gruson [ctb] , David Santiago Quevedo [ctb] , Miguel Gamez [ctb], Sumali Bajaj [ctb] [...truncated...]
Maintainer: Zulma M. Cucunuba <zulma.cucunuba@javeriana.edu.co>
Repository: CRAN
Date/Publication: 2025-03-31 10:00:02 UTC

More information about serofoi at CRAN
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New package eyeris with initial version 1.0.0
Package: eyeris
Title: Flexible, Extensible, & Reproducible Processing of Pupil Data
Version: 1.0.0
Date: 2025-03-28
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states (see Clewett et al., 2020 <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie, 2018 <doi:10.3758/s13428-018-1075-y>; Strauch, 2024 <doi:10.1016/j.tins.2024.06.002>). Yet, despite decades of pupillometry research, many established packages and workflows to date unfortunately lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles (see Wilkinson et al., 2016 <doi:10.1038/sdata.2016.18> for more information). 'eyeris', on the other hand, follows a design philosophy that provides users with an intuitive, modular, performant, and extensible pupillometry data preprocessing framework out-of-the-box. 'eyeris' introduces a Brain Imaging Data Structure (BIDS)-like organization for derivative (i.e., prepro [...truncated...]
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: eyelinker, dplyr, gsignal, purrr, zoo, cli, rlang, stringr, utils, stats, graphics, grDevices, tidyr, progress, data.table, withr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: MIT + file LICENSE
URL: https://shawnschwartz.com/eyeris/, https://github.com/shawntz/eyeris/
BugReports: https://github.com/shawntz/eyeris/issues
NeedsCompilation: no
Packaged: 2025-03-28 15:50:53 UTC; sts
Author: Shawn Schwartz [aut, cre, cph]
Maintainer: Shawn Schwartz <stschwartz@stanford.edu>
Repository: CRAN
Date/Publication: 2025-03-31 10:00:06 UTC

More information about eyeris at CRAN
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New package filibustr with initial version 0.3.0
Package: filibustr
Title: Data Utilities for Congressional Research
Version: 0.3.0
Description: Provides easy-to-understand and consistent interfaces for accessing data on the U.S. Congress. The functions in 'filibustr' streamline the process for importing data on Congress into R, removing the need to download and work from CSV files and the like. Data sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate website (<https://www.senate.gov/>), and more.
License: MIT + file LICENSE
URL: https://github.com/feinleib/filibustr, https://feinleib.github.io/filibustr/
BugReports: https://github.com/feinleib/filibustr/issues
Depends: R (>= 4.1.0)
Imports: cli, dplyr, haven, httr2, lifecycle, readr, rlang, rvest, stringr, tidyr, tools
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-30 17:06:13 UTC; mhfeinleib
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-31 07:00:01 UTC

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New package brokenstick with initial version 2.6.0
Package: brokenstick
Title: Broken Stick Model for Irregular Longitudinal Data
Version: 2.6.0
Description: Data on multiple individuals through time are often sampled at times that differ between persons. Irregular observation times can severely complicate the statistical analysis of the data. The broken stick model approximates each subject’s trajectory by one or more connected line segments. The times at which segments connect (breakpoints) are identical for all subjects and under control of the user. A well-fitting broken stick model effectively transforms individual measurements made at irregular times into regular trajectories with common observation times. Specification of the model requires three variables: time, measurement and subject. The model is a special case of the linear mixed model, with time as a linear B-spline and subject as the grouping factor. The main assumptions are: subjects are exchangeable, trajectories between consecutive breakpoints are straight, random effects follow a multivariate normal distribution, and unobserved data are missing at random. The package conta [...truncated...]
Depends: R (>= 3.5.0)
Imports: coda, dplyr, lme4, matrixsampling, methods, rlang, splines, stats, tidyr
Suggests: AGD, bookdown, ggplot2, grDevices, gridExtra, knitr, lattice, MASS, Matrix, mice, mvtnorm, plyr, svglite, testthat, rmarkdown
URL: doi:10.18637/jss.v106.i07, https://growthcharts.org/brokenstick/
BugReports: https://github.com/growthcharts/brokenstick/issues
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-28 14:47:54 UTC; buurensv
Author: Stef van Buuren [aut, cre]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Repository: CRAN
Date/Publication: 2025-03-31 05:40:02 UTC

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Sun, 30 Mar 2025

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

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

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Fri, 28 Mar 2025

New package sae4health with initial version 1.2.0
Package: sae4health
Title: Small Area Estimation for Key Health and Demographic Indicators from Household Surveys
Version: 1.2.0
Description: Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R 'shiny' application that helps public health analysts, policymakers, and researchers generate subnational estimates and prevalence maps for 150+ binary indicators from Demographic and Health Surveys (DHS). Basing its core SAE analysis workflow on the 'surveyPrev' package, the app ensures methodological rigor through guided model selection, automated fitting, and interactive visualization. For more details, visit <https://sae4health.stat.uw.edu/>.
License: AGPL-3
URL: https://sae4health.stat.uw.edu/, https://github.com/wu-thomas/sae4health
BugReports: https://github.com/wu-thomas/sae4health/issues
Depends: R (>= 4.3)
Imports: config, dplyr, DT, ggplot2, golem (>= 0.4.1), grid, gridExtra, htmltools, htmlwidgets, leaflet, R6, sf, sp, shiny (>= 1.7.4), shinyBS, shinydashboard, shinyFeedback, shinyjs, shinyWidgets, SUMMER, surveyPrev, survey, geodata, bookdown, markdown, haven, ggridges, ggthemes, RColorBrewer, viridisLite, scales, patchwork, leaflegend, leafsync, methods, graphics, plotly, readr, sn
Suggests: INLA, testthat (>= 3.0.0)
Additional_repositories: https://inla.r-inla-download.org/R/testing/
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Language: en-US
Packaged: 2025-03-26 20:16:41 UTC; wu-th
Author: Yunhan Wu [cre, aut], Qianyu Dong [aut], Zehang R Li [aut], Jon Wakefield [aut]
Maintainer: Yunhan Wu <wu-thomas@outlook.com>
Repository: CRAN
Date/Publication: 2025-03-28 18:20:01 UTC

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New package msda with initial version 1.0.4
Package: msda
Title: Multi-Class Sparse Discriminant Analysis
Version: 1.0.4
Date: 2025-03-24
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Depends: Matrix, MASS
Imports: methods
Description: Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously. It is an implementation of the work proposed by Mai, Q., Yang, Y., and Zou, H. (2019) <doi:10.5705/ss.202016.0117>.
LazyData: yes
License: GPL-2
URL: https://github.com/archer-yang-lab/msda
Packaged: 2025-03-27 00:45:59 UTC; jiaozi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2025-03-28 18:40:02 UTC
Author: Qing Mai [aut], Yi Yang [aut, cre], Hui Zou [aut]

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New package dynemu with initial version 1.0.0
Package: dynemu
Title: Emulation of Dynamic Simulators via One-Step-Ahead Approach
Version: 1.0.0
Maintainer: Junoh Heo <heojunoh@msu.edu>
Description: Performs emulation of dynamic simulators using Gaussian process via one-step ahead approach. The package implements a flexible framework for approximating time-dependent outputs from computationally expensive dynamic systems. It is specifically designed for nonlinear dynamic systems where full simulations may be costly. The underlying Gaussian process model accounts for temporal dependency through the one-step-ahead formulation, allowing for accurate emulation of complex dynamics. Hyperparameters are estimated via maximum likelihood. See Heo (2025, <doi:10.48550/arXiv.2503.20250>) for exact method, and Mohammadi, Challenor, and Goodfellow (2019, <doi:10.1016/j.csda.2019.05.006>) for methodological details.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: deSolve, plgp, stats, utils, MASS
Suggests: lhs
NeedsCompilation: no
Packaged: 2025-03-27 18:34:32 UTC; junoh
Author: Junoh Heo [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-28 18:50:01 UTC

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New package massiveGST with initial version 1.2.4
Package: massiveGST
Title: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test
Version: 1.2.4
Date: 2025-03-25
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>
Description: Friendly implementation of the Mann-Whitney-Wilcoxon test for competitive gene set enrichment analysis.
Depends: R (>= 4.4), formattable (>= 0.2.1), WriteXLS (>= 6.7.0), igraph (>= 2.1.4), visNetwork (>= 2.1.2)
Suggests: knitr, rmarkdown
License: GPL (>= 3)
URL: <https://github.com/stefanoMP/massiveGST>, <http://www.massivegenesetstest.org/>
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-28 12:18:03 UTC; stefano
Author: Stefano Maria Pagnotta [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-03-28 12:50:01 UTC

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Thu, 27 Mar 2025

New package pcpr with initial version 1.0.0
Package: pcpr
Title: Principal Component Pursuit for Environmental Epidemiology
Version: 1.0.0
Description: Implementation of the pattern recognition technique Principal Component Pursuit tailored to environmental health data, as described in Gibson et al (2022) <doi:10.1289/EHP10479>.
License: GPL (>= 3)
URL: https://columbia-prime.github.io/pcpr/, https://github.com/Columbia-PRIME/pcpr
BugReports: https://github.com/Columbia-PRIME/pcpr/issues
Depends: R (>= 3.5.0)
Imports: checkmate, dplyr, foreach, furrr, future, magrittr, progressr, purrr, rlang, tidyselect
Suggests: GGally, ggplot2, knitr, lubridate, metR, rmarkdown, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-26 18:44:18 UTC; lgc2035
Author: Lawrence G. Chillrud [aut, cre, cph] , Jaime Benavides [aut] , Elizabeth A. Gibson [aut] , Junhui Zhang [aut] , Jingkai Yan [aut] , John N. Wright [aut], Jeff Goldsmith [aut], Marianthi-Anna Kioumourtzoglou [aut] , Columbia University [fnd]
Maintainer: Lawrence G. Chillrud <lawrencechillrud@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-27 18:20:02 UTC

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New package VegSpecIndex with initial version 0.1.0
Package: VegSpecIndex
Title: Vegetation and Spectral Indices for Environmental Assessment
Version: 0.1.0
Maintainer: Tanuj Misra <tanujmisra102@gmail.com>
Description: Earth system dynamics, such as plant dynamics, water bodies, and fire regimes, are widely monitored using spectral indicators obtained from multispectral remote sensing products. There is a great need for spectral index catalogues and computing tools as a result of the quick rise of suggested spectral indices. Unfortunately, the majority of these resources lack a standard Application Programming Interface, are out-of-date, closed-source, or are not linked to a catalogue. We now introduce 'VegSpecIndex', a standardised list of spectral indices for studies of the earth system. A thorough inventory of spectral indices is offered by 'VegSpecIndex' and is connected to an R library. For every spectral index, 'VegSpecIndex' provides a comprehensive collection of information, such as names, formulae, and source references. The user community may add more items to the catalogue, which will keep 'VegSpecIndex' up to date and allow for further scientific uses. Additionally, the R library makes it [...truncated...]
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-26 11:51:11 UTC; PC
Author: Avijit Ghosh [aut, ctb, cph], Ram S Chaurasia [aut, ctb, cph], Tanuj Misra [aut, cre, ctb, cph], Amit Kumar Singh [aut, ctb, cph], Shailendra Kumar [aut, ctb, cph], Abhishek Chakraborty [aut, ctb, cph], Devanand [aut, ctb, cph], J P Singh [aut, ctb, [...truncated...]
Repository: CRAN
Date/Publication: 2025-03-27 17:50:06 UTC

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New package STCCGEV with initial version 1.0.0
Package: STCCGEV
Title: Conditional Copula Model for Crop Yield Forecasting
Version: 1.0.0
Description: Provides functions to model and forecast crop yields using a spatial temporal conditional copula approach. The package incorporates extreme weather covariates and Bayesian Structural Time Series models to analyze crop yield dependencies across multiple regions. Includes tools for fitting, simulating, and visualizing results. This method build upon established R packages, including 'Hofert' 'et' 'al'. (2025) <doi:10.32614/CRAN.package.copula>, 'Scott' (2024) <doi:10.32614/CRAN.package.bsts>, and 'Stephenson' 'et' 'al'. (2024) <doi:10.32614/CRAN.package.evd>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: bsts, copula, evd, ggplot2, grDevices, rootSolve, stats, utils
Depends: R (>= 4.0.0)
LazyData: true
LazyDataCompression: xz
Suggests: knitr, rmarkdown, testthat (>= 3.0.0),
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-26 05:39:16 UTC; liyongkun
Author: Marie Michaelides [aut], Melina Mailhot [aut], Yongkun Li [aut, cre]
Maintainer: Yongkun Li <yongkun.li@concordia.ca>
Repository: CRAN
Date/Publication: 2025-03-27 17:30:04 UTC

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New package neuroSCC with initial version 1.0.0
Package: neuroSCC
Title: Bridging Simultaneous Confidence Corridors and PET Neuroimaging
Version: 1.0.0
Maintainer: Juan A. Arias Lopez <juanantonio.arias.lopez@usc.es>
Description: Tools for the structured processing of PET neuroimaging data in preparation for the estimation of Simultaneous Confidence Corridors (SCCs) for one-group, two-group, or single-patient vs group comparisons. The package facilitates PET image loading, data restructuring, integration into a Functional Data Analysis framework, contour extraction, identification of significant results, and performance evaluation. It bridges established packages (e.g., 'oro.nifti') with novel statistical methodologies (e.g., 'ImageSCC') and enables reproducible analysis pipelines, including comparison with Statistical Parametric Mapping ('SPM').
License: MIT + file LICENSE
URL: https://iguanamarina.github.io/neuroSCC/, https://github.com/iguanamarina/PhD-2023-SCC-vs-SPM-Group-vs-Group, https://github.com/iguanamarina/PhD-2024-SCC-vs-SPM-SinglePatient-vs-Group
BugReports: https://github.com/iguanamarina/neuroSCC/issues
Depends: R (>= 4.2.0)
Imports: contoureR, dplyr, graphics, memisc, oro.nifti, stats, tidyr, utils
Suggests: BPST, ImageSCC, knitr, rcmdcheck, remotes, rmarkdown, roxygen2 (>= 7.1.0), Triangulation
Additional_repositories: https://iguanamarina.github.io/neuroSCC-drat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-26 15:20:33 UTC; juana
Author: Juan A. Arias Lopez [aut, cre, cph] , Virgilio Gomez Rubio [rev] , Pablo Aguiar Fernandez [ths] , Andrew Haddon Kemp [ths]
Repository: CRAN
Date/Publication: 2025-03-27 18:00:00 UTC

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New package mars with initial version 0.2.2
Package: mars
Title: Meta Analysis and Research Synthesis
Version: 0.2.2
Description: Includes functions for conducting univariate and multivariate meta-analysis. This includes the estimation of the asymptotic variance-covariance matrix of effect sizes. For more details see Becker (1992) <doi:10.2307/1165128>, Cooper, Hedges, and Valentine (2019) <doi:10.7758/9781610448864>, and Schmid, Stijnen, and White (2020) <doi:10.1201/9781315119403>.
Depends: R (>= 4.2)
Imports: Matrix, corpcor, matrixcalc
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, dplyr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-26 16:11:16 UTC; blebeau
Author: Brandon LeBeau [aut, cre] , Ariel M. Aloe [aut], Betsy Jane Becker [ctb], Seohee Park [ctb], Roberto C. Toro Rodriguez [ctb]
Maintainer: Brandon LeBeau <lebebr01+mars@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-27 18:00:05 UTC

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New package HMDA with initial version 0.1
Package: HMDA
Title: Holistic Multimodel Domain Analysis for Exploratory Machine Learning
Version: 0.1
Depends: R (>= 3.5.0)
Description: Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological cond [...truncated...]
Imports: curl (>= 4.3.0), h2o (>= 3.34.0.0), shapley (>= 0.5), autoEnsemble (>= 0.3), h2otools (>= 0.4), splitTools (>= 1.0.1), psych (>= 2.4.6), dplyr (>= 1.1.4), ggplot2 (>= 3.4.2)
License: MIT + file LICENSE
Encoding: UTF-8
URL: http://dx.doi.org/10.13140/RG.2.2.32473.63846, https://github.com/haghish/HMDA, https://www.sv.uio.no/psi/english/people/academic/haghish/
BugReports: https://github.com/haghish/HMDA/issues
NeedsCompilation: no
Packaged: 2025-03-26 11:39:13 UTC; haghish
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Repository: CRAN
Date/Publication: 2025-03-27 17:40:02 UTC

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New package flexord with initial version 1.0.0
Package: flexord
Title: Flexible Clustering of Ordinal and Mixed-with-Ordinal Data
Version: 1.0.0
Description: Extends the capabilities for flexible partitioning and model-based clustering available in the packages 'flexclust' and 'flexmix' to handle ordinal and mixed-with-ordinal data types via new distance, centroid and driver functions that make various assumptions regarding ordinality. Using them within the flex-scheme allows for easy comparisons across methods.
Imports: flexclust (>= 1.5.0), methods, mvtnorm, flexmix
Suggests: rmarkdown, knitr
License: GPL-2
Encoding: UTF-8
URL: https://zettlchen.github.io/flexord/
BugReports: https://github.com/dernst/flexord/issues
VignetteBuilder: rmarkdown, knitr
Depends: R (>= 4.3)
NeedsCompilation: no
Packaged: 2025-03-26 12:02:37 UTC; zettlchen
Author: Lena Ortega Menjivar [aut, cre] , Dominik Ernst [aut] , Theresa Scharl [ctb] , Bettina Gruen [ctb] , Ivan Kondofersky [ctb]
Maintainer: Lena Ortega Menjivar <lena.ortega-menjivar@boku.ac.at>
Repository: CRAN
Date/Publication: 2025-03-27 17:50:02 UTC

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New package fChange with initial version 2.0.0
Package: fChange
Title: Functional Change Point Detection and Analysis
Version: 2.0.0
Description: Analyze functional data and its change points. Includes functionality to store and process data, summarize and validate assumptions, characterize and perform inference of change points, and provide visualizations. Data is stored as discretely collected observations without requiring the selection of basis functions. For more details see chapter 8 of Horvath and Rice (2024) <doi:10.1007/978-3-031-51609-2>. Additional papers are forthcoming. Focused works are also included in the documentation of corresponding functions.
Encoding: UTF-8
Imports: dplyr, fastmatrix, fda, ftsa, ggplot2, ggpubr, graphics, grDevices, MASS, methods, plot3D, plotly, rainbow, RColorBrewer, Rcpp, RcppArmadillo, Rfast, sandwich, scales, stats, tensorA, tidyr, vars
LinkingTo: Rcpp, RcppArmadillo
Suggests: CompQuadForm, fda.usc, forecast, funData, jmuOutlier, knitr, lattice, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: true
URL: https://jrvanderdoes.github.io/fChange/
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2025-03-26 16:36:05 UTC; jerem
Author: Jeremy VanderDoes [aut, cre, cph] , Gregory Rice [aut], Martin Wendler [aut]
Maintainer: Jeremy VanderDoes <jeremy.vanderdoes@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-27 18:00:09 UTC

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New package marlod with initial version 0.2.0
Package: marlod
Title: Marginal Modeling for Exposure Data with Values Below the LOD
Version: 0.2.0
Depends: R (>= 2.10)
Imports: MASS, survival, quantreg, stats, knitr, utils
Maintainer: I-Chen Chen <okv0@cdc.gov>
Description: Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates. For more details see Chen IC, Bertke SJ, Curwin BD (2021) <doi:10.1038/s41370-021-00345-1>, Chen IC, Bertke SJ, Estill CF (2024) <doi:10.1038/s41370-024-00640-7>, Chen IC, Bertke SJ, Dahm MM (2024) <doi:10.1093/annweh/wxae068>, and Chen IC (2025) <doi:10.1038/s41370-025-00752-8>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: yes
Repository: CRAN
LazyData: true
Suggests: rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Packaged: 2025-03-26 17:52:03 UTC; okv0
Author: I-Chen Chen [cre, aut] , Philip Westgate [ctb], Liya Fu [ctb]
Date/Publication: 2025-03-27 11:50:18 UTC

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Wed, 26 Mar 2025

New package varycoef with initial version 0.3.5
Package: varycoef
Title: Modeling Spatially Varying Coefficients
Version: 0.3.5
Description: Implements a maximum likelihood estimation (MLE) method for estimation and prediction of Gaussian process-based spatially varying coefficient (SVC) models (Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>). Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can be applied such that the method scales to large data. Further, it implements a joint variable selection of the fixed and random effects (Dambon et al. (2021b) <doi:10.1080/13658816.2022.2097684>). The package and its capabilities are described in (Dambon et al. (2021c) <doi:10.48550/arXiv.2106.02364>).
License: GPL-2
URL: https://github.com/jakobdambon/varycoef
BugReports: https://github.com/jakobdambon/varycoef/issues
Depends: R (>= 3.5.0)
Imports: glmnet, lhs, methods, mlr, mlrMBO, optimParallel (>= 0.8-1), ParamHelpers, pbapply, smoof, spam
Suggests: DiceKriging, knitr, lattice, latticeExtra, parallel, rmarkdown, sp, spData, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-26 10:30:06 UTC; jakob
Author: Jakob A. Dambon [aut, cre] , Fabio Sigrist [ctb] , Reinhard Furrer [ctb]
Maintainer: Jakob A. Dambon <jakob.dambon@math.ethz.ch>
Repository: CRAN
Date/Publication: 2025-03-26 17:30:02 UTC

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New package asympDiag with initial version 0.3.0
Package: asympDiag
Title: Diagnostic Tools for Asymptotic Theory
Version: 0.3.0
Description: Leveraging Monte Carlo simulations, this package provides tools for diagnosing regression models. It implements a parametric bootstrap framework to compute statistics, generates diagnostic envelopes to assess goodness-of-fit, and evaluates type I error control for Wald tests. By simulating data under the assumption that the model is true, it helps to identify model mis-specifications and enhances the reliability of the model inferences.
License: MIT + file LICENSE
URL: https://github.com/Alvaro-Kothe/asympDiag
BugReports: https://github.com/Alvaro-Kothe/asympDiag/issues
Imports: cli
Suggests: glmmTMB, lme4, MASS, Matrix, rlang, sandwich, survival, testthat (>= 3.0.0), vctrs, withr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-25 19:43:18 UTC; alvarojsk
Author: Alvaro Kothe [aut, cre, cph] , Alexandre Patriota [aut]
Maintainer: Alvaro Kothe <kothe65@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-26 11:10:06 UTC

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New package meddra.read with initial version 0.0.1
Package: meddra.read
Title: Load and Use 'MedDRA' Data for Clinical Trials
Version: 0.0.1
Description: 'MedDRA' data is used for defining adverse events in clinical studies. You can load and merge the data for use in categorizing the adverse events using this package. The package requires the data licensed from 'MedDRA' <https://www.meddra.org/>.
License: MIT + file LICENSE
Imports: dplyr
Suggests: spelling, testthat (>= 3.0.0)
Encoding: UTF-8
URL: https://humanpred.github.io/meddra.read/
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-25 16:28:07 UTC; bill
Author: Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Repository: CRAN
Date/Publication: 2025-03-26 10:40:13 UTC

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New package AOUSDOHtools with initial version 1.0.4
Package: AOUSDOHtools
Title: Analyzing AOU SDOH Survey Data
Version: 1.0.4
Description: Functions for processing and analyzing survey data from the All of Us Social Determinants of Health (AOUSDOH) program, including tools for calculating health and well-being scores, recoding variables, and simplifying survey data analysis. For more details see - Koleck TA, Dreisbach C, Zhang C, Grayson S, Lor M, Deng Z, Conway A, Higgins PDR, Bakken S (2024) <doi:10.1093/jamia/ocae214>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, covr, devtools, usethis
URL: https://github.com/zhd52/AOUSDOHtools
BugReports: https://github.com/zhd52/AOUSDOHtools/issues
NeedsCompilation: no
Packaged: 2025-03-25 16:45:09 UTC; ZHD52
Author: Zhirui Deng [aut, cre], Theresa A. Koleck [ctb], Caitlin Dreisbach [ctb], Chen Zhang [ctb], Peter D.R. Higgins [ctb], DreisbachLab [cph]
Maintainer: Zhirui Deng <zhd52@pitt.edu>
Repository: CRAN
Date/Publication: 2025-03-26 10:50:02 UTC

More information about AOUSDOHtools at CRAN
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Tue, 25 Mar 2025

New package erboost with initial version 1.5
Package: erboost
Title: Nonparametric Multiple Expectile Regression via ER-Boost
Version: 1.5
Date: 2025-03-24
Depends: R (>= 2.12.0), lattice, splines
Description: Expectile regression is a nice tool for estimating the conditional expectiles of a response variable given a set of covariates. This package implements a regression tree based gradient boosting estimator for nonparametric multiple expectile regression, proposed by Yang, Y., Qian, W. and Zou, H. (2018) <doi:10.1080/00949655.2013.876024>. The code is based on the 'gbm' package originally developed by Greg Ridgeway.
License: GPL-3
Packaged: 2025-03-25 03:24:55 UTC; jiaozi
NeedsCompilation: yes
Date/Publication: 2025-03-25 16:10:01 UTC
Author: Yi Yang [aut, cre] , Hui Zou [aut] , Greg Ridgeway [ctb, cph]
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Repository: CRAN

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New package TDboost with initial version 1.6
Package: TDboost
Title: A Boosted Tweedie Compound Poisson Model
Version: 1.6
Date: 2025-03-24
Depends: R (>= 2.12.0), lattice
Description: An implementation of a boosted Tweedie compound Poisson model proposed by Yang, Y., Qian, W. and Zou, H. (2018) <doi:10.1080/07350015.2016.1200981>. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing high-order interactions among predictors. This package is based on the 'gbm' package originally developed by Greg Ridgeway.
LazyData: yes
License: GPL-3
Packaged: 2025-03-25 02:55:30 UTC; jiaozi
NeedsCompilation: yes
Date/Publication: 2025-03-25 16:00:02 UTC
Author: Yi Yang [aut, cre] , Hui Zou [aut] , Wei Qian [aut] , Greg Ridgeway [ctb, cph]
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Repository: CRAN

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New package Spower with initial version 0.2.2
Package: Spower
Title: Power Analyses using Monte Carlo Simulations
Version: 0.2.2
Description: Provides a general purpose simulation-based power analysis API for routine and customized simulation experimental designs. The package focuses exclusively on Monte Carlo simulation variants of (expected) prospective power analyses, criterion power analyses, compromise power analyses, sensitivity analyses, and prospective/post-hoc power analyses. The default simulation experiment functions found within the package provide stochastic variants of the power analyses subroutines found in the G*Power 3 software (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>, along with various other power analysis examples (e.g., mediation analyses). Supporting functions are also included, such as for building empirical power curve estimates, which utilize a similar API structure.
Depends: SimDesign (>= 2.19.1), R (>= 4.1.0), stats
Imports: cocor, car, polycor, parallelly, methods, ggplot2, plotly, lavaan, EnvStats
Suggests: knitr, rmarkdown, bookdown, VGAM, copula, pwr
VignetteBuilder: knitr
License: GPL (>= 3)
Encoding: UTF-8
Repository: CRAN
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
URL: https://github.com/philchalmers/Spower
BugReports: https://github.com/philchalmers/Spower/issues?state=open
NeedsCompilation: no
Packaged: 2025-03-24 14:39:32 UTC; phil
Author: Phil Chalmers [aut, cre]
Date/Publication: 2025-03-25 15:40:02 UTC

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New package rdhte with initial version 0.0.1
Package: rdhte
Title: Heterogeneous Treatment Effects in Regression Discontinuity Designs
Version: 0.0.1
Description: Understanding heterogeneous causal effects based on pretreatment covariates is a crucial step in modern empirical work in data science. Building on the recent developments in Calonico et al (2025) <https://rdpackages.github.io/references/Calonico-Cattaneo-Farrell-Palomba-Titiunik_2025_HTERD.pdf>, this package provides tools for estimation and inference of heterogeneous treatment effects in Regression Discontinuity (RD) Designs. The package includes two main commands: 'rdhte' to conduct estimation and robust bias-corrected inference for conditional RD treatment effects (given choice of bandwidth parameter); and 'rdbwhte', which implements automatic bandwidth selection methods.
License: GPL-2
Imports: rdrobust, sandwich
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-24 18:03:11 UTC; sebastian
Author: Sebastian Calonico [aut, cre], Matias D. Cattaneo [aut], Max H. Farrell [aut], Filippo Palomba [aut], Rocio Titiunik [aut]
Maintainer: Sebastian Calonico <scalonico@ucdavis.edu>
Repository: CRAN
Date/Publication: 2025-03-25 15:50:02 UTC

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New package RcppPlanc with initial version 2.0.0
Package: RcppPlanc
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Version: 2.0.0
Date: 2025-03-21f
Description: 'Rcpp' bindings for 'PLANC', a highly parallel and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library. Wraps algorithms described in Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and Eswar et. al (2021) <doi:10.1145/3432185>. Implements algorithms described in Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>, Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Encoding: UTF-8
Imports: methods, Rcpp, Matrix, hdf5r.Extra
Suggests: knitr, withr, rmarkdown, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
License: GPL (>= 2)
SystemRequirements: C++17, cmake >= 3.21.0, hdf5, git, v8, patch, gnumake, hwloc, GNU make
Depends: R (>= 3.5)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-03-24 18:22:34 UTC; andrew
Author: Andrew Robbins [aut, cre] , Yichen Wang [aut], Joshua Welch [cph] , Ramakrishnan Kannan [cph] , UT-Batelle [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Repository: CRAN
Date/Publication: 2025-03-25 15:50:13 UTC

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New package prism with initial version 0.2.3
Package: prism
Title: Access Data from the Oregon State Prism Climate Project
Description: Allows users to access the Oregon State Prism climate data (<https://prism.nacse.org/>). Using the web service API data can easily downloaded in bulk and loaded into R for spatial analysis. Some user friendly visualizations are also provided.
URL: https://docs.ropensci.org/prism/, https://github.com/ropensci/prism
BugReports: https://github.com/ropensci/prism/issues
Version: 0.2.3
License: MIT + file LICENSE
Imports: ggplot2, raster, httr, dplyr, stringr, magrittr, readr, utils
VignetteBuilder: knitr
Suggests: covr, knitr, rmarkdown, testthat (>= 2.1.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-24 17:43:59 UTC; RAButler
Author: Hart Edmund [aut, ccp], Kendon Bell [aut], Alan Butler [ctb, cre]
Maintainer: Alan Butler <rabutler@usbr.gov>
Repository: CRAN
Date/Publication: 2025-03-25 15:50:05 UTC

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New package groupedHyperframe with initial version 0.1.0
Package: groupedHyperframe
Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame Object
Version: 0.1.0
Date: 2025-03-24
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Description: An S3 class 'groupedHyperframe' that inherits from hyper data frame. Batch processes on point-pattern hyper column. Aggregation of function-value-table hyper column(s) and numeric hyper column(s) over a nested grouping structure.
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
License: GPL-2
Depends: R (>= 4.4)
Language: en-US
Imports: cli, parallel, stats, nlme, matrixStats, pracma, spatstat.explore, spatstat.geom
Suggests: knitr, survival, spatstat.data, spatstat.univar, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-03-24 17:48:27 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre] , Inna Chervoneva [aut]
Repository: CRAN
Date/Publication: 2025-03-25 15:50:09 UTC

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New package PlotNormTest with initial version 1.0.1
Package: PlotNormTest
Title: Graphical Univariate/Multivariate Assessments for Normality Assumption
Version: 1.0.1
Maintainer: Huong Tran <quynhhuong5335@gmail.com>
Description: Graphical methods testing multivariate normality assumption. Methods including assessing score function, and moment generating functions,independent transformations and linear transformations. For more details see Tran (2024),"Contributions to Multivariate Data Science: Assessment and Identification of Multivariate Distributions and Supervised Learning for Groups of Objects." , PhD thesis, <https://our.oakland.edu/items/c8942577-2562-4d2f-8677-cb8ec0bf6234>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Rdpack, ggplot2, stats, Matrix, MatrixExtra, MASS, rlang
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
SysDataCompression: xz
NeedsCompilation: no
Packaged: 2025-03-24 14:00:35 UTC; huongtran
Author: Huong Tran [aut, cre] , Ravindra Khattree [aut]
Repository: CRAN
Date/Publication: 2025-03-25 09:10:05 UTC

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New package ip2location.io with initial version 0.0.0-2
Package: ip2location.io
Title: Batch IP Data Retrieval and Storage Using 'IP2Location.io'
Version: 0.0.0-2
Description: A system for submitting multiple IP information queries to 'IP2Location.io'’s IP Geolocation API and storing the resulting data in a dataframe. You provide a vector of IP addresses and your 'IP2Location.io' API key. The package returns a dataframe with one row per IP address and a column for each available data field (data fields not included in your API plan will contain NAs). This is the second submission of the package to CRAN.
License: MIT + file LICENSE
Imports: dplyr, httr, jsonlite, tidyselect
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), mockery
NeedsCompilation: no
Packaged: 2025-03-24 14:29:07 UTC; georgeac
Author: Oriane Georgeac [aut, cre]
Maintainer: Oriane Georgeac <oriane.georgeac@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-25 09:10:02 UTC

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New package GoMiner with initial version 1.0
Package: GoMiner
Version: 1.0
Date: 2025-03-16
Title: Automate the Mapping Between a List of Genes and Gene Ontology Categories
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Author: Barry Zeeberg [aut, cre]
Depends: R (>= 4.2.0)
Imports: minimalistGODB, HGNChelper, stats, gplots, grDevices, utils
LazyData: true
LazyDataCompression: xz
Description: In gene-expression microarray studies, for example, one generally obtains a list of dozens or hundreds of genes that differ in expression between samples and then asks 'What does all of this mean biologically?' Alternatively, gene lists can be derived conceptually in addition to experimentally. For instance, one might want to analyze a group of genes known as housekeeping genes. The work of the Gene Ontology (GO) Consortium <geneontology.org> provides a way to address that question. GO organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. The role of 'GoMiner' is to automate the mapping between a list of genes and GO, and to provide a statistical summary of the results as well as a visualization.
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-03-24 16:04:19 UTC; barryzeeberg
Repository: CRAN
Date/Publication: 2025-03-25 09:20:02 UTC

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New package gghourglass with initial version 0.0.1
Package: gghourglass
Title: Plot Records per Time of Day
Version: 0.0.1
Author: Pepijn de Vries [aut, cre] , Sander Lagerveld [dtc]
Description: Splits date and time of day components from continuous 'datetime' objects, then plots them using grammar of graphics ('ggplot2'). Plots can also be decorated with solar cycle information (e.g., sunset, sunrise, etc.). This is useful for data that are associated with the solar cycle.
Depends: R (>= 4.1.0)
Imports: dplyr (>= 1.1.4), ggplot2 (>= 3.4.4), lubridate (>= 1.9.3), rlang (>= 1.1.2), suncalc (>= 0.5.1)
Suggests: readr (>= 2.1.4), testthat (>= 3.0.0), usethis (>= 2.2.2), vdiffr
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://pepijn-devries.github.io/gghourglass/
NeedsCompilation: no
Packaged: 2025-03-24 14:00:08 UTC; vries171
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Repository: CRAN
Date/Publication: 2025-03-25 09:30:02 UTC

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New package dartR with initial version 2.9.9.5
Package: dartR
Title: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
Version: 2.9.9.5
Date: 2025-03-24
Description: Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2 [...truncated...]
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr, dartR.data
Imports: ape,crayon,data.table,fields,foreach,gridExtra,MASS,methods,patchwork,plyr,PopGenReport,raster,reshape2,shiny,SNPRelate,sp (>= 1.6.1),StAMPP,stats,stringr,tidyr,utils, gsubfn, purrr
Suggests: boot, devtools, directlabels, dismo, doParallel, expm, gdistance, ggtern, gganimate, ggrepel, grid, gtable, ggthemes, gplots, HardyWeinberg, hierfstat, igraph, iterpc, knitr, label.switching, lattice, leaflet, leaflet.minicharts, markdown, mmod, networkD3, parallel, pegas, pheatmap, plotly, poppr, proxy, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown, rrBLUP, scales, seqinr, shinyBS, shinyjs, shinythemes, shinyWidgets, SIBER, snpStats, stringi, terra, tibble, vcfR, zoo, viridis, vegan
License: GPL (>= 3)
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-25 00:35:23 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Diana Robledo-Ruiz [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb]
URL: https://green-striped-gecko.github.io/dartR/, https://github.com/green-striped-gecko/dartR
BugReports: https://groups.google.com/g/dartr?pli=1
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2025-03-25 09:50:02 UTC

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Mon, 24 Mar 2025

New package corella with initial version 0.1.4
Package: corella
Title: Prepare, Manipulate and Check Data to Comply with Darwin Core Standard
Version: 0.1.4
Description: Helps users standardise data to the Darwin Core Standard, a global data standard to store, document, and share biodiversity data like species occurrence records. The package provides tools to manipulate data to conform with, and check validity against, the Darwin Core Standard. Using 'corella' allows users to verify that their data can be used to build 'Darwin Core Archives' using the 'galaxias' package.
Depends: R (>= 4.3.0)
Imports: cli, dplyr, glue, hms, lubridate, purrr, rlang, sf, stringr, tibble, tidyr, uuid
Suggests: gt, knitr, nanoparquet, ozmaps, readr, rmarkdown, testthat (>= 3.0.0), withr
License: GPL-3
URL: https://corella.ala.org.au
BugReports: https://github.com/AtlasOfLivingAustralia/corella/issues
Maintainer: Dax Kellie <dax.kellie@csiro.au>
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-24 02:03:35 UTC; kel329
Author: Dax Kellie [aut, cre], Shandiya Balasubramanium [aut], Martin Westgate [aut]
Repository: CRAN
Date/Publication: 2025-03-24 15:10:06 UTC

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New package quadkeyr with initial version 0.1.0
Package: quadkeyr
Title: Generate Raster Images from QuadKey-Identified Datasets
Version: 0.1.0
Description: A set of functions of increasing complexity allows users to (1) convert QuadKey-identified datasets, based on 'Microsoft's Bing Maps Tile System', into Simple Features data frames, (2) transform Simple Features data frames into rasters, and (3) process multiple 'Meta' ('Facebook') QuadKey-identified human mobility files directly into raster files. For more details, see D’Andrea et al. (2024) <doi:10.21105/joss.06500>.
License: MIT + file LICENSE
URL: https://docs.ropensci.org/quadkeyr/, https://github.com/ropensci/quadkeyr
BugReports: https://github.com/ropensci/quadkeyr/issues
Encoding: UTF-8
Suggests: bslib (>= 0.6.1), DT (>= 0.31), ggplot2 (>= 3.4.4), knitr, leaflet (>= 2.2.1), magick (>= 2.8.5), rmarkdown, rnaturalearth (>= 1.0.0), shinytest2 (>= 0.3.2), testthat (>= 3.1.10), tidyr (>= 1.3.0), viridis (>= 0.6.4), withr
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
LazyData: true
Imports: dplyr (>= 1.1.2), lubridate (>= 1.9.2), purrr (>= 1.0.1), readr (>= 2.1.4), rlang (>= 1.1.2), sf (>= 1.0.14), shiny (>= 1.7.4), stars (>= 0.6.2)
NeedsCompilation: no
Packaged: 2025-03-24 00:53:18 UTC; runner
Author: Florencia D'Andrea [aut, cre] , Pilar Fernandez [aut] , Maria Paula Caldas [rev] for rOpenSci, see https://github.com/ropensci/software-review/issues/619), Vincent van Hees [rev] for rOpenSci, see https://github.com/ropensci/software-review/issues/ [...truncated...]
Maintainer: Florencia D'Andrea <florencia.dandrea@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 15:00:02 UTC

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New package jumps with initial version 1.0
Package: jumps
Title: Hodrick-Prescott Filter with Jumps
Version: 1.0
Date: 2025-03-20
Maintainer: Matteo Pelagatti <matteo.pelagatti@unimib.it>
Description: A set of functions to compute the Hodrick-Prescott (HP) filter with automatically selected jumps. The original HP filter extracts a smooth trend from a time series, and our version allows for a small number of automatically identified jumps. See Maranzano and Pelagatti (2024) <doi:10.2139/ssrn.4896170> for details.
License: GPL-3
Imports: Rcpp (>= 1.0.10), stats, nloptr
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, xts
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2025-03-23 21:43:25 UTC; pelagatti
Author: Matteo Pelagatti [aut, cre, cph] , Paolo Maranzano [aut, cph]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-03-24 15:00:06 UTC

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New package immunogenetr with initial version 0.1.0
Package: immunogenetr
Title: A Comprehensive Toolkit for Clinical HLA Informatics
Version: 0.1.0
Maintainer: Nicholas Brown <nicholas.brown@pennmedicine.upenn.edu>
Description: A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of genotype list string (GL string, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL string; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL string; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL string.
License: GPL (>= 3)
URL: https://github.com/k96nb01/immunogenetr_package
BugReports: https://github.com/k96nb01/immunogenetr_package/issues
Depends: R (>= 4.1.0)
Imports: cli, dplyr, glue, magrittr, purrr, rlang, stringr, tibble, tidyr, tidyselect, xml2
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-22 16:30:03 UTC; drnic
Author: Nicholas Brown [cre, aut] , Busra Coskun [aut]
Repository: CRAN
Date/Publication: 2025-03-24 14:10:05 UTC

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New package xpect with initial version 1.0
Package: xpect
Title: Probabilistic Time Series Forecasting with XGBoost and Conformal Inference
Version: 1.0
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Description: Implements a probabilistic approach to time series forecasting combining XGBoost regression with conformal inference methods. The package provides functionality for generating predictive distributions, evaluating uncertainty, and optimizing hyperparameters using Bayesian, coarse-to-fine, or random search strategies.
License: GPL-3
Encoding: UTF-8
Imports: normalp (>= 0.7.2), glogis (>= 1.0-2), gld (>= 2.6.6), edfun (>= 0.2.0), purrr (>= 1.0.1), ald (>= 1.3.1), evd (>= 2.3-6.1), GeneralizedHyperbolic (>= 0.8-6), cubature (>= 2.1.0), furrr (>= 0.3.1), future (>= 1.33.0), xgboost (>= 1.7.5.1), rBayesianOptimization (>= 1.2.0), lubridate (>= 1.9.2), ggplot2 (>= 3.5.1), scales (>= 1.3.0)
URL: https://rpubs.com/giancarlo_vercellino/xpect
Suggests: testthat (>= 3.0.0)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2025-03-20 19:52:24 UTC; gianc
Author: Giancarlo Vercellino [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-03-24 11:30:01 UTC

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New package snazzieR with initial version 0.1.0
Package: snazzieR
Title: Chic and Sleek Functions for Beautiful Statisticians
Version: 0.1.0
Maintainer: Aidan J. Wagner <JesusButForGayPeople@proton.me>
Description: Because your linear models deserve better than console output. A sleek color palette and kable styling to make your regression results look sharper than they are. See the package manual at <https://github.com/JesusButForGayPeople/snazzieR/releases/download/v0.1.0/snazzieR_0.1.0.pdf>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, knitr, kableExtra, stats
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-03-21 18:33:21 UTC; shared-psychosis
Author: Aidan J. Wagner [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-24 11:50:02 UTC

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New package SMAHP with initial version 0.0.5
Package: SMAHP
Title: Survival Mediation Analysis of High-Dimensional Proteogenomic Data
Version: 0.0.5
Description: SMAHP (pronounced as SOO-MAP) is a novel multi-omics framework for causal mediation analysis of high-dimensional proteogenomic data with survival outcomes. The full methodological details can be found in our recent preprint by Ahn S et al. (2025) <doi:10.48550/arXiv.2503.08606>.
License: GPL-3
Encoding: UTF-8
Imports: data.table, fdrtool, ncvreg, penAFT, survival, stats, glmnet
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Language: en-US
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2025-03-21 18:47:12 UTC; fuw01
Author: Seungjun Ahn [aut] , Weijia Fu [cre, aut] , Zhigang Li [ctb]
Maintainer: Weijia Fu <weijia.fu@mountsinai.org>
Repository: CRAN
Date/Publication: 2025-03-24 12:00:12 UTC

More information about SMAHP at CRAN
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New package shinyproxyLogs with initial version 0.1.0
Package: shinyproxyLogs
Title: Tools for Analyzing 'ShinyProxy' Containers Logs
URL: https://tsenegas.github.io/shinyproxyLogs/
BugReports: https://github.com/tsenegas/shinyproxyLogs/issues
Version: 0.1.0
Description: Provides functions to parse and analyze logs generated by 'ShinyProxy' containers. It extracts metadata from log file names, reads log contents, and computes summary statistics (such as the total number of lines and lines containing error messages), facilitating efficient monitoring and debugging of 'ShinyProxy' deployments.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr, purrr, stringr, tibble
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-03-20 20:02:40 UTC; tsenegas
Author: Thibault Senegas [aut, cre]
Maintainer: Thibault Senegas <senegas.th@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 11:20:02 UTC

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New package rsahmi with initial version 0.0.2
Package: rsahmi
Title: Single-Cell Analysis of Host-Microbiome Interactions
Version: 0.0.2
Description: A computational resource designed to accurately detect microbial nucleic acids while filtering out contaminants and false-positive taxonomic assignments from standard transcriptomic sequencing of mammalian tissues. For more details, see Ghaddar (2023) <doi:10.1038/s43588-023-00507-1>. This implementation leverages the 'polars' package for fast and systematic microbial signal recovery and denoising from host tissue genomic sequencing.
License: MIT + file LICENSE
ByteCompile: true
Encoding: UTF-8
OS_type: unix
SystemRequirements: kraken2, seqkit
Imports: blit (>= 0.1.0), cli, rlang (>= 1.1.0), ShortRead, utils
Suggests: polars (>= 0.17.0)
Additional_repositories: https://community.r-multiverse.org
URL: https://github.com/Yunuuuu/rsahmi
BugReports: https://github.com/Yunuuuu/rsahmi/issues
NeedsCompilation: no
Packaged: 2025-03-21 18:48:11 UTC; yun
Author: Yun Peng [aut, cre]
Maintainer: Yun Peng <yunyunp96@163.com>
Repository: CRAN
Date/Publication: 2025-03-24 12:00:05 UTC

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New package redquack with initial version 0.1.1
Package: redquack
Title: Transfer 'REDCap' Data to 'DuckDB'
Version: 0.1.1
Description: Provides a single function to transfer 'REDCap' (Research Electronic Data Capture) data to a 'DuckDB' database. Processes data in chunks to handle large datasets while minimizing memory usage. Features include resuming incomplete transfers, converting column types, tracking progress, logging operations in the database.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: audio, beepr, cli, DBI, dplyr, duckdb, httr2, readr, utils
Suggests: arrow, testthat (>= 3.0.0)
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-03-22 03:27:31 UTC; dylanpieper
Author: Dylan Pieper [aut, cre]
Maintainer: Dylan Pieper <dylanpieper@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 12:00:08 UTC

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New package positron.tutorials with initial version 0.1.2
Package: positron.tutorials
Title: Tutorials for Learning 'Positron' and Related Tools
Version: 0.1.2
Description: Collection of tutorials for working with 'Positron'. Covers scripts, 'Quarto' documents, 'Git', 'GitHub', and 'Quarto' websites. Makes extensive use of the tools in the 'tutorial.helpers' package.
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/PPBDS/positron.tutorials/issues
URL: https://ppbds.github.io/positron.tutorials/, https://github.com/PPBDS/positron.tutorials
Imports: dplyr, mime, purrr, rvest, tibble
Suggests: gert, gitcreds, knitr, learnr, palmerpenguins, quarto, rsconnect, testthat (>= 3.0.0), tidyverse, tutorial.helpers, usethis
NeedsCompilation: no
Packaged: 2025-03-20 23:54:20 UTC; dkane
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 11:40:02 UTC

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New package LJexm with initial version 1.0.4
Package: LJexm
Title: Extract, Convert, and Merge 'pdf' Files from 'zip' Files
Version: 1.0.4
Description: Extracts 'zip' files, converts 'Word' and 'Excel' documents to 'pdf' files using 'VBScript', and merges 'pdf' files into a single file. This package is only supported on 'Windows' due to 'VBScript' dependencies.
License: GPL (>= 3)
Encoding: UTF-8
Imports: fs, pdftools, rstudioapi, utils
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-03-21 16:14:37 UTC; lijin
Author: Lijin Arakkandathil Thekkathil [aut, cre]
Maintainer: Lijin Arakkandathil Thekkathil <lijin5673@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-24 11:50:06 UTC

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New package capybara with initial version 0.9.0
Package: capybara
Title: Fast and Memory Efficient Fitting of Linear Models with High-Dimensional Fixed Effects
Version: 0.9.0
Imports: data.table, Formula, generics, ggplot2, kendallknight, MASS, stats
Suggests: broom, knitr, rmarkdown, testthat (>= 3.0.0), units
Depends: R(>= 3.5.0)
Description: Fast and user-friendly estimation of generalized linear models with multiple fixed effects and cluster the standard errors. The method to obtain the estimated fixed-effects coefficients is based on Stammann (2018) <doi:10.48550/arXiv.1707.01815> and Gaure (2013) <doi:10.1016/j.csda.2013.03.024>.
License: Apache License (>= 2)
BugReports: https://github.com/pachadotdev/capybara/issues
URL: https://pacha.dev/capybara/, https://github.com/pachadotdev/capybara
LazyData: true
Encoding: UTF-8
NeedsCompilation: yes
LinkingTo: cpp11, cpp11armadillo
VignetteBuilder: knitr
Packaged: 2025-03-20 18:38:17 UTC; pacha
Author: Mauricio Vargas Sepulveda [aut, cre]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2025-03-24 11:20:05 UTC

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New package usdoj with initial version 1.1.1
Package: usdoj
Title: For Accessing U.S. Department of Justice (DOJ) Open Data
Version: 1.1.1
Maintainer: Steph Buongiorno <steph.buon@gmail.com>
Depends: R (>= 3.4.4)
Imports: anytime, dplyr, httr, jsonlite, stringr, tibble
URL: https://github.com/ropengov/usdoj
BugReports: https://github.com/ropengov/usdoj/issues
Description: Fetch data from the <https://www.justice.gov/developer/api-documentation/api_v1> API such as press releases, blog entries, and speeches. Optional parameters allow users to specify the number of results starting from the earliest or latest entries, and whether these results contain keywords. Data is cleaned for analysis and returned in a dataframe.
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-23 15:54:22 UTC; steph
Author: Steph Buongiorno [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-24 09:40:02 UTC

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Sun, 23 Mar 2025

New package tidysynth with initial version 0.2.1
Package: tidysynth
Title: A Tidy Implementation of the Synthetic Control Method
Version: 0.2.1
Description: A synthetic control offers a way of evaluating the effect of an intervention in comparative case studies. The package makes a number of improvements when implementing the method in R. These improvements allow users to inspect, visualize, and tune the synthetic control more easily. A key benefit of a tidy implementation is that the entire preparation process for building the synthetic control can be accomplished in a single pipe.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: magrittr, tibble, dplyr, ggplot2, tidyr, forcats, rlang, kernlab, rgenoud, optimx, stats
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-03-23 22:05:22 UTC; ed769
Author: Eric Dunford [aut, cre]
Maintainer: Eric Dunford <ed769@georgetown.edu>
Repository: CRAN
Date/Publication: 2025-03-24 00:50:02 UTC

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Sat, 22 Mar 2025

New package rpc with initial version 2.0.3
Package: rpc
Title: Ridge Partial Correlation
Version: 2.0.3
Date: 2025-03-20
Encoding: UTF-8
Maintainer: Somak Dutta <somakd@iastate.edu>
Description: Computes the ridge partial correlation coefficients in a high or ultra-high dimensional linear regression problem. An extended Bayesian information criterion is also implemented for variable selection. Users provide the matrix of covariates as a usual dense matrix or a sparse matrix stored in a compressed sparse column format. Detail of the method is given in the manual.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.11), Matrix
Suggests: MatrixExtra
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2025-03-20 15:42:25 UTC; somakd
Author: Somak Dutta [aut, cre, cph], An Nguyen [aut, ctb], Run Wang [ctb], Vivekananda Roy [ctb]
Repository: CRAN
Date/Publication: 2025-03-22 12:10:02 UTC

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New package SONO with initial version 1.1
Package: SONO
Title: Scores of Nominal Outlyingness (SONO)
Version: 1.1
Description: Computes scores of outlyingness for data sets consisting of nominal variables and includes various evaluation metrics for assessing performance of outlier identification algorithms producing scores of outlyingness. The scores of nominal outlyingness are computed based on the framework of Costa and Papatsouma (2025) <doi:10.48550/arXiv.2408.07463>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: data.table (>= 1.14.0), DescTools (>= 0.99.0), ggplot2 (>= 3.3.5), Rdpack (>= 2.0), rje (>= 0.9)
NeedsCompilation: no
Packaged: 2025-03-20 12:50:26 UTC; ec1917
Author: Efthymios Costa [aut, cre]
Maintainer: Efthymios Costa <efthymios.costa17@imperial.ac.uk>
Repository: CRAN
Date/Publication: 2025-03-22 11:50:07 UTC

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New package simpr.interaction with initial version 0.1.0
Package: simpr.interaction
Title: Calculating Parameters for Simulation-Based Regression Interaction Power Analysis
Version: 0.1.0
Description: Provides functionality for analytically calculating parameters (via the 'InteractionPoweR' package) useful for simulation of moderated multiple regression, based on the correlations among the predictors and outcome and the reliability of predictors.
Imports: InteractionPoweR
License: GPL-2
Encoding: UTF-8
URL: https://github.com/statisfactions/simpr.interaction/
BugReports: https://github.com/statisfactions/simpr.interaction/issues/
NeedsCompilation: no
Packaged: 2025-03-20 08:59:14 UTC; EthanBrown
Author: Ethan C. Brown [aut, cre]
Maintainer: Ethan C. Brown <ethancbrown@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-22 11:30:02 UTC

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New package SHIP with initial version 2.0.3
Package: SHIP
Title: Shrinkage Covariance Incorporating Prior Knowledge
Version: 2.0.3
Description: Implements estimation methods for shrinkage covariance matrices using user-specified covariance targets. The covariance target is a structured matrix towards which the unbiased sample covariance is shrunk, optionally incorporating prior knowledge. Shrinkage intensity is computed analytically. The method is described and applied to microarray gene expression data in Jelizarow et al. (2010) <doi:10.1093/bioinformatics/btq323>.
License: GPL (>= 2)
Encoding: UTF-8
Imports: stats
URL: https://github.com/vguillemot/SHIP
BugReports: https://github.com/vguillemot/SHIP/issues
NeedsCompilation: no
Packaged: 2025-03-20 12:53:13 UTC; vguillem
Author: Vincent Guillemot [aut, cre], Monika Jelizarow [aut]
Maintainer: Vincent Guillemot <vincent.guillemot@pasteur.fr>
Repository: CRAN
Date/Publication: 2025-03-22 11:50:11 UTC

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New package EstimateBreed with initial version 1.0.0
Package: EstimateBreed
Title: Estimation of Environmental Variables and Genetic Parameters
Version: 1.0.0
Date: 2025-03-16
Maintainer: Willyan Junior Adorian Bandeira <bandeira.wjab@gmail.com>
Description: Performs analyzes and estimates of environmental covariates and genetic parameters related to selection strategies and development of superior genotypes. It has two main functionalities, the first being about prediction models of covariates and environmental processes, while the second deals with the estimation of genetic parameters and selection strategies. Designed for researchers and professionals in genetics and environmental sciences, the package combines statistical methods for modeling and data analysis. This includes the plastochron estimate proposed by Porta et al. (2024) <doi:10.1590/1807-1929/agriambi.v28n10e278299>, Stress indices for genotype selection referenced by Ghazvini et al. (2024) <doi:10.1007/s10343-024-00981-1>, the Environmental Stress Index described by Tazzo et al. (2024) <https://revistas.ufg.br/vet/article/view/77035>, industrial quality indices of wheat genotypes (Szareski et al., 2019), <doi:10.4238/gmr18223>, Ear Indexes estimation [...truncated...]
License: GPL (>= 3)
URL: https://github.com/willyanjnr/EstimateBreed
Depends: R (>= 4.1.0)
Imports: dplyr, ggplot2, hrbrthemes, broom, purrr, ggrepel, grid, httr, jsonlite, lubridate, nasapower, tidyr, viridis, cowplot, sommer, lme4, minque, utils, car, lmtest
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), roxygen2, DT
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
LazyLoad: true
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-20 12:40:34 UTC; willy
Author: Willyan Junior Adorian Bandeira [aut, cre] , Ivan Ricardo Carvalho [aut, ctb] , Murilo Vieira Loro [aut, ctb] , Leonardo Cesar Pradebon [aut, ctb] , Jose Antonio Gonzalez da Silva [aut, ctb]
Repository: CRAN
Date/Publication: 2025-03-22 11:50:14 UTC

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New package BayesPIM with initial version 1.0.0
Package: BayesPIM
Title: Bayesian Prevalence-Incidence Mixture Model
Version: 1.0.0
Description: Models time-to-event data from interval-censored screening studies. It accounts for latent prevalence at baseline and incorporates misclassification due to imperfect test sensitivity. For usage details, see the package vignette ("BayesPIM_intro"). Further details can be found in T. Klausch, B. I. Lissenberg-Witte, and V. M. Coupe (2024), "A Bayesian prevalence-incidence mixture model for screening outcomes with misclassification", <doi:10.48550/arXiv.2412.16065>.
License: MIT + file LICENSE
URL: https://github.com/thomasklausch2/bayespim
BugReports: https://github.com/thomasklausch2/BayesPIM/issues
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp, mvtnorm, MASS, ggamma, doParallel, foreach, parallel, actuar
Depends: R (>= 3.5.0), coda
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-03-20 09:17:37 UTC; thoma
Author: Thomas Klausch [aut, cre]
Maintainer: Thomas Klausch <t.klausch@amsterdamumc.nl>
Repository: CRAN
Date/Publication: 2025-03-22 11:40:02 UTC

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Fri, 21 Mar 2025

New package PLNmodels with initial version 1.2.2
Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.2.2
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.
URL: https://pln-team.github.io/PLNmodels/
BugReports: https://github.com/pln-team/PLNmodels/issues
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Imports: cli, corrplot, dplyr, future, future.apply, ggplot2, glassoFast, grDevices, grid, gridExtra, igraph, magrittr, MASS, Matrix, methods, nloptr, parallel, pscl, purrr, R6, Rcpp, rlang, scales, stats, tidyr, torch
Suggests: factoextra, knitr, rmarkdown, spelling, testthat
LinkingTo: nloptr, Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: yes
Packaged: 2025-03-21 11:05:39 UTC; jchiquet
Author: Julien Chiquet [aut, cre] , Mahendra Mariadassou [aut] , Stephane Robin [aut], Francois Gindraud [aut], Julie Aubert [ctb], Bastien Batardiere [ctb], Giovanni Poggiato [ctb], Cole Trapnell [ctb], Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Repository: CRAN
Date/Publication: 2025-03-21 17:40:06 UTC

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New package mregions2 with initial version 1.1.2
Package: mregions2
Title: Access Data from Marine Regions: Gazetteer & Data Products
Version: 1.1.2
Description: Explore and retrieve marine spatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: checkmate, glue, httr2, magrittr, sf, utils, rdflib, ISOcodes, memoise, cli, dplyr, xml2, wrapr, methods, curl, digest
URL: https://github.com/ropensci/mregions2, https://docs.ropensci.org/mregions2/
BugReports: https://github.com/ropensci/mregions2/issues
Suggests: ows4R (>= 0.3), httptest2, jsonlite, knitr, leaflet, leaflet.extras2, mapview, rmarkdown, testthat, wk, purrr, withr
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2025-03-21 12:34:01 UTC; salvadorf@vliz.be
Author: Salvador Jesus Fernandez Bejarano [aut, cre], Lotte Pohl [aut], Julia Gustavsen [rev], Muralidhar M.A. [rev], Sheila M. Saia [rev]
Maintainer: Salvador Jesus Fernandez Bejarano <salvador.fernandez@vliz.be>
Repository: CRAN
Date/Publication: 2025-03-21 17:40:02 UTC

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New package trps with initial version 0.1.0
Package: trps
Title: Bayesian Trophic Position Models using 'stan'
Version: 0.1.0
Description: Bayesian trophic position models using 'stan' by leveraging 'brms' for stable isotope data. Trophic position models are derived by using equations from Post (2002) <doi:10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2>, Vander Zanden and Vadeboncoeur (2002) <doi:10.1890/0012-9658(2002)083[2152:FAIOBA]2.0.CO;2>, and Heuvel et al. (2024) <doi:10.1139/cjfas-2024-0028>.
License: CC0
Encoding: UTF-8
LazyData: true
Imports: brms, cli, dplyr, lifecycle
Suggests: bayesplot, ggdist, ggplot2, grid, knitr, purrr, rmarkdown, testthat (>= 3.0.0), tidybayes, tidyr, viridis
Depends: R (>= 4.1.0)
URL: https://benjaminhlina.github.io/trps/, https://github.com/benjaminhlina/trps
BugReports: https://github.com/benjaminhlina/trps/issues
VignetteBuilder: knitr
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2025-03-19 17:24:31 UTC; benhlina
Author: Benjamin L. Hlina [aut, cre]
Maintainer: Benjamin L. Hlina <benjamin.hlina@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-21 16:00:02 UTC

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New package robustSFA with initial version 0.2.0
Package: robustSFA
Title: Robust Estimation of Stochastic Frontier Models with MDPDE
Version: 0.2.0
Maintainer: Junmo Song <junmo.song@gmail.com>
Description: This provides a robust estimator for stochastic frontier models, employing the Minimum Density Power Divergence Estimator (MDPDE) for enhanced robustness against outliers. Additionally, it includes a function to recommend the optimal tuning parameter, alpha, which controls the robustness of the MDPDE. The methods implemented in this package are based on Song et al. (2017) <doi:10.1016/j.csda.2016.08.005>.
License: GPL-3
Encoding: UTF-8
Imports: stats, truncnorm, Rcpp,frontier
NeedsCompilation: yes
LinkingTo: Rcpp, BH
Packaged: 2025-03-19 06:05:25 UTC; jsong
Author: Junmo Song [aut, cre], Dong-hyun Oh [aut]
Repository: CRAN
Date/Publication: 2025-03-21 15:50:02 UTC

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New package mrgdp with initial version 0.3.2
Package: mrgdp
Title: Mexican Regional Gross Domestic Product
Version: 0.3.2
Maintainer: Marco Antonio Perez-Mendez <mperez.mendez@izt.uam.mx>
Description: Download Mexican economic census for several years (2004, 2009, 2014 and 2019) and all federal entities. Filter the census data table by municipal data and build a data.frame for all federal entities and several years.
License: GPL-2
Encoding: UTF-8
Imports: dplyr
Suggests: knitr, rmarkdown, vroom
VignetteBuilder: knitr
URL: <https://github.com/MarcoAPerezM/mrgdp>, https://github.com/MarcoAPerezM/mrgdp
BugReports: https://github.com/MarcoAPerezM/mrgdp/issues
NeedsCompilation: no
Packaged: 2025-03-19 02:09:20 UTC; marcoantonio
Author: Marco Antonio Perez-Mendez [aut, cre] , Jocabed Sanchez Martinez [aut], Hortensia Moreno-Macias [aut] , Laboratorio de Desigualadad Socioeconomica Regional DeSERLab [cph]
Repository: CRAN
Date/Publication: 2025-03-21 15:50:05 UTC

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New package mooplot with initial version 0.1.0
Package: mooplot
Title: Graphical Visualizations for Multi-Objective Optimization
Version: 0.1.0
Description: Visualization of multi-dimensional data arising in multi-objective optimization, including plots of the empirical attainment function (EAF), M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>, and symmetric Vorob'ev expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) <doi:10.1016/j.ejor.2014.07.032>, among others.
Depends: R (>= 4.0)
Imports: Rdpack, collapse (>= 2.0.8), grDevices, graphics, matrixStats, moocore
Suggests: extrafont, viridisLite, spelling, testthat (>= 3.0.0), withr
License: LGPL (>= 2)
BugReports: https://github.com/multi-objective/mooplot/issues/
URL: https://multi-objective.github.io/mooplot/r/, https://github.com/multi-objective/mooplot/
LazyLoad: true
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2025-03-19 08:50:09 UTC; manu
Author: Manuel Lopez-Ibanez [aut, cre] , Carlos Fonseca [ctb], Luis Paquete [ctb], Mickael Binois [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Repository: CRAN
Date/Publication: 2025-03-21 15:50:08 UTC

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New package MariNET with initial version 1.0.0
Package: MariNET
Title: Build Network Based on Linear Mixed Models from EHRs
Version: 1.0.0
Description: Analyzing longitudinal clinical data from Electronic Health Records (EHRs) using linear mixed models (LMM) and visualizing the results as networks. It includes functions for fitting LMM, normalizing adjacency matrices, and comparing networks. The package is designed for researchers in clinical and biomedical fields who need to model longitudinal data and explore relationships between variables For more details see Bates et al. (2015) <doi:10.18637/jss.v067.i01>.
License: GPL-3
Imports: dplyr, lme4, qgraph
Encoding: UTF-8
Suggests: knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
Depends: R (>= 3.5)
LazyData: true
NeedsCompilation: no
Packaged: 2025-03-19 15:26:54 UTC; marina
Author: Vargas-Fernandez Marina [aut, cre], Martorell-Marugan Jordi [aut], Carmona-Saez Pedro [aut]
Maintainer: Vargas-Fernandez Marina <marina.vargas@genyo.es>
Repository: CRAN
Date/Publication: 2025-03-21 16:00:06 UTC

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Thu, 20 Mar 2025

New package MiscMetabar with initial version 0.14.2
Package: MiscMetabar
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.14.2
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
License: AGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1.0), phyloseq, ggplot2 (>= 3.5.0), dada2, dplyr, purrr
Suggests: adespatial, ANCOMBC, BiocManager, Biostrings, circlize, ComplexUpset, DECIPHER, DESeq2, devtools, DT, edgeR, formattable, ggalluvial, ggfittext, gghalves, ggh4x, ggstatsplot, ggridges, ggVennDiagram, glmulti, gtsummary, grDevices, grid, gridExtra, here, httr, iNEXT, indicspecies, IRanges, jsonlite, knitr, magrittr, methods, mia, mixtools, multcompView, networkD3, pak, patchwork, pbapply, permute, phangorn, phyloseqGraphTest, pkgnet, plotly, plyr, reshape2, rmarkdown, rotl, Rtsne, scales, seqinr, SRS, stringr, SummarizedExperiment, testthat (>= 3.0.0), tibble, tidyr, treemapify, umap, uwot, vegan, venneuler, vctrs, viridis, withr, spelling
URL: https://github.com/adrientaudiere/MiscMetabar, https://adrientaudiere.github.io/MiscMetabar/
BugReports: https://github.com/adrientaudiere/MiscMetabar/issues
Imports: ape, lifecycle, rlang, stats
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-03-20 13:49:05 UTC; adrien
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Repository: CRAN
Date/Publication: 2025-03-20 15:20:02 UTC

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New package LJmp3converter with initial version 1.0.5
Package: LJmp3converter
Title: Convert Video Files to MP3 Format using 'FFmpeg'
Version: 1.0.5
Description: Converts video files to 'MP3' using 'FFmpeg', which is dynamically downloaded to avoid bundling any third-party binaries. Users must ensure compliance with the license terms of 'FFmpeg' when using the package. See <https://github.com/BtbN/FFmpeg-Builds/releases/download/latest/ffmpeg-master-latest-win64-gpl.zip> for details.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: fs, tools, utils, rstudioapi, httr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-03-18 17:38:40 UTC; lijin
Author: Lijin Arakkandathil Thekkathil [aut, cre]
Maintainer: Lijin Arakkandathil Thekkathil <lijin5673@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-20 09:20:08 UTC

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New package kanova with initial version 0.3-12
Package: kanova
Version: 0.3-12
Date: 2025-03-19
Title: Pseudo Anova for K-Functions
Author: Rolf Turner [aut, cre]
Maintainer: Rolf Turner <rolfturner@posteo.net>
Description: One-way and two-way analysis of variance for replicated point patterns, grouped by one or two classification factors, on the basis of the corresponding K-functions.
Imports: spatstat.geom, spatstat.explore, spatstat.random
Suggests: R.rsp, Devore7
VignetteBuilder: R.rsp
LazyData: true
Depends: R (>= 3.2.2)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-03-18 22:04:12 UTC; rolf
Repository: CRAN
Date/Publication: 2025-03-20 09:40:02 UTC

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New package firebase.auth.rest with initial version 1.0.0
Package: firebase.auth.rest
Title: R Wrapper for 'Firebase Authentication REST API'
Version: 1.0.0
Description: A convenient and user-friendly interface to interact with the 'Firebase Authentication REST API': <https://firebase.google.com/docs/reference/rest/auth>. It enables R developers to integrate 'Firebase Authentication' services seamlessly into their projects, allowing for user authentication, account management, and other authentication-related tasks.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/kennedymwavu/firebase.auth.rest
BugReports: https://github.com/kennedymwavu/firebase.auth.rest/issues
Imports: httr2 (>= 0.2.3)
NeedsCompilation: no
Packaged: 2025-03-18 18:14:34 UTC; mwavu
Author: Kennedy Mwavu [aut, cre, cph]
Maintainer: Kennedy Mwavu <mwavukennedy@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-20 09:20:02 UTC

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New package fibos with initial version 1.2.3
Package: fibos
Title: Occlusion Surface Using the Occluded Surface and Fibonacci Occluded Surface
Version: 1.2.3
Maintainer: Herson Soares <hersonhebert@hotmail.com>
Description: The Occluded Surface (OS) algorithm is a widely used approach for analyzing atomic packing in biomolecules as described by Pattabiraman N, Ward KB, Fleming PJ (1995) <doi:10.1002/jmr.300080603>. Here, we introduce 'fibos', an 'R' and 'Python' package that extends the 'OS''' methodology, as presented in Soares HHM, Romanelli JPR, Fleming PJ, da Silveira CH (2024) <doi:10.1101/2024.11.01.621530>.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
Imports: fs, dplyr, readr, stringr, tidyr, reticulate, glue
NeedsCompilation: yes
Packaged: 2025-03-19 01:10:35 UTC; hersonhebert
Author: Herson Soares [cre, aut], Carlos Silveira [aut], Joao Romanelli [aut], Patrick Fleming [aut], Posit Software, PBC [cph, fnd]
Repository: CRAN
Date/Publication: 2025-03-20 09:50:02 UTC

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New package corrRF with initial version 1.1.0
Package: corrRF
Title: Clustered Random Forests for Optimal Prediction and Inference of Clustered Data
Version: 1.1.0
Maintainer: Elliot H. Young <ey244@cam.ac.uk>
Description: A clustered random forest algorithm for fitting random forests for data of independent clusters, that exhibit within cluster dependence. Details of the method can be found in Young and Buehlmann (2025) <doi:10.48550/arXiv.2503.12634>.
License: GPL-3
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp, rpart
Depends: R (>= 4.2.0)
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: yes
Packaged: 2025-03-18 17:40:09 UTC; elliotyoung
Author: Elliot H. Young [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-20 09:20:06 UTC

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Wed, 19 Mar 2025

New package cpmBigData with initial version 0.0.2
Package: cpmBigData
Title: Fitting Semiparametric Cumulative Probability Models for Big Data
Version: 0.0.2
Description: A big data version for fitting cumulative probability models using the orm() function from the 'rms' package. See Liu et al. (2017) <DOI:10.1002/sim.7433> for details.
Depends: R (>= 4.0.0)
License: GPL (>= 2)
Encoding: UTF-8
Imports: rms (>= 7.0.0),Hmisc (>= 5.2.2),doParallel (>= 1.0.11),parallel (>= 3.5.2),foreach (>= 1.2.0),iterators (>= 1.0.0),benchmarkme (>= 1.0.4)
NeedsCompilation: no
Packaged: 2025-02-28 21:49:04 UTC; lic3
Author: Chun Li [cre, aut], Guo Chen [aut]
Maintainer: Chun Li <cli77199@usc.edu>
Repository: CRAN
Date/Publication: 2025-03-20 01:00:12 UTC

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New package tndata with initial version 0.1.0
Package: tndata
Title: Fetch Datasets from the Official Tunisian Data Catalog
Version: 0.1.0
Description: Simplifies access to Tunisian government open data from <https://data.gov.tn/fr/>. Queries datasets by theme, author, or keywords, retrieves metadata, and gets structured results ready for analysis; all through the official 'CKAN' API.
License: Apache License (>= 2)
Encoding: UTF-8
Imports: dplyr, fs, glue, httr, httr2, jsonlite, logger, lubridate, purrr, stringr
Depends: R (>= 4.1.0)
URL: https://github.com/aymennasri/tndata, http://aymennasri.me/tndata/
BugReports: https://github.com/aymennasri/tndata/issues
NeedsCompilation: no
Packaged: 2025-03-18 13:02:55 UTC; aymen
Author: Aymen Nasri [aut, cre, cph]
Maintainer: Aymen Nasri <aymennasrii@proton.me>
Repository: CRAN
Date/Publication: 2025-03-19 13:20:02 UTC

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New package kernopt with initial version 1.0.0
Package: kernopt
Title: Estimating Count Data Distributions with Discrete Optimal Symmetric Kernel
Version: 1.0.0
Maintainer: Thomas Fillon <thomas.fillon@univ-ubs.fr>
Description: Implementation of Discrete Symmetric Optimal Kernel for estimating count data distributions, as described by T. Senga Kiessé and G. Durrieu (2024) <doi:10.1016/j.spl.2024.110078>.The nonparametric estimator using the discrete symmetric optimal kernel was illustrated on simulated data sets and a real-word data set included in the package, in comparison with two other discrete symmetric kernels.
License: GPL (>= 3)
Encoding: UTF-8
Imports: stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
LazyData: true
URL: https://thomasfillon.github.io/kernopt/, https://github.com/thomasfillon/kernopt
BugReports: https://github.com/thomasfillon/kernopt/issues
NeedsCompilation: no
Packaged: 2025-03-18 14:11:14 UTC; rstudio
Author: Tristan Senga Kiesse [aut] , Gilles Durrieu [aut] , Thomas Fillon [aut, cre] , INRAE, Institut Agro, CNRS - UMR SAS [cph], Universite de Bretagne Sud, CNRS - UMR 6205 LMBA [cph]
Repository: CRAN
Date/Publication: 2025-03-19 13:20:05 UTC

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New package globpso with initial version 1.3.0
Package: globpso
Title: Swarm Intelligence Optimization
Version: 1.3.0
Date: 2025-03-08
Author: Ping-Yang Chen [aut, cre], Russell Eberhart [ctb], Kennedy Kennedy [ctb], Jun Sun [ctb], Bin Feng [ctb], Wenbo Xu [ctb], Mohammad Reza Bonyadi [ctb], Zbigniew Michalewicz [ctb], Ran Cheng [ctb], Yaochu Jin [ctb], Milan Stehlik [ctb], Weng Kee Wong [c [...truncated...]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>
Description: A fast and flexible general-purpose implementation of Particle Swarm Optimization (PSO) and Differential Evolution (DE) for solving global minimization problems is provided. It is designed to handle complex optimization tasks with nonlinear, non-differentiable, and multi-modal objective functions defined by users. There are five types of PSO variants: Particle Swarm Optimization (PSO, Eberhart & Kennedy, 1995) <doi:10.1109/MHS.1995.494215>, Quantum-behaved particle Swarm Optimization (QPSO, Sun et al., 2004) <doi:10.1109/CEC.2004.1330875>, Locally convergent rotationally invariant particle swarm optimization (LcRiPSO, Bonyadi & Michalewicz, 2014) <doi:10.1007/s11721-014-0095-1>, Competitive Swarm Optimizer (CSO, Cheng & Jin, 2015) <doi:10.1109/TCYB.2014.2322602> and Double exponential particle swarm optimization (DExPSO, Stehlik et al., 2024) <doi:10.1016/j.asoc.2024.111913>. For the DE algorithm, six types in Storn, R. & Price, K. (1997) & [...truncated...]
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 1.0.12), RcppArmadillo (>= 0.12.6.6.1), methods, utils
LinkingTo: Rcpp, RcppArmadillo,
Suggests: knitr, rmarkdown
NeedsCompilation: yes
Packaged: 2025-03-18 07:42:56 UTC; User
Repository: CRAN
Date/Publication: 2025-03-19 13:10:02 UTC

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New package CohortPathways with initial version 0.0.1
Package: CohortPathways
Title: Create Pathways from Target to Event Cohorts
Version: 0.0.1
Date: 2025-03-18
Maintainer: Gowtham Rao <rao@ohdsi.org>
Description: Software tool designed to compute the temporal relationship defined as pathways between any two instantiated cohorts. The cohorts are input as Target and event cohorts.
Depends: DatabaseConnector (>= 5.0.0), R (>= 4.1.0)
Imports: checkmate, dplyr, lifecycle, rlang, SqlRender, tidyr
Suggests: remotes, testthat, withr
License: Apache License
Encoding: UTF-8
Language: en-US
URL: https://github.com/OHDSI/CohortPathways
BugReports: https://github.com/OHDSI/CohortPathways/issues
NeedsCompilation: no
Packaged: 2025-03-18 15:18:14 UTC; gowth
Author: Gowtham Rao [aut, cre], Chris Knoll [aut], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2025-03-19 13:30:02 UTC

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New package CANE with initial version 0.1.0
Package: CANE
Title: Comprehensive Groups of Experiments Analysis for Numerous Environments
Version: 0.1.0
Maintainer: Vinayaka <vinayaka.b3vs@gmail.com>
Description: In many cases, experiments must be repeated across multiple seasons or locations to ensure applicability of findings. A single experiment conducted in one location and season may yield limited conclusions, as results can vary under different environmental conditions. In agricultural research, treatment × location and treatment × season interactions play a crucial role. Analyzing a series of experiments across diverse conditions allows for more generalized and reliable recommendations. The 'CANE' package facilitates the pooled analysis of experiments conducted over multiple years, seasons, or locations. It is designed to assess treatment interactions with environmental factors (such as location and season) using various experimental designs. The package supports pooled analysis of variance (ANOVA) for the following designs: (1) 'PooledCRD()': completely randomized design; (2) 'PooledRBD()': randomized block design; (3) 'PooledLSD()': Latin square design; (4) 'PooledSPD()': split plot de [...truncated...]
Imports: agricolae, dplyr, emmeans, stats
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
NeedsCompilation: no
Packaged: 2025-03-18 14:47:42 UTC; DELL
Author: Vinayaka [aut, cre] , T. Lakshmi Pathy [aut, ctb] , K. Gopalareddy [aut, ctb] , Shweta Kumari [aut, ctb] , P. Murali [aut, ctb] , P. Govindaraj [aut, ctb], P. Rama Chandra Prasad [aut, ctb] , L.N. Vinaykumar [aut, ctb]
Repository: CRAN
Date/Publication: 2025-03-19 13:30:05 UTC

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New package Waypoint with initial version 1.1.0
Package: Waypoint
Title: Convert, Validate, Format and Print Geographic Coordinates and Waypoints
Version: 1.1.0
Date: 2025-03-17
Description: Convert, validate, format and elegantly print geographic coordinates and waypoints (paired latitude and longitude values) in decimal degrees, degrees and minutes, and degrees, minutes and seconds using high performance C++ code to enable rapid conversion and formatting of large coordinate and waypoint datasets.
License: MIT + file LICENSE
Imports: methods, Rcpp (>= 1.0.13)
LinkingTo: Rcpp
Encoding: UTF-8
URL: https://mark-eis.github.io/Waypoint/
NeedsCompilation: yes
Packaged: 2025-03-17 22:54:08 UTC; runner
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark.eisler@bristol.ac.uk>
Depends: R (>= 4.1.0)
Repository: CRAN
Date/Publication: 2025-03-19 13:00:01 UTC

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New package MultiNMix with initial version 0.1.0
Package: MultiNMix
Title: Multi-Species N-Mixture (MNM) Models with 'nimble'
Version: 0.1.0
Description: Simulating data and fitting multi-species N-mixture models using 'nimble'. Includes features for handling zero-inflation and temporal correlation, Bayesian inference, model diagnostics, parameter estimation, and predictive checks. Designed for ecological studies with zero-altered or time-series data. Mimnagh, N., Parnell, A., Prado, E., & Moral, R. A. (2022) <doi:10.1007/s10651-022-00542-7>. Royle, J. A. (2004) <doi:10.1111/j.0006-341X.2004.00142.x>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: clusterGeneration, mvtnorm, extraDistr, rstan, stats, abind, methods, coda
Depends: nimble, R (>= 3.5)
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
LazyData: true
URL: https://github.com/niamhmimnagh/MultiNMix
BugReports: https://github.com/niamhmimnagh/MultiNMix/issues
NeedsCompilation: no
Packaged: 2025-03-17 17:21:20 UTC; niamh
Author: Niamh Mimnagh [aut, cre], Rafael de Andrade Moral [aut]
Maintainer: Niamh Mimnagh <niamhmimnagh@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-19 12:50:02 UTC

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New package CohortSurvival with initial version 1.0.0
Package: CohortSurvival
Title: Estimate Survival from Common Data Model Cohorts
Version: 1.0.0
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
License: Apache License (>= 2)
Encoding: UTF-8
Imports: CDMConnector (>= 2.0.0), omopgenerics (>= 1.1.0), checkmate, cli, clock, DBI, dplyr, magrittr, broom, PatientProfiles (>= 1.3.1), rlang (>= 0.4.11), survival (>= 3.7.0), stringr, tibble, tidyr, purrr
Suggests: testthat (>= 3.0.0), CodelistGenerator, roxygen2, knitr, tictoc, rmarkdown, ggplot2, patchwork, cmprsk, duckdb, gt, flextable, scales, visOmopResults (>= 1.0.0)
VignetteBuilder: knitr
URL: https://darwin-eu-dev.github.io/CohortSurvival/
NeedsCompilation: no
Packaged: 2025-03-17 15:18:40 UTC; lopezk
Author: Kim Lopez-Gueell [aut, cre] , Edward Burn [aut] , Marti Catala [aut] , Xintong Li [aut] , Danielle Newby [aut] , Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Repository: CRAN
Date/Publication: 2025-03-19 12:50:06 UTC

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New package autodb with initial version 2.3.1
Package: autodb
Title: Automatic Database Normalisation for Data Frames
Version: 2.3.1
Description: Automatic normalisation of a data frame to third normal form, with the intention of easing the process of data cleaning. (Usage to design your actual database for you is not advised.) Originally inspired by the 'AutoNormalize' library for 'Python' by 'Alteryx' (<https://github.com/alteryx/autonormalize>), with various changes and improvements. Automatic discovery of functional or approximate dependencies, normalisation based on those, and plotting of the resulting "database" via 'Graphviz', with options to exclude some attributes at discovery time, or remove discovered dependencies at normalisation time.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Language: en-GB
Depends: R (>= 4.1.0)
Imports: rlang
Suggests: spelling, DiagrammeR (>= 1.0.7), testthat (>= 3.1.4), R.utils (>= 2.11.0), hedgehog (>= 0.1), tibble(>= 3.2.1), knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
URL: https://charnelmouse.github.io/autodb/, https://github.com/CharnelMouse/autodb
BugReports: https://github.com/CharnelMouse/autodb/issues
NeedsCompilation: no
Packaged: 2025-03-17 14:49:55 UTC; Mark
Author: Mark Webster [aut, cre]
Maintainer: Mark Webster <markwebster204@yahoo.co.uk>
Repository: CRAN
Date/Publication: 2025-03-19 12:40:02 UTC

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Tue, 18 Mar 2025

New package DataSimilarity with initial version 0.1.1
Package: DataSimilarity
Title: Quantifying Similarity of Datasets and Multivariate Two- And k-Sample Testing
Version: 0.1.1
Date: 2025-03-18
Depends: R (>= 3.5.0)
Imports: boot, stats
Suggests: ade4, approxOT, Ball, caret, clue, cramer, crossmatch, dbscan, densratio, DWDLargeR, e1071, Ecume, energy, expm, FNN, gTests, gTestsMulti, HDLSSkST, hypoRF, kernlab, kerTests, KMD, knitr, LPKsample, Matrix, mvtnorm, nbpMatching, pROC, purrr, randtoolbox, rlemon, rpart, rpart.plot, testthat, RSNNS
Description: A collection of methods for quantifying the similarity of two or more datasets, many of which can be used for two- or k-sample testing. It provides newly implemented methods as well as wrapper functions for existing methods that enable calling many different methods in a unified framework. The methods were selected from the review and comparison of Stolte et al. (2024) <doi:10.1214/24-SS149>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2025-03-18 16:10:24 UTC; stolte
Author: Marieke Stolte [aut, cre, cph] , Luca Sauer [aut], David Alvarez-Melis [ctb] , Nabarun Deb [ctb] , <https://github.com/NabarunD/MultiDistFree.git>), Bodhisattva Sen [ctb] , <https://github.com/NabarunD/MultiDistFree.git>)
Maintainer: Marieke Stolte <stolte@statistik.tu-dortmund.de>
Repository: CRAN
Date/Publication: 2025-03-18 21:10:06 UTC

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New package TPXG with initial version 1.0
Package: TPXG
Title: Two Parameter Xgamma & Poisson Xgamma: Regression & Distribution Functions
Version: 1.0
Date: 2025-03-12
Author: Nikolaos Kontemeniotis [aut, cre], Michail Tsagris [aut]
Maintainer: Nikolaos Kontemeniotis <kontemeniotisn@gmail.com>
Depends: R (>= 4.0)
Imports: Rfast2, stats
Suggests: Rfast
Description: The two-parameter Xgamma and Poisson Xgamma distributions are analyzed, covering standard distribution and regression functions, maximum likelihood estimation, quantile functions, probability density and mass functions, cumulative distribution functions, and random number generation. References include: "Sen, S., Chandra, N. and Maiti, S. S. (2018). On properties and applications of a two-parameter XGamma distribution. Journal of Statistical Theory and Applications, 17(4): 674--685. <doi:10.2991/jsta.2018.17.4.9>." "Wani, M. A., Ahmad, P. B., Para, B. A. and Elah, N. (2023). A new regression model for count data with applications to health care data. International Journal of Data Science and Analytics. <doi:10.1007/s41060-023-00453-1>."
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-03-17 11:59:31 UTC; nikolask
Repository: CRAN
Date/Publication: 2025-03-18 15:10:09 UTC

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New package StatRec with initial version 1.0.0
Package: StatRec
Title: A Statistical Method for Multi-Item Rating and Recommendation Problems
Imports: Rcpp (>= 1.0.14)
Version: 1.0.0
Maintainer: Sjoerd Hermes <sjoerd.hermes@wur.nl>
Description: Implements the methodological developments found in Hermes (2025) <doi:10.48550/arXiv.2503.02786>, and allows for the statistical modeling of data consisting of multiple users that provide an ordinal rating for one or multiple items.
License: GPL-3
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2025-03-17 08:55:04 UTC; sjoerd
Author: Sjoerd Hermes [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-18 15:10:13 UTC

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New package SLmetrics with initial version 0.3-3
Package: SLmetrics
Title: Machine Learning Performance Evaluation on Steroids
Version: 0.3-3
Description: Performance evaluation metrics for supervised and unsupervised machine learning, statistical learning and artificial intelligence applications. Core computations are implemented in 'C++' for scalability and efficiency.
License: GPL (>= 3)
Encoding: UTF-8
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, reticulate, rmarkdown, testthat (>= 3.0.0)
Imports: grDevices, lattice, Rcpp
Depends: R (>= 4.3)
URL: https://serkor1.github.io/SLmetrics/, https://github.com/serkor1/SLmetrics
BugReports: https://github.com/serkor1/SLmetrics/issues
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-03-17 13:41:49 UTC; serkan
Author: Serkan Korkmaz [cre, aut, cph]
Maintainer: Serkan Korkmaz <serkor1@duck.com>
Repository: CRAN
Date/Publication: 2025-03-18 15:20:10 UTC

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New package ResIndex with initial version 0.1.0
Package: ResIndex
Title: Generate Simple yet Effective Metric of Feature Importance for Classification Problems
Version: 0.1.0
Description: An intuitive and explainable metric of Feature Importance for Classification Problems. Resolution Index measures the extent to which a Feature clusters different classes when data is sorted on it. User provides a DataFrame, column name of the Class, sample size and number of iterations used for calculation. Resolution Index for each Feature is returned, which can be effectively used to rank Features and reduce Dimensionality of Training data. For more details on Feature Selection see Theng and Bhoyar (2023) <doi:10.1007/s10115-023-02010-5>.
License: LGPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-03-17 08:13:17 UTC; 703254631
Author: Anand Jha [aut, cre]
Maintainer: Anand Jha <anandorjha18@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-18 15:10:15 UTC

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