Fri, 07 Feb 2025

Package centr updated to version 0.2.2 with previous version 0.2.1 dated 2024-12-22

Title: Weighted and Unweighted Spatial Centers
Description: Generate mean and median weighted or unweighted spatial centers. Functions are analogous to their identically named counterparts within 'ArcGIS Pro'. Median center methodology based off of Kuhn and Kuenne (1962) <doi:10.1111/j.1467-9787.1962.tb00902.x>.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>

Diff between centr versions 0.2.1 dated 2024-12-22 and 0.2.2 dated 2025-02-07

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Package bsitar updated to version 0.3.2 with previous version 0.2.1 dated 2024-03-19

Title: Bayesian Super Imposition by Translation and Rotation Growth Curve Analysis
Description: The Super Imposition by Translation and Rotation (SITAR) model is a shape-invariant nonlinear mixed effect model that fits a natural cubic spline mean curve to the growth data and aligns individual-specific growth curves to the underlying mean curve via a set of random effects (see Cole, 2010 <doi:10.1093/ije/dyq115> for details). The non-Bayesian version of the SITAR model can be fit by using the already available R package 'sitar'. While the 'sitar' package allows modelling of a single outcome only, the 'bsitar' package offers great flexibility in fitting models of varying complexities, including joint modelling of multiple outcomes such as height and weight (multivariate model). Additionally, the 'bsitar' package allows for the simultaneous analysis of an outcome separately for subgroups defined by a factor variable such as gender. This is achieved by fitting separate models for each subgroup (for example males and females for gender variable). An advantage of this approach is [...truncated...]
Author: Satpal Sandhu [aut, cre, cph]
Maintainer: Satpal Sandhu <satpal.sandhu@bristol.ac.uk>

Diff between bsitar versions 0.2.1 dated 2024-03-19 and 0.3.2 dated 2025-02-07

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Package emayili updated to version 0.9.3 with previous version 0.9.2 dated 2025-01-28

Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph], Matt Dennis [ctb], Antoine Bichat [ctb] , Daniel Fahey [ctb], Johann R. Kleinbub [ctb], Panagiotis Moulos [ctb], Swechhya Bista [ctb], Colin Fay [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>

Diff between emayili versions 0.9.2 dated 2025-01-28 and 0.9.3 dated 2025-02-07

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Thu, 06 Feb 2025

Package stoppingrule updated to version 0.5.2 with previous version 0.5.1 dated 2024-12-05

Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies.
Author: Michael J. Martens [aut, cre], Qinghua Lian [aut], Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>

Diff between stoppingrule versions 0.5.1 dated 2024-12-05 and 0.5.2 dated 2025-02-06

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Package galah updated to version 2.1.1 with previous version 2.1.0 dated 2024-11-18

Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre], Dax Kellie [aut], Matilda Stevenson [aut], Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>

Diff between galah versions 2.1.0 dated 2024-11-18 and 2.1.1 dated 2025-02-06

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Package bndesr updated to version 1.0.4 with previous version 1.0.3 dated 2023-06-06

Title: Access Data from the Brazilian Development Bank (BNDES)
Description: Allows access to data on BNDES disbursements and contracts since 1995. The package makes it easy to import data from the bank into R.<https://www.bndes.gov.br/SiteBNDES/bndes/bndes_en>.
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>

Diff between bndesr versions 1.0.3 dated 2023-06-06 and 1.0.4 dated 2025-02-06

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Package SomaDataIO updated to version 6.2.0 with previous version 6.1.0 dated 2024-03-26

Title: Input/Output 'SomaScan' Data
Description: Load and export 'SomaScan' data via the 'Standard BioTools, Inc.' structured text file called an ADAT ('*.adat'). For file format see <https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
Author: Stu Field [aut] , Caleb Scheidel [cre], Standard BioTools, Inc. [cph, fnd]
Maintainer: Caleb Scheidel <calebjscheidel@gmail.com>

Diff between SomaDataIO versions 6.1.0 dated 2024-03-26 and 6.2.0 dated 2025-02-06

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New package shapr with initial version 1.0.2
Package: shapr
Version: 1.0.2
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, progress, coro, parsnip, recipes, workflows, tune, dials, yardstick, hardhat, rsample, rlang, cli
LinkingTo: RcppArmadillo, Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-01-30 11:54:59 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: 2025-02-07 00:40:02 UTC

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New package params with initial version 0.7.7
Package: params
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options().
Version: 0.7.7
Depends: R (>= 3.0.2), whisker
Imports: utils, RcppTOML, glue, readr (>= 1.4.0), purrr
Suggests: openxlsx, readxl, testthat, knitr, utf8
License: GPL-2
URL: https://github.com/sahilseth/params
BugReports: https://github.com/sahilseth/params/issues
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-02-06 19:40:55 UTC; seths3
Author: Sahil Seth [aut, cre], Yihui Xie [ctb]
Maintainer: Sahil Seth <me@sahilseth.com>
Repository: CRAN
Date/Publication: 2025-02-07 00:40:07 UTC

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New package MBNMAdose with initial version 0.5.0
Package: MBNMAdose
Title: Dose-Response MBNMA Models
Version: 0.5.0
Language: en-GB
Date: 2025-02-06
URL: https://hugaped.github.io/MBNMAdose/
Maintainer: Hugo Pedder <hugopedder@gmail.com>
Description: Fits Bayesian dose-response model-based network meta-analysis (MBNMA) that incorporate multiple doses within an agent by modelling different dose-response functions, as described by Mawdsley et al. (2016) <doi:10.1002/psp4.12091>. By modelling dose-response relationships this can connect networks of evidence that might otherwise be disconnected, and can improve precision on treatment estimates. Several common dose-response functions are provided; others may be added by the user. Various characteristics and assumptions can be flexibly added to the models, such as shared class effects. The consistency of direct and indirect evidence in the network can be assessed using unrelated mean effects models and/or by node-splitting at the treatment level.
License: GPL-3
Depends: R (>= 3.0.2)
Imports: grDevices, stats, graphics, utils, scales, dplyr (>= 0.7.4), R2jags (>= 0.5-7), rjags (>= 4-8), magrittr (>= 1.5), checkmate (>= 1.8.5), Rdpack (>= 0.11-0), igraph (>= 2.0.1.1), ggplot2 (>= 2.2.1), reshape2 (>= 1.4.3)
Suggests: overlapping (>= 1.5.0), RColorBrewer (>= 1.1-2), mcmcplots (>= 0.4.3), coda (>= 0.19-4), testthat (>= 1.0.2), crayon (>= 1.3.4), forestplot (>= 1.10), ggdist (>= 2.4.0), zoo (>= 1.8-8), lspline (>= 1.0-0), formatR (>= 1.14), netmeta, knitr, rmarkdown
SystemRequirements: JAGS (>= 4.3.0) (https://mcmc-jags.sourceforge.net/)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-06 19:58:33 UTC; hp17602
Author: Hugo Pedder [aut, cre] , Adil Karim [ctb]
Repository: CRAN
Date/Publication: 2025-02-07 00:40:23 UTC

More information about MBNMAdose at CRAN
Permanent link

Package geostatsp updated to version 2.0.8 with previous version 2.0.6 dated 2024-02-20

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector' objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://www.wim.uni-mannheim.de/schlather/publications/software>.
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>

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Package ellmer updated to version 0.1.1 with previous version 0.1.0 dated 2025-01-09

Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] , Joe Cheng [aut], Aaron Jacobs [aut], Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

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Package sreg updated to version 1.0.1 with previous version 1.0.0 dated 2024-06-25

Title: Stratified Randomized Experiments
Description: Estimate average treatment effects (ATEs) in stratified randomized experiments. 'sreg' is designed to accommodate scenarios with multiple treatments and cluster-level treatment assignments, and accommodates optimal linear covariate adjustment based on baseline observable characteristics. 'sreg' computes estimators and standard errors based on Bugni, Canay, Shaikh (2018) <doi:10.1080/01621459.2017.1375934>; Bugni, Canay, Shaikh, Tabord-Meehan (2024+) <doi:10.48550/arXiv.2204.08356>; and Jiang, Linton, Tang, Zhang (2023+) <doi:10.48550/arXiv.2201.13004>.
Author: Juri Trifonov [aut, cre, cph], Yuehao Bai [aut], Azeem Shaikh [aut], Max Tabord-Meehan [aut]
Maintainer: Juri Trifonov <jutrifonov@uchicago.edu>

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Package aws.wrfsmn updated to version 0.0.5 with previous version 0.0.4 dated 2025-01-10

Title: Data Processing of SMN Hi-Res Weather Forecast from 'AWS'
Description: Exploration of Weather Research & Forecasting ('WRF') Model data of Servicio Meteorologico Nacional (SMN) from Amazon Web Services (<https://registry.opendata.aws/smn-ar-wrf-dataset/>) cloud. The package provides the possibility of data downloading, processing and correction methods. It also has map management and series exploration of available meteorological variables of 'WRF' forecast.
Author: Gonzalo Diaz [cre, aut]
Maintainer: Gonzalo Diaz <gonzalomartindiaz22@gmail.com>

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Package checkglobals updated to version 0.1.3 with previous version 0.1.0 dated 2023-06-02

Title: Static Analysis of R-Code Dependencies
Description: A minimal R-package to approximately detect global and imported functions or variables from R-source code or R-packages by static code analysis.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

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Package adegenet updated to version 2.1.11 with previous version 2.1.10 dated 2023-01-26

Title: Exploratory Analysis of Genetic and Genomic Data
Description: Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Author: Thibaut Jombart [aut] , Zhian N. Kamvar [aut, cre] , Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maie [ctb], Libor Morkovsky [ [...truncated...]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

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Package TOSTER updated to version 0.8.4 with previous version 0.8.3 dated 2024-05-08

Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut], Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>

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New package sphereML with initial version 0.1.0
Package: sphereML
Title: Analyzing Students' Performance Dataset in Physics Education Research (SPHERE) using Machine Learning (ML)
Version: 0.1.0
Maintainer: Purwoko Haryadi Santoso <purwokoharyadisantoso@unsulbar.ac.id>
Description: A simple package facilitating ML based analysis for physics education research (PER) purposes. The implemented machine learning technique is random forest optimized by item response theory (IRT) for feature selection and genetic algorithm (GA) for hyperparameter tuning. The data analyzed here has been made available in the CRAN repository through the 'spheredata' package. The SPHERE stands for Students' Performance in Physics Education Research (PER). The students are the eleventh graders learning physics at the high school curriculum. We follow the stream of multidimensional students' assessment as probed by some research based assessments in PER. The goal is to predict the students' performance at the end of the learning process. Three learning domains are measured including conceptual understanding, scientific ability, and scientific attitude. Furthermore, demographic backgrounds and potential variables predicting students' performance on physics are also demonstrated.
BugReports: https://github.com/santosoph/sphereML/issues
URL: https://github.com/santosoph/sphereML
License: MIT + file LICENSE
Imports: shiny, shinydashboard, spheredata, lavaan, semPlot, CTT, mirt, shinycssloaders, FSelectorRcpp, randomForest, caret, caTools, pROC, GA, readxl
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-06 14:43:15 UTC; ASUS
Author: Purwoko Haryadi Santoso [aut, cre] , Edi Istiyono [ctb], Haryanto Haryanto [ctb]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-06 20:10:01 UTC

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Package easylabel updated to version 0.3.3 with previous version 0.3.2 dated 2025-01-09

Title: Interactive Scatter Plot and Volcano Plot Labels
Description: Interactive labelling of scatter plots, volcano plots and Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover over points to see where specific points are located and click points on/off to easily label them. Labels can be dragged around the plot to place them optimally. Plots can be exported directly to PDF for publication. For plots with large numbers of points, points can optionally be rasterized as a bitmap, while all other elements (axes, text, labels & lines) are preserved as vector objects. This can dramatically reduce file size for plots with millions of points such as Manhattan plots, and is ideal for publication.
Author: Myles Lewis [aut, cre] , Katriona Goldmann [aut] , Cankut Cubuk [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>

Diff between easylabel versions 0.3.2 dated 2025-01-09 and 0.3.3 dated 2025-02-06

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Package trtswitch updated to version 0.1.3 with previous version 0.1.2 dated 2024-12-05

Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>

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New package tall with initial version 0.1.0
Package: tall
Title: Text Analysis for All
Version: 0.1.0
Description: An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs. It is a versatile, general-purpose tool for analyzing textual data. 'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/massimoaria/tall, https://www.k-synth.com/tall/
BugReports: https://github.com/massimoaria/tall/issues
Depends: R (>= 3.5.0), shiny
Imports: graphics, dplyr (>= 1.1.0), shinyWidgets, shinydashboardPlus, chromote, later, promises, tidyr, purrr, plotly, stringr, Rcpp (>= 1.0.3), RSpectra, rlang, DT, openxlsx, visNetwork, igraph, udpipe, topicmodels, pdftools, textrank, strucchange, sparkline, tidygraph, readxl, readtext, jsonlite, fontawesome, ca, ldatuning, shinycssloaders, shinyjs, shinyFiles, readr, curl, pagedown, doParallel
LazyData: true
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2025-02-06 11:55:33 UTC; massimoaria
Author: Massimo Aria [aut, cre, cph] , Maria Spano [aut] , Luca D'Aniello [aut] , Corrado Cuccurullo [ctb] , Michelangelo Misuraca [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Repository: CRAN
Date/Publication: 2025-02-06 20:00:02 UTC

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New package oneinfl with initial version 1.0.0
Package: oneinfl
Title: Estimates OIPP and OIZTNB Regression Models
Version: 1.0.0
Author: Ryan T. Godwin [aut, cre]
Maintainer: Ryan T. Godwin <ryan.godwin@umanitoba.ca>
Description: Estimates one-inflated positive Poisson (OIPP) and one-inflated zero-truncated negative binomial (OIZTNB) regression models. A suite of ancillary statistical tools are also provided, including: estimation of positive Poisson (PP) and zero-truncated negative binomial (ZTNB) models; marginal effects and their standard errors; diagnostic likelihood ratio and Wald tests; plotting; predicted counts and expected responses; and random variate generation. The models and tools, as well as four applications, are shown in Godwin, R. T. (2024). "One-inflated zero-truncated count regression models" arXiv preprint <doi:10.48550/arXiv.2402.02272>.
License: GPL (>= 3)
Imports: graphics, stats
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-06 03:39:21 UTC; ryang
Repository: CRAN
Date/Publication: 2025-02-06 19:40:02 UTC

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New package jellyfisher with initial version 1.0.4
Package: jellyfisher
Title: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
Version: 1.0.4
Description: Generates interactive Jellyfish plots to visualize spatiotemporal tumor evolution by integrating sample and phylogenetic trees into a unified plot. This approach provides an intuitive way to analyze tumor heterogeneity and evolution over time and across anatomical locations. The Jellyfish plot visualization design was first introduced by Lahtinen, Lavikka, et al. (2023, <doi:10.1016/j.ccell.2023.04.017>). This package also supports visualizing ClonEvol results, a tool developed by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal evolution from multi-sample sequencing data. The 'clonevol' package is not available on CRAN but can be installed from its GitHub repository (<https://github.com/hdng/clonevol>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/HautaniemiLab/jellyfisher, https://hautaniemilab.github.io/jellyfisher/
BugReports: https://github.com/HautaniemiLab/jellyfisher/issues
Imports: htmlwidgets, dplyr, stringr
Suggests: knitr, rmarkdown, clonevol
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-05 12:40:36 UTC; klavikka
Author: Kari Lavikka [cph, aut, cre]
Maintainer: Kari Lavikka <kari.lavikka@helsinki.fi>
Repository: CRAN
Date/Publication: 2025-02-06 19:30:02 UTC

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New package EEAaq with initial version 1.0.0
Package: EEAaq
Title: Handle Air Quality Data from the European Environment Agency Data Portal
Version: 1.0.0
Description: This software downloads and manages air quality data from the European Environmental Agency (EEA) dataflow (<https://www.eea.europa.eu/data-and-maps/data/aqereporting-9>). See the web page <https://eeadmz1-downloads-webapp.azurewebsites.net/> for details on the EEA's Air Quality Download Service. The package allows dynamically mapping the stations, summarising and time aggregating the measurements and building spatial interpolation maps. See the web page <https://www.eea.europa.eu/en> for further information on EEA activities and history. Further details, as well as, an extended vignette of the main functions included in the package, are available at the GitHub web page dedicated to the project.
URL: https://github.com/PaoloMaranzano/EEAaq_R
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: arrow, curl, dplyr, ggplot2, ggpubr, gifski, grDevices, gstat, htmlwidgets, httr, leaflet, lubridate, raster, readr, sf, stats, tibble, tidyr, utils
Encoding: UTF-8
Suggests: knitr, rmarkdown, rvest, readxl, digest, gh, base64enc, stringr
NeedsCompilation: no
Packaged: 2025-02-05 14:43:18 UTC; paulm
Author: Paolo Maranzano [aut, cre, cph] , Riccardo Borgoni [aut, cph] , Samir Doghmi [aut, cph], Agostino Tassan Mazzocco [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-06 19:30:06 UTC

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New package DiscreteDLM with initial version 1.0.0
Package: DiscreteDLM
Title: Bayesian Distributed Lag Model Fitting for Binary and Count Response Data
Version: 1.0.0
Maintainer: Daniel Dempsey <daniel.dempsey0@gmail.com>
Description: Tools for fitting Bayesian Distributed Lag Models (DLMs) to longitudinal response data that is a count or binary. Count data is fit using negative binomial regression and binary is fit using quantile regression. The contribution of the lags are fit via b-splines. In addition, infers the predictor inclusion uncertainty. Multimomial models are not supported. Based on Dempsey and Wyse (2025) <doi:10.48550/arXiv.2403.03646>.
License: GPL-3
Encoding: UTF-8
Imports: statmod, BayesLogit, dlnm, splines, dplyr, ggplot2, ggridges, reshape2
URL: https://github.com/DanDempsey/DiscreteDLM
BugReports: https://github.com/DanDempsey/DiscreteDLM/issues
NeedsCompilation: yes
Packaged: 2025-02-06 01:49:36 UTC; bluff
Author: Daniel Dempsey [aut, cre] , Jason Wyse [ctb] , Christian E. Galarza [ctb] .), Victor H. Lachos [ctb] .)
Repository: CRAN
Date/Publication: 2025-02-06 19:40:10 UTC

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Package arcpullr updated to version 0.3.0 with previous version 0.2.9 dated 2024-03-11

Title: Pull Data from an 'ArcGIS REST' API
Description: Functions to efficiently query 'ArcGIS REST' APIs <https://developers.arcgis.com/rest/>. Both spatial and SQL queries can be used to retrieve data. Simple Feature (sf) objects are utilized to perform spatial queries. This package was neither produced nor is maintained by Esri.
Author: Paul Frater [aut, cre] , Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>

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Package sate updated to version 2.3.0 with previous version 2.2.1 dated 2024-12-05

Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials. Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the probability that a jury will find a defendant guilty given jurors' preferences for a guilty verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical trial conditions to conduct harmful error analysis. The relationship between individual jurors' verdict preferences and the probability that a jury returns a guilty verdict has been studied by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>, and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>

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Package easystats updated to version 0.7.4 with previous version 0.7.3 dated 2024-07-22

Title: Framework for Easy Statistical Modeling, Visualization, and Reporting
Description: A meta-package that installs and loads a set of packages from 'easystats' ecosystem in a single step. This collection of packages provide a unifying and consistent framework for statistical modeling, visualization, and reporting. Additionally, it provides articles targeted at instructors for teaching 'easystats', and a dashboard targeted at new R users for easily conducting statistical analysis by accessing summary results, model fit indices, and visualizations with minimal programming.
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Brenton M. Wiernik [aut] , Etienne Bacher [aut] , Remi Theriault [aut]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

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Package BayesianMCPMod updated to version 1.0.2 with previous version 1.0.1 dated 2024-04-05

Title: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod
Description: Bayesian MCPMod (Fleischer et al. (2022) <doi:10.1002/pst.2193>) is an innovative method that improves the traditional MCPMod by systematically incorporating historical data, such as previous placebo group data. This R package offers functions for simulating, analyzing, and evaluating Bayesian MCPMod trials with normally distributed endpoints. It enables the assessment of trial designs incorporating historical data across various true dose-response relationships and sample sizes. Robust mixture prior distributions, such as those derived with the Meta-Analytic-Predictive approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be specified for each dose group. Resulting mixture posterior distributions are used in the Bayesian Multiple Comparison Procedure and modeling steps. The modeling step also includes a weighted model averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>). Estimated dose-response relationships can be bootstrapped and visualiz [...truncated...]
Author: Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd], Stephan Wojciekowski [aut, cre], Lars Andersen [aut], Jonas Schick [ctb], Sebastian Bossert [aut]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>

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Package vistla updated to version 2.1.0 with previous version 2.0.4 dated 2025-01-25

Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs. In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits. Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>

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Package dibble updated to version 0.3.1 with previous version 0.3.0 dated 2024-06-23

Title: Dimensional Data Frames
Description: Provides a 'dibble' that implements data cubes (derived from 'dimensional tibble'), and allows broadcasting by dimensional names.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>

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New package watcher with initial version 0.1.0
Package: watcher
Title: Watch the File System for Changes
Version: 0.1.0
Description: R binding for 'libfswatch', a file system monitoring library. Watch files, or directories recursively, for changes in the background. Log activity, or run an R function every time a change event occurs.
License: MIT + file LICENSE
BugReports: https://github.com/r-lib/watcher/issues
URL: https://r-lib.github.io/watcher/, https://github.com/r-lib/watcher/
Encoding: UTF-8
SystemRequirements: 'libfswatch', or 'cmake' to compile from package sources
Depends: R (>= 3.6)
Imports: later, R6, rlang
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2025-02-05 21:55:22 UTC; cg334
Author: Charlie Gao [aut, cre] , Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Repository: CRAN
Date/Publication: 2025-02-06 14:20:02 UTC

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Package TreatmentPatterns updated to version 3.0.0 with previous version 2.7.0 dated 2024-11-27

Title: Analyzes Real-World Treatment Patterns of a Study Population of Interest
Description: Computes treatment patterns within a given cohort using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). As described in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] , Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>

Diff between TreatmentPatterns versions 2.7.0 dated 2024-11-27 and 3.0.0 dated 2025-02-06

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More information about TreatmentPatterns at CRAN
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Package SLOS updated to version 1.0.1 with previous version 1.0.0 dated 2025-01-20

Title: ICU Length of Stay Prediction and Efficiency Evaluation
Description: Provides tools for predicting ICU length of stay and assessing ICU efficiency. It is based on the methodologies proposed by Peres et al. (2022, 2023), which utilize data-driven approaches for modeling and validation, offering insights into ICU performance and patient outcomes. References: Peres et al. (2022)<https://pubmed.ncbi.nlm.nih.gov/35988701/>, Peres et al. (2023)<https://pubmed.ncbi.nlm.nih.gov/37922007/>. More information: <https://github.com/igor-peres/ICU-Length-of-Stay-Prediction>.
Author: Igor Peres [aut], Joana da Matta [cre]
Maintainer: Joana da Matta <joana.damatta02@gmail.com>

Diff between SLOS versions 1.0.0 dated 2025-01-20 and 1.0.1 dated 2025-02-06

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Package urlparse updated to version 0.2.0 with previous version 0.1.0 dated 2025-01-13

Title: Fast Simple URL Parser
Description: A fast and simple 'URL' parser package for 'R'. This package provides functions to parse 'URLs' into their components, such as scheme, user, password, host, port, path, query, and fragment.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

Diff between urlparse versions 0.1.0 dated 2025-01-13 and 0.2.0 dated 2025-02-06

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New package SynergyLMM with initial version 1.0.0
Package: SynergyLMM
Title: Statistical Framework for in Vivo Drug Combination Studies
Version: 1.0.0
Description: A framework for evaluating drug combination effects in preclinical in vivo studies. 'SynergyLMM' provides functions to analyze longitudinal tumor growth experiments using linear mixed-effects models, perform time-dependent analyses of synergy and antagonism, evaluate model diagnostics and performance, and assess both post-hoc and a priori statistical power. The calculation of drug combination synergy follows the statistical framework provided by Demidenko and Miller (2019, <doi:10.1371/journal.pone.0224137>). The implementation and analysis of linear mixed-effect models is based on the methods described by Pinheiro and Bates (2000, <doi:10.1007/b98882>), and Gałecki and Burzykowski (2013, <doi:10.1007/978-1-4614-3900-4>).
License: GPL (>= 3)
Encoding: UTF-8
Imports: magrittr (>= 2.0.3), rlang, dplyr (>= 1.1.4), ggplot2 (>= 3.5.1), cowplot (>= 1.1.3), nlme (>= 3.1-165), nlmeU, fBasics, car, MASS, performance, lattice, marginaleffects, clubSandwich
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 4.0)
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/RafRomB/SynergyLMM
BugReports: https://github.com/RafRomB/SynergyLMM/issues
NeedsCompilation: no
Packaged: 2025-02-05 15:05:35 UTC; rafrombec
Author: Rafael Romero-Becerra [aut, cre] , Zhi Zhao [ctb], Tero Aittokallio [ctb]
Maintainer: Rafael Romero-Becerra <r.r.becerra@medisin.uio.no>
Repository: CRAN
Date/Publication: 2025-02-06 13:30:02 UTC

More information about SynergyLMM at CRAN
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New package pseudoCure with initial version 1.0.0
Package: pseudoCure
Title: A Pseudo-Observations Approach for Analyzing Survival Data with a Cure Fraction
Version: 1.0.0
Date: 2025-02-05
Description: A collection of easy-to-use tools for regression analysis of survival data with a cure fraction proposed in Su et al. (2022) <doi:10.1177/09622802221108579>. The modeling framework is based on the Cox proportional hazards mixture cure model and the bounded cumulative hazard (promotion time cure) model. The pseudo-observations approach is utilized to assess covariate effects and embedded in the variable selection procedure.
License: GPL (>= 2)
Depends: R (>= 4.2.0)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2025-02-05 14:30:37 UTC; schiou
Encoding: UTF-8
Imports: Rcpp, MASS, ggplot2, ggpubr, rlang
Author: Sy Han Chiou [aut, cre], Chien-Lin Su [aut], Feng-Chang Lin [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@smu.edu>
Repository: CRAN
Date/Publication: 2025-02-06 13:10:02 UTC

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Package insight updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-09

Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut, ctb] , Indrajeet Patil [aut, ctb] , Philip Waggoner [aut, ctb] , Mattan S. Ben-Shachar [aut, ctb] , Brenton M. Wiernik [aut, ctb] , Vincent Arel-Bundock [aut, ctb] , Etienne Bacher [aut, ctb] , Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

Diff between insight versions 1.0.1 dated 2025-01-09 and 1.0.2 dated 2025-02-06

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Package Coxmos updated to version 1.1.1 with previous version 1.1.0 dated 2025-01-18

Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets. It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis, including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression, Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies, and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources for interpreting results. While references are available within the corresponding functions, key literature is mentioned below. Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>, Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>, Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>, Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev] , Sonia Tarazona Campos [ths], Ana Conesa Cegarra [ths], Kassu Mehari Beyene [ctb], Luis Meira Machado [ctb], Marta Sestelo [ctb], Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>

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Package bvhar updated to version 2.2.0 with previous version 2.1.2 dated 2024-10-11

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

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Package ggalign updated to version 0.1.0 with previous version 0.0.5 dated 2024-11-14

Title: A 'ggplot2' Extension for Consistent Axis Alignment
Description: A 'ggplot2' extension offers various tools for organizing and arranging plots. It is designed to consistently align a specific axis across multiple 'ggplot' objects, making it especially useful for plots requiring data order manipulation. A typical use case includes organizing combinations like a dendrogram and a heatmap.
Author: Yun Peng [aut, cre] , Shixiang Wang [aut] , Guangchuang Yu [aut]
Maintainer: Yun Peng <yunyunp96@163.com>

Diff between ggalign versions 0.0.5 dated 2024-11-14 and 0.1.0 dated 2025-02-06

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Package convertid updated to version 0.1.10 with previous version 0.1.8 dated 2023-11-29

Title: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre], Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>

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Package VGAMdata updated to version 1.1-13 with previous version 1.1-12 dated 2024-09-17

Title: Data Supporting the 'VGAM' Package
Description: Mainly data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology). This package now contains some old VGAM family functions which have been replaced by newer ones (often because they are now special cases).
Author: Thomas Yee [aut, cre, cph] , James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

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Package DrugExposureDiagnostics updated to version 1.1.1 with previous version 1.1.0 dated 2024-12-22

Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] , Edward Burn [aut] , Theresa Burkard [aut] , Yuchen Guo [ctb] , Marti Catala [ctb] , Mike Du [ctb] , Xintong Li [ctb] , Ross Williams [ctb] , Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>

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Package ChainLadder updated to version 0.2.20 with previous version 0.2.19 dated 2024-07-21

Title: Statistical Methods and Models for Claims Reserving in General Insurance
Description: Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.
Author: Markus Gesmann [aut, cre], Daniel Murphy [aut], Yanwei Zhang [aut], Alessandro Carrato [aut], Giuseppe Crupi [ctb], Christophe Dutang [ctb], Arnaud Lacoume [ctb], Arthur Charpentier [ctb], Mario Wuthrich [aut], Fabio Concina [aut], Eric Dal Moro [au [...truncated...]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

Diff between ChainLadder versions 0.2.19 dated 2024-07-21 and 0.2.20 dated 2025-02-06

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Package windex updated to version 2.1.0 with previous version 2.0.8 dated 2024-04-26

Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.
Author: Kevin Arbuckle [aut, cre], Amanda Minter [aut]
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>

Diff between windex versions 2.0.8 dated 2024-04-26 and 2.1.0 dated 2025-02-06

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Package sgs updated to version 0.3.4 with previous version 0.3.3 dated 2025-02-03

Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>

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Package netmeta updated to version 3.1-1 with previous version 3.1-0 dated 2025-02-04

Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis": - frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>; - additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>; - network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>; - rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>; - ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] , Ulrike Krahn [aut], Jochem Koenig [aut] , Orestis Efthimiou [aut] , Annabel Davies [aut] , Theodoros Papakonstantinou [aut] , Theodoros Evrenoglou [ctb] , Krzysztof Ciomek [ctb] , Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>

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Package dfr updated to version 0.1.4 with previous version 0.1.3 dated 2025-02-03

Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>

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Package CvmortalityMult updated to version 1.0.8 with previous version 1.0.7 dated 2024-08-31

Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models. References. Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>. Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>. Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>. Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>. Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>. Santolino, M. (2023) <doi:10.3390/risks11100170>.
Author: David Atance [aut, cre] , Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>

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Package bamdit updated to version 3.4.4 with previous version 3.4.3 dated 2024-11-22

Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>

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Package deductive updated to version 1.0.1 with previous version 1.0.0 dated 2021-03-29

Title: Data Correction and Imputation Using Deductive Methods
Description: Attempt to repair inconsistencies and missing values in data records by using information from valid values and validation rules restricting the data.
Author: Mark van der Loo [cre, aut] , Edwin de Jonge [aut] , Reijer Idema [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package RcppArmadillo updated to version 14.2.3-1 with previous version 14.2.2-1 dated 2024-12-06

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

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Package SPAS updated to version 2025.2.1 with previous version 2024.1.31 dated 2024-01-25

Title: Stratified-Petersen Analysis System
Description: The Stratified-Petersen Analysis System (SPAS) is designed to estimate abundance in two-sample capture-recapture experiments where the capture and recaptures are stratified. This is a generalization of the simple Lincoln-Petersen estimator. Strata may be defined in time or in space or both, and the s strata in which marking takes place may differ from the t strata in which recoveries take place. When s=t, SPAS reduces to the method described by Darroch (1961) <doi:10.2307/2332748>. When s<t, SPAS implements the methods described in Plante, Rivest, and Tremblay (1988) <doi:10.2307/2533994>. Schwarz and Taylor (1998) <doi:10.1139/f97-238> describe the use of SPAS in estimating return of salmon stratified by time and geography. A related package, BTSPAS, deals with temporal stratification where a spline is used to model the distribution of the population over time as it passes the second capture location. This is the R-version of the (now obsolete) standalone Windows [...truncated...]
Author: Carl James Schwarz [aut, cre]
Maintainer: Carl James Schwarz <cschwarz.stat.sfu.ca@gmail.com>

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Package cppcontainers (with last version 1.0.4) was removed from CRAN

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

2025-01-15 1.0.4
2025-01-09 1.0.3
2024-11-14 1.0.1
2024-11-13 1.0.0

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Wed, 05 Feb 2025

Package gemini.R updated to version 0.8.0 with previous version 0.6.1 dated 2024-12-10

Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API, enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R. This package facilitates seamless integration with Google Gemini, allowing for advanced language processing, text generation, and other AI-driven capabilities within the R environment. For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] , Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>

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Package leidenbase updated to version 0.1.32 with previous version 0.1.31 dated 2024-09-25

Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition (). It runs the equivalent of the 'leidenalg' find_partition() function, which is given in the 'leidenalg' distribution file 'leiden/src/functions.py'. This package includes the required source code files from the official 'leidenalg' distribution and functions from the R 'igraph' package. The 'leidenalg' distribution is available from <https://github.com/vtraag/leidenalg/> and the R 'igraph' package is available from <https://igraph.org/r/>. The Leiden algorithm is described in the article by Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>. Leidenbase includes code from the packages: igraph version 0.9.8 with license GPL (>= 2), leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre], Vincent Traag [ctb], Gabor Csardi [ctb], Tamas Nepusz [ctb], Szabolcs Horvat [ctb], Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>

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Package Lifertable updated to version 0.1.0 with previous version 0.0.1 dated 2024-02-29

Title: Life and Fertility Tables Specially for Insects
Description: Life and Fertility Tables are appropriate to study the dynamics of arthropods populations. This package provides utilities for constructing Life Tables and Fertility Tables, related demographic parameters, and some simple graphs of interest. It also offers functions to transform the obtained data into a known format for better manipulation. This document is based on the article by Maia, Luiz, and Campanhola "Statistical Inference on Associated Fertility Life Table Parameters Using Jackknife Technique Computational Aspects" (April 2000, Journal of Economic Entomology, Volume 93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.
Author: Carlos Abimael Sarmiento Sanchez [aut, cre], Lauro Soto Rojas [ctb], Alejandro Corona Ambriz [ctb], Gabriel Arcangel Rodriguez Yam [ctb], Yolanda Franco Islas [ctb], Noe Ramirez Negrete [ctb]
Maintainer: Carlos Abimael Sarmiento Sanchez <cass9918@hotmail.com>

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Package ggeffects updated to version 2.2.0 with previous version 2.1.0 dated 2025-01-20

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] , Frederik Aust [ctb] , Sam Crawley [ctb] , Mattan S. Ben-Shachar [ctb] , Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

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Package signnet updated to version 1.0.5 with previous version 1.0.4 dated 2024-01-08

Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes several measures for structural balance as introduced by Cartwright and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various centrality indices, and projections of signed two-mode networks introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>

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Package rstanemax updated to version 0.1.8 with previous version 0.1.7 dated 2024-12-06

Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] , Danielle Navarro [aut] , Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>

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Package tinyplot updated to version 0.3.0 with previous version 0.2.1 dated 2024-08-26

Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support for automatic legends, facets, themes, and various other enhancements.
Author: Grant McDermott [aut, cre] , Vincent Arel-Bundock [aut] , Achim Zeileis [aut] , Etienne Bacher [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>

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Package geomorph updated to version 4.0.10 with previous version 4.0.9 dated 2024-11-15

Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Author: Dean Adams [aut, cre], Michael Collyer [aut], Antigoni Kaliontzopoulou [aut], Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>

Diff between geomorph versions 4.0.9 dated 2024-11-15 and 4.0.10 dated 2025-02-05

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New package WpProj with initial version 0.2.3
Package: WpProj
Title: Linear p-Wasserstein Projections
Version: 0.2.3
Date: 2025-02-03
Description: Performs Wasserstein projections from the predictive distributions of any model into the space of predictive distributions of linear models. We utilize L1 penalties to also reduce the complexity of the model space. This package employs the methods as described in Dunipace, Eric and Lorenzo Trippa (2020) <doi:10.48550/arXiv.2012.09999>.
License: GPL (== 3.0)
Depends: R (>= 4.0)
Imports: approxOT (>= 1.2), glmnet, oem, Rcpp, rlang, ROI, ROI.plugin.ecos, ROI.plugin.lpsolve, Matrix, rqPen, quantreg, doParallel, foreach, doRNG, dplyr, stats, magrittr, methods, slam, lifecycle
LinkingTo: approxOT (>= 1.2), BH, Rcpp (>= 1.0.0), RcppCGAL, RcppEigen, RcppProgress, RSpectra
Suggests: ggplot2, ggsci, ggridges, testthat (>= 2.1.0), transport, Rmosek, spelling, ECOSolveR
URL: https://github.com/ericdunipace/WpProj
BugReports: https://github.com/ericdunipace/WpProj/issues
SystemRequirements: C++17
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2025-02-03 23:43:13 UTC; eifer
Author: Eric Dunipace [aut, cre] , Clemens Schmid [ctb] , Espen Bernton [ctb] , Mathieu Gerber [ctb] , Pierre Jacob [ctb] , Bin Dai [ctb] , Jared Huling [ctb] , Yixuan Qiu [ctb] , Dominic Schuhmacher [ctb] , Nicolas Bonneel [ctb]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Repository: CRAN
Date/Publication: 2025-02-05 18:20:02 UTC

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New package SPIChanges with initial version 0.1.0
Package: SPIChanges
Title: Improves the Interpretation of the Standardized Precipitation Index Under Changing Climate Conditions
Version: 0.1.0
Description: Improves the interpretation of the Standardized Precipitation Index under changing climate conditions. The package uses the nonstationary approach proposed in Blain et al. (2022) <doi:10.1002/joc.7550> to detect trends in rainfall quantities and to quantify the effect of such trends on the probability of a drought event occurring.
License: MIT + file LICENSE
URL: https://github.com/gabrielblain/SPIChanges
BugReports: https://github.com/gabrielblain/SPIChanges/issues
Depends: R (>= 2.10)
Imports: gamlss, gamlss.dist, lubridate, MuMIn, rlang, spsUtil, stats, brglm2, zoo
Suggests: archive, curl, doParallel, dplyr, foreach, ggplot2, grid, knitr, ncdf4, patchwork, RColorBrewer, rmarkdown, roxyglobals, sf, purrr, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-04 18:56:44 UTC; Gabriel
Author: Gabriel Constantino Blain [aut, cre] , Graciela R. Sobierajski [aut] , Leticia L. Martins [aut] , Adam H. Sparks [aut]
Maintainer: Gabriel Constantino Blain <gabriel.blain@sp.gov.br>
Repository: CRAN
Date/Publication: 2025-02-05 18:10:08 UTC

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New package matriz with initial version 1.0.1
Package: matriz
Title: Literature Matrix Synthesis Tools for Epidemiology and Health Science Research
Version: 1.0.1
Maintainer: JP Monteagudo <jpmonteagudo2014@gmail.com>
Description: An easy-to-use workflow that provides tools to create, update and fill literature matrices commonly used in research, specifically epidemiology and health sciences research. The project is born out of need as an easy–to–use tool for my research methods classes.
License: AGPL (>= 3)
Encoding: UTF-8
URL: https://github.com/jpmonteagudo28/matriz
BugReports: https://github.com/jpmonteagudo28/matriz/issues
Suggests: testthat (>= 3.0.0)
Imports: dplyr, readr, readxl, rlang, stringr, writexl
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-02-04 21:21:53 UTC; jpmonteagudo
Author: JP Monteagudo [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-05 18:30:01 UTC

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New package Horsekicks with initial version 1.0.2
Package: Horsekicks
Title: Provide Extensions to the Prussian Army Death by Horsekick Data
Version: 1.0.2
Author: Bill Venables [aut, cre], Antony Unwin [ctb]
Maintainer: Bill Venables <bill.venables@gmail.com>
Description: We provide extensions to the classical dataset "Example 4: Death by the kick of a horse in the Prussian Army" first used by Ladislaus von Bortkeiwicz in his treatise on the Poisson distribution "Das Gesetz der kleinen Zahlen", <DOI:10.1017/S0370164600019453>. As well as an extended time series for the horse-kick death data, we also provide, in parallel, deaths by falling from a horse and by drowning.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown, ggplot2, dplyr, tidyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-05 00:12:42 UTC; Bill
Repository: CRAN
Date/Publication: 2025-02-05 18:40:02 UTC

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Package espadon updated to version 1.10.0 with previous version 1.9.0 dated 2024-11-25

Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] , Jean-Marc Fontbonne [aut] , Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>

Diff between espadon versions 1.9.0 dated 2024-11-25 and 1.10.0 dated 2025-02-05

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New package CircNNTSRSymmetric with initial version 0.1.0
Package: CircNNTSRSymmetric
Title: Circular Data using Symmetric NNTS Models
Version: 0.1.0
Description: The statistical analysis of circular data using distributions based on symmetric Nonnegative Trigonometric Sums (NNTS). It includes functions to perform empirical analysis and estimate the parameters of density functions. Fernandez-Duran, J.J. and Gregorio-Dominguez, M.M. (2025), "Multimodal Symmetric Circular Distributions Based on Nonnegative Trigonometric Sums and a Likelihood Ratio Test for Reflective Symmetry", <doi:10.48550/arXiv.2412.19501>.
Depends: stats, CircNNTSR
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-04 19:36:04 UTC; mercedesgregorio
Author: Juan Jose Fernandez-Duran [aut], Maria Mercedes Gregorio-Dominguez [aut, cre]
Maintainer: Maria Mercedes Gregorio-Dominguez <mercedes@itam.mx>
Repository: CRAN
Date/Publication: 2025-02-05 18:20:06 UTC

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Package BKT updated to version 0.1.0 with previous version 0.0.1 dated 2025-01-30

Title: Bayesian Knowledge Tracing Model
Description: Fitting, cross-validating, and predicting with Bayesian Knowledge Tracing (BKT) models. It is designed for analyzing educational datasets to trace student knowledge over time. The package includes functions for fitting BKT models, evaluating their performance using various metrics, and making predictions on new data. It provides the similar functionality as the Python package pyBKT authored by Zachary A. Pardos (zp@berkeley.edu) at <https://github.com/CAHLR/pyBKT>.
Author: Yuhao Yuan [aut, cre], Biying Zhou [aut], Feng Ji [aut]
Maintainer: Yuhao Yuan <yuanyuhaoapply@163.com>

Diff between BKT versions 0.0.1 dated 2025-01-30 and 0.1.0 dated 2025-02-05

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New package BayesAT with initial version 0.1.0
Package: BayesAT
Title: Bayesian Adaptive Trial
Version: 0.1.0
Maintainer: Yuan Zhong <aqua.zhong@gmail.com>
Description: Bayesian adaptive trial algorithm implements multiple-stage interim analysis. Package includes data generating function, and Bayesian hypothesis testing function.
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-04 20:11:36 UTC; adamzhong
Author: Yuan Zhong [aut, cre], Zeynep Baskurt [aut], Wei Xu [aut]
Repository: CRAN
Date/Publication: 2025-02-05 18:20:09 UTC

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Package ReturnCurves updated to version 1.0.1 with previous version 1.0 dated 2024-07-04

Title: Estimation of Return Curves
Description: Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
Author: Lidia Andre [aut, cre], Callum Murphy-Barltrop [aut]
Maintainer: Lidia Andre <lidia.andre@unamur.be>

Diff between ReturnCurves versions 1.0 dated 2024-07-04 and 1.0.1 dated 2025-02-05

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Package purrr updated to version 1.0.4 with previous version 1.0.2 dated 2023-08-10

Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Hadley Wickham [aut, cre] , Lionel Henry [aut], Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between purrr versions 1.0.2 dated 2023-08-10 and 1.0.4 dated 2025-02-05

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Package paleobuddy updated to version 1.1.0 with previous version 1.0.0 dated 2021-12-21

Title: Simulating Diversification Dynamics
Description: Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
Author: Bruno do Rosario Petrucci [aut, cre] , Matheus Januario [aut] , Tiago Quental [aut]
Maintainer: Bruno do Rosario Petrucci <petrucci@iastate.edu>

Diff between paleobuddy versions 1.0.0 dated 2021-12-21 and 1.1.0 dated 2025-02-05

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Package crew.aws.batch updated to version 0.0.8 with previous version 0.0.7 dated 2024-11-17

Title: A Crew Launcher Plugin for AWS Batch
Description: In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.aws.batch' package extends the 'mirai'-powered 'crew' package with a worker launcher plugin for AWS Batch. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre] , Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>

Diff between crew.aws.batch versions 0.0.7 dated 2024-11-17 and 0.0.8 dated 2025-02-05

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Package twoStageDesignTMLE updated to version 1.0.1.2 with previous version 1.0 dated 2024-09-05

Title: Targeted Maximum Likelihood Estimation for Two-Stage Study Design
Description: An inverse probability of censoring weighted (IPCW) targeted maximum likelihood estimator (TMLE) for evaluating a marginal point treatment effect from data where some variables were collected on only a subset of participants using a two-stage design (or marginal mean outcome for a single arm study). A TMLE for conditional parameters defined by a marginal structural model (MSM) is also available.
Author: Susan Gruber [aut, cre], Mark van der Laan [aut]
Maintainer: Susan Gruber <sgruber@TLrevolution.com>

Diff between twoStageDesignTMLE versions 1.0 dated 2024-09-05 and 1.0.1.2 dated 2025-02-05

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Package transfR updated to version 1.1.0 with previous version 1.0.11 dated 2023-10-02

Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring streamflow measurements from gauged to ungauged catchments. Inverse modelling enables to estimate net rainfall from streamflow measurements following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>. Resulting net rainfall is then estimated on the ungauged catchments by spatial interpolation in order to finally simulate streamflow following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] , Christophe Cudennec [ths] , Tom Loree [ctb], Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>

Diff between transfR versions 1.0.11 dated 2023-10-02 and 1.1.0 dated 2025-02-05

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Package PlotFTIR updated to version 1.1.0 with previous version 1.0.0 dated 2024-11-13

Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions. L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] , Ulrich Makanda [trl] , His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>

Diff between PlotFTIR versions 1.0.0 dated 2024-11-13 and 1.1.0 dated 2025-02-05

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Package NMsim updated to version 0.1.6 with previous version 0.1.5 dated 2024-11-14

Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre], Brian Reilly [ctb], Sanaya Shroff [ctb], Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>

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Package GaussianHMM1d updated to version 1.1.2 with previous version 1.1.1 dated 2023-07-08

Title: Inference, Goodness-of-Fit and Forecast for Univariate Gaussian Hidden Markov Models
Description: Inference, goodness-of-fit test, and prediction densities and intervals for univariate Gaussian Hidden Markov Models (HMM). The goodness-of-fit is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Chapter 10.2 of Remillard (2013) <doi:10.1201/b14285>.
Author: Bouchra R. Nasri [aut, cre, cph], Bruno N Remillard [aut, ctb, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>

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Package crew.cluster updated to version 0.3.4 with previous version 0.3.3 dated 2024-11-17

Title: Crew Launcher Plugins for Traditional High-Performance Computing Clusters
Description: In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre] , Michael Gilbert Levin [aut] , Brendan Furneaux [aut] , Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>

Diff between crew.cluster versions 0.3.3 dated 2024-11-17 and 0.3.4 dated 2025-02-05

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Package bspline updated to version 2.3.0 with previous version 2.2.2 dated 2024-07-02

Title: B-Spline Interpolation and Regression
Description: Build and use B-splines for interpolation and regression. In case of regression, equality constraints as well as monotonicity and/or positivity of B-spline weights can be imposed. Moreover, knot positions (not only spline weights) can be part of optimized parameters too. For this end, 'bspline' is able to calculate Jacobian of basis vectors as function of knot positions. User is provided with functions calculating spline values at arbitrary points. These functions can be differentiated and integrated to obtain B-splines calculating derivatives/integrals at any point. B-splines of this package can simultaneously operate on a series of curves sharing the same set of knots. 'bspline' is written with concern about computing performance that's why the basis and Jacobian calculation is implemented in C++. The rest is implemented in R but without notable impact on computing speed.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>

Diff between bspline versions 2.2.2 dated 2024-07-02 and 2.3.0 dated 2025-02-05

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Package sessioninfo updated to version 1.2.3 with previous version 1.2.2 dated 2021-12-06

Title: R Session Information
Description: Query and print information about the current R session. It is similar to 'utils::sessionInfo()', but includes more information about packages, and where they were installed from.
Author: Gabor Csardi [cre], Hadley Wickham [aut], Winston Chang [aut], Robert Flight [aut], Kirill Mueller [aut], Jim Hester [aut], R Core team [ctb], Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

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Package GWnnegPCA updated to version 0.0.5 with previous version 0.0.4 dated 2020-11-18

Title: Geographically Weighted Non-Negative Principal Components Analysis
Description: Implements a geographically weighted non-negative principal components analysis, which consists of the fusion of geographically weighted and sparse non-negative principal components analyses <doi:10.17608/k6.auckland.9850826.v1>.
Author: Narumasa Tsutsumida [aut, cre]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>

Diff between GWnnegPCA versions 0.0.4 dated 2020-11-18 and 0.0.5 dated 2025-02-05

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Package fishmethods updated to version 1.13-1 with previous version 1.12-1 dated 2023-04-27

Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson [aut, cre]
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>

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Package DAISIE updated to version 4.5.0 with previous version 4.4.1 dated 2023-10-21

Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Author: Rampal S. Etienne [aut, cre] , Luis Valente [aut] , Albert B. Phillimore [aut] , Bart Haegeman [aut] , Joshua W. Lambert [aut] , Pedro Santos Neves [aut] , Shu Xie [aut] , Richel J.C. Bilderbeek [aut] , Hanno Hildenbrandt [aut] , Torsten Hauffe [ctb] [...truncated...]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

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Package ympes updated to version 1.8.0 with previous version 1.7.0 dated 2024-11-27

Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both for interactive use and for inclusion within other packages. These include functions for minimal input assertions, visualising colour palettes, quoting user input, searching rows of a data frame and capturing string tokens.
Author: Tim Taylor [aut, cre, cph] , R Core Team [cph] , Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package PhenotypeR updated to version 0.1.2 with previous version 0.1.1 dated 2025-01-17

Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] , Marti Catala [aut] , Xihang Chen [aut] , Marta Alcalde-Herraiz [aut] , Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

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Package HVT updated to version 25.2.2 with previous version 25.2.1 dated 2025-02-04

Title: Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut], Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>

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Package grates updated to version 1.4.1 with previous version 1.4.0 dated 2025-01-17

Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating grouped date classes. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package boiwsa updated to version 1.1.3 with previous version 1.1.2 dated 2024-09-23

Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment of weekly data. The package provides a user-friendly interface for computing seasonally adjusted estimates of weekly data and includes functions for the creation of country-specific prior adjustment variables, as well as diagnostic tools to assess the quality of the adjustments. The method is described in more detail in Ginker (2023) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph] , Jon Lachman [ctb]
Maintainer: Tim Ginker <tim.ginker@gmail.com>

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Package aifeducation updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-28

Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial Intelligence (AI) is a challenging task. Relevant data is often only available in handwritten forms, or the use of data is restricted by privacy policies. This often leads to small data sets. Furthermore, in the educational and social sciences, data is often unbalanced in terms of frequencies. To support educators as well as educational and social researchers in using the potentials of AI for their work, this package provides a unified interface for neural nets in 'PyTorch' to deal with natural language problems. In addition, the package ships with a shiny app, providing a graphical user interface. This allows the usage of AI for people without skills in writing python/R scripts. The tools integrate existing mathematical and statistical methods for dealing with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al. (2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] , Tykhonova Yuliia [aut] , Pargmann Julia [ctb] , Leube Anna [ctb] , Riebenbauer Elisabeth [ctb] , Rebmann Karin [ctb], Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>

Diff between aifeducation versions 1.0.1 dated 2025-01-28 and 1.0.2 dated 2025-02-05

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New package SurvMetrics with initial version 0.5.1
Package: SurvMetrics
Title: Predictive Evaluation Metrics in Survival Analysis
Version: 0.5.1
Date: 2025-01-16
Author: Hanpu Zhou [aut], Xuewei Cheng [aut], Sizheng Wang [aut], Yi Zou [aut], Hong Wang [aut, cre]
Maintainer: Hong Wang <wh@csu.edu.cn>
Description: An implementation of popular evaluation metrics that are commonly used in survival prediction including Concordance Index, Brier Score, Integrated Brier Score, Integrated Square Error, Integrated Absolute Error and Mean Absolute Error. For a detailed information, see (Ishwaran H, Kogalur UB, Blackstone EH and Lauer MS (2008) <doi:10.1214/08-AOAS169>) , (Moradian H, Larocque D and Bellavance F (2017) <doi:10.1007/s10985-016-9372-1>), (Hanpu Zhou, Hong Wang, Sizheng Wang and Yi Zou (2023) <doi:10.32614/rj-2023-009>) for different evaluation metrics.
License: GPL (>= 2)
Encoding: UTF-8
Imports: survminer, stats, survival, MASS,pec
Suggests: knitr, rmarkdown, caret, ggplot2, ggpubr, randomForestSRC, testthat (>= 3.0.0)
NeedsCompilation: no
URL: https://github.com/whcsu/SurvMetrics
Packaged: 2025-02-04 12:39:33 UTC; flood
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-05 11:50:28 UTC

More information about SurvMetrics at CRAN
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Package super updated to version 0.0.5 with previous version 0.0.4 dated 2024-12-16

Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the 'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] , Jim Hester [aut] , Jennifer Bryan [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package statgenIBD updated to version 1.0.8 with previous version 1.0.7 dated 2024-02-02

Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (<https://www.jstor.org/stable/29713>) and Huang (<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Author: Martin Boer [aut] , Bart-Jan van Rossum [aut, cre] , Wenhao Li [ctb] , Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Permanent link

Package SmallCountRounding updated to version 1.2.0 with previous version 1.1.0 dated 2024-12-09

Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre], Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>

Diff between SmallCountRounding versions 1.1.0 dated 2024-12-09 and 1.2.0 dated 2025-02-05

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Package shinyscholar updated to version 0.2.5 with previous version 0.2.4 dated 2025-01-29

Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph], Tim Lucas [aut] , Jamie M. Kass [ctb], Gonzalo E. Pinilla-Buitrago [ctb], Andrea Paz [ctb], Bethany A. Johnson [ctb], Valentina Grisales-Betancur [ctb], Dean Attali [ctb], Matthew E. Aiello-Lammens [ctb], Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>

Diff between shinyscholar versions 0.2.4 dated 2025-01-29 and 0.2.5 dated 2025-02-05

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More information about shinyscholar at CRAN
Permanent link

Package scplot updated to version 0.5.0 with previous version 0.4.0 dated 2024-06-29

Title: Plot Function for Single-Case Data Frames
Description: Add-on for the 'scan' package that creates plots from single-case data frames ('scdf'). It includes functions for styling single-case plots, adding phase-based lines to indicate various statistical parameters, and predefined themes for presentations and publications. More information and in depth examples can be found in the online book "Analyzing Single-Case Data with R and 'scan" Jürgen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>

Diff between scplot versions 0.4.0 dated 2024-06-29 and 0.5.0 dated 2025-02-05

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More information about scplot at CRAN
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Package scan updated to version 0.62.0 with previous version 0.61.0 dated 2024-07-01

Title: Single-Case Data Analyses for Single and Multiple Baseline Designs
Description: A collection of procedures for analysing, visualising, and managing single-case data. These include piecewise linear regression models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u', 'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions support outlier detection, handling missing values, scaling, and custom transformations. An export function helps to generate html, word, and latex tables in a publication friendly style. More details can be found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] , Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>

Diff between scan versions 0.61.0 dated 2024-07-01 and 0.62.0 dated 2025-02-05

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Package netrankr updated to version 1.2.4 with previous version 1.2.3 dated 2023-12-19

Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] , Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>

Diff between netrankr versions 1.2.3 dated 2023-12-19 and 1.2.4 dated 2025-02-05

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More information about netrankr at CRAN
Permanent link

Package modelbased updated to version 0.9.0 with previous version 0.8.9 dated 2024-10-26

Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models, used in the computation of marginal means, contrast analysis and predictions. For a list of supported models, see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] , Daniel Luedecke [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package archive updated to version 1.1.11 with previous version 1.1.10 dated 2024-11-08

Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] , Gabor Csardi [aut, cre], Ondrej Holy [cph] , RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between archive versions 1.1.10 dated 2024-11-08 and 1.1.11 dated 2025-02-05

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Package pqrBayes updated to version 1.0.5 with previous version 1.0.4 dated 2025-01-24

Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity, outliers and heavy-tailed distributions in the response variable. In addition, it can flexibly model dynamic patterns of regression coefficients through nonparametric varying coefficient functions. In this package, we have implemented the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient Bayesian shrinkage estimation, variable selection and statistical inference. In particular, valid Bayesian inferences on sparse quantile varying coefficient functions can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed and alternative models can be efficiently performed by using the package.
Author: Kun Fan [aut], Cen Wu [aut, cre], Jie Ren [aut], Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>

Diff between pqrBayes versions 1.0.4 dated 2025-01-24 and 1.0.5 dated 2025-02-05

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Package nanostringr updated to version 0.5.0 with previous version 0.4.2 dated 2024-06-11

Title: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are used to determine which samples passed or failed QC. Gene expression should first be normalized to housekeeping genes, before a reference-based approach is used to adjust for batch effects. Raw NanoString data can be imported in the form of Reporter Code Count (RCC) files.
Author: Derek Chiu [aut, cre] , Aline Talhouk [aut] , Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

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Package jskm updated to version 0.5.10 with previous version 0.5.8 dated 2025-01-08

Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] , yoonkyoung Chun [aut], Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jskm versions 0.5.8 dated 2025-01-08 and 0.5.10 dated 2025-02-05

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Package correctR updated to version 0.3.1 with previous version 0.2.1 dated 2024-03-13

Title: Corrected Test Statistics for Comparing Machine Learning Models on Correlated Samples
Description: Calculate a set of corrected test statistics for cases when samples are not independent, such as when classification accuracy values are obtained over resamples or through k-fold cross-validation, as proposed by Nadeau and Bengio (2003) <doi:10.1023/A:1024068626366> and presented in Bouckaert and Frank (2004) <doi:10.1007/978-3-540-24775-3_3>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>

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New package tergo with initial version 0.1.8
Package: tergo
Title: Style Your Code Fast
Version: 0.1.8
Description: Provides a set of functions that allow users for styling their R code according to the 'tidyverse' style guide. The package uses a native Rust implementation to ensure the highest performance. Learn more about 'tergo' at <https://rtergo.pagacz.io>.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: Cargo (Rust's package manager), rustc
NeedsCompilation: yes
Biarch: true
Depends: R (>= 4.1.0)
Suggests: rextendr (== 0.3.1), roxygen2, rstudioapi (>= 0.7), devtools, pkgdown, desc, knitr, rmarkdown
URL: https://rtergo.pagacz.io, https://github.com/kpagacz/tergo
BugReports: https://github.com/kpagacz/tergo/issues
VignetteBuilder: knitr
Packaged: 2025-02-04 17:13:56 UTC; kpagacz
Author: Konrad Pagacz [aut, cre], Maciej Nasinski [ctb], The authors of the dependency Rust crates [ctb]
Maintainer: Konrad Pagacz <konrad.pagacz@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-05 09:20:02 UTC

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Package diceR updated to version 3.0.0 with previous version 2.2.0 dated 2024-01-22

Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble clustering framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>. Results from a diverse set of algorithms are pooled together using methods such as majority voting, K-Modes, LinkCluE, and CSPA. There are options to compare cluster assignments across algorithms using internal and external indices, visualizations such as heatmaps, and significance testing for the existence of clusters.
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

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Package EpiNow2 updated to version 1.7.0 with previous version 1.6.1 dated 2024-10-31

Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
Description: Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.
Author: Sam Abbott [aut] , Joel Hellewell [aut] , Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut] , Michael DeWitt [aut] , James M. Azam [aut] , Robin Thompson [ctb], Sophie Meakin [ctb], James Munday [ctb], Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>

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Package ClassComparison updated to version 3.3.5 with previous version 3.3.2 dated 2024-08-17

Title: Classes and Methods for "Class Comparison" Problems on Microarrays
Description: Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Tue, 04 Feb 2025

Package AhoCorasickTrie updated to version 0.1.3 with previous version 0.1.2 dated 2020-09-29

Title: Fast Searching for Multiple Keywords in Multiple Texts
Description: Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.
Author: Matt Chambers [aut, cre], Tomas Petricek [aut, cph], Vanderbilt University [cph]
Maintainer: Matt Chambers <matt.chambers42@gmail.com>

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Package Umpire updated to version 2.0.11 with previous version 2.0.10 dated 2020-11-10

Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes [aut, cre], Jiexin Zhang [aut], Caitlin E. Coombes [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package multilevLCA updated to version 2.0.0 with previous version 1.5.2 dated 2024-10-12

Title: Estimates and Plots Single-Level and Multilevel Latent Class Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <doi:10.48550/arXiv.2305.07276>.
Author: Roberto Di Mari [aut, cre], Johan Lyrvall [aut], Zsuzsa Bakk [ctb], Jennifer Oser [ctb], Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>

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Package metadat updated to version 1.4-0 with previous version 1.2-0 dated 2022-04-06

Title: Meta-Analysis Datasets
Description: A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Author: Wolfgang Viechtbauer [aut, cre] , Thomas White [aut] , Daniel Noble [aut] , Alistair Senior [aut] , W. Kyle Hamilton [aut] , Guido Schwarzer [dtc]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>

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Package posologyr updated to version 1.2.8 with previous version 1.2.7 dated 2024-09-13

Title: Individual Dose Optimization using Population Pharmacokinetics
Description: Personalize drug regimens using individual pharmacokinetic (PK) and pharmacokinetic-pharmacodynamic (PK-PD) profiles. By combining therapeutic drug monitoring (TDM) data with a population model, 'posologyr' offers accurate posterior estimates and helps compute optimal individualized dosing regimens. The empirical Bayes estimates are computed following the method described by Kang et al. (2012) <doi:10.4196/kjpp.2012.16.2.97>.
Author: Cyril Leven [aut, cre, cph] , Matthew Fidler [ctb] , Emmanuelle Comets [ctb], Audrey Lavenu [ctb], Marc Lavielle [ctb]
Maintainer: Cyril Leven <cyril.leven@chu-brest.fr>

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Package plotthis updated to version 0.5.1 with previous version 0.5.0 dated 2025-01-09

Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly. It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects. It is particularly useful for creating complex plots with multiple layers, facets, and annotations. It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees. The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem. The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>

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Package MixtureMissing updated to version 3.0.4 with previous version 3.0.3 dated 2024-10-15

Title: Robust and Flexible Model-Based Clustering for Data Sets with Missing Values at Random
Description: Implementations of various robust and flexible model-based clustering methods for data sets with missing values at random. Two main models are: Multivariate Contaminated Normal Mixture (MCNM, Tong and Tortora, 2022, <doi:10.1007/s11634-021-00476-1>) and Multivariate Generalized Hyperbolic Mixture (MGHM, Wei et al., 2019, <doi:10.1016/j.csda.2018.08.016>). Mixtures via some special or limiting cases of the multivariate generalized hyperbolic distribution are also included: Normal-Inverse Gaussian, Symmetric Normal-Inverse Gaussian, Skew-Cauchy, Cauchy, Skew-t, Student's t, Normal, Symmetric Generalized Hyperbolic, Hyperbolic Univariate Marginals, Hyperbolic, and Symmetric Hyperbolic.
Author: Hung Tong [aut, cre], Cristina Tortora [aut, ths, dgs]
Maintainer: Hung Tong <hungtongmx@gmail.com>

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Package gmoTree updated to version 1.4.1 with previous version 1.4.0 dated 2025-02-04

Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments. Import 'oTree' data and clean them by using functions that handle messy data, dropouts, and other problematic cases. Create IDs, calculate the time, transfer variables between app data frames, and delete sensitive information. Review your experimental data prior to running the experiment and automatically generate a detailed summary of the variables used in your 'oTree' code. Information on 'oTree' is found in Chen, D. L., Schonger, M., & Wickens, C. (2016) <doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>

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Package constrainedKriging updated to version 0.2-11 with previous version 0.2-10 dated 2025-02-01

Title: Constrained, Covariance-Matching Constrained and Universal Point or Block Kriging
Description: Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target value [...truncated...]
Author: Christoph Hofer [aut], Andreas Papritz [ctb, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>

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Package QuadratiK updated to version 1.1.3 with previous version 1.1.2 dated 2024-10-29

Title: Collection of Methods Constructed using Kernel-Based Quadratic Distances
Description: It includes test for multivariate normality, test for uniformity on the d-dimensional Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson kernel-based density and clustering algorithm for spherical data. For more information see Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024) <doi:10.48550/arXiv.2402.02290> Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>, Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>, and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Author: Giovanni Saraceno [aut, cre] , Marianthi Markatou [aut], Raktim Mukhopadhyay [aut], Mojgan Golzy [aut], Hingee Kassel [rev], Emi Tanaka [rev]
Maintainer: Giovanni Saraceno <giovanni.saraceno@unipd.it>

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Package metasnf updated to version 2.0.0 with previous version 1.1.1 dated 2024-11-08

Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre], Xiaoqiao Xu [aut], Prajkta Kallurkar [aut], Ana Patricia Balbon [aut], Maria T Secara [aut], Adam Taback [aut], Denise Sabac [aut], Nicholas Chan [aut], Shihao Ma [aut], Bo Wang [aut], Daniel Felsky [aut], Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>

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More information about metasnf at CRAN
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Package FIESTA updated to version 3.7.0 with previous version 3.6.4 dated 2024-06-07

Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut], Gretchen Moisen [aut], Paul Patterson [aut], Chris Toney [aut], Grayson White [aut, cre] , Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>

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Package irboost updated to version 0.2-1.0 with previous version 0.1-1.5 dated 2024-04-18

Title: Iteratively Reweighted Boosting for Robust Analysis
Description: Fit a predictive model using iteratively reweighted boosting (IRBoost) to minimize robust loss functions within the CC-family (concave-convex). This constitutes an application of iteratively reweighted convex optimization (IRCO), where convex optimization is performed using the functional descent boosting algorithm. IRBoost assigns weights to facilitate outlier identification. Applications include robust generalized linear models and robust accelerated failure time models. Wang (2025) <doi:10.6339/24-JDS1138>.
Author: Zhu Wang [aut, cre]
Maintainer: Zhu Wang <zhuwang@gmail.com>

Diff between irboost versions 0.1-1.5 dated 2024-04-18 and 0.2-1.0 dated 2025-02-04

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Package SSBtools updated to version 1.7.0 with previous version 1.6.0 dated 2024-12-04

Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices are included (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] , Daniel Lupp [aut] , Bjoern-Helge Mevik [ctb], Vidar Norstein Klungre [rev] , Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>

Diff between SSBtools versions 1.6.0 dated 2024-12-04 and 1.7.0 dated 2025-02-04

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New package SQLFormatteR with initial version 0.0.1
Package: SQLFormatteR
Title: Format SQL Queries
Version: 0.0.1
Description: A convenient interface for formatting 'SQL' queries directly within 'R'. It acts as a wrapper around the 'sql_format' Rust crate. The package allows you to format 'SQL' code with customizable options, including indentation, case formatting, and more, ensuring your 'SQL' queries are clean, readable, and consistent.
License: MIT + file LICENSE
URL: https://dataupsurge.github.io/SQLFormatteR/, https://github.com/dataupsurge/SQLFormatteR
BugReports: https://github.com/dataupsurge/SQLFormatteR/issues
Imports: assertthat
Suggests: covr (>= 3.6.4), docopt (>= 0.7.1), git2r (>= 0.35.0), jsonlite (>= 1.8.9), lintr (>= 3.1.2), optparse (>= 1.7.5), precommit (>= 0.4.3), rextendr (>= 0.3.1), roxygen2 (>= 7.3.2), styler (>= 1.10.3), testthat (>= 3.0.0)
Encoding: UTF-8
SystemRequirements: Cargo (Rust's package manager), rustc >= 1.65.0
NeedsCompilation: yes
Packaged: 2025-02-04 11:11:05 UTC; morgan
Author: Morgan Durand [aut, cre, cph], Authors of the dependent Rust crates [aut]
Maintainer: Morgan Durand <morgan@dataupsurge.com>
Repository: CRAN
Date/Publication: 2025-02-04 17:40:15 UTC

More information about SQLFormatteR at CRAN
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New package shiny2docker with initial version 0.0.1
Package: shiny2docker
Title: Generate Dockerfiles for 'Shiny' Applications
Version: 0.0.1
Description: Automates the creation of Dockerfiles for deploying 'Shiny' applications. By integrating with 'renv' for dependency management and leveraging Docker-based solutions, it simplifies the process of containerizing 'Shiny' apps, ensuring reproducibility and consistency across different environments.
License: MIT + file LICENSE
Imports: attachment (>= 0.4.3), dockerfiler, here, yesno
Encoding: UTF-8
URL: https://github.com/VincentGuyader/shiny2docker
BugReports: https://github.com/VincentGuyader/shiny2docker/issues
Suggests: shiny, renv, testthat (>= 3.0.0), knitr, rmarkdown, rstudioapi
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-04 10:29:45 UTC; PC
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Repository: CRAN
Date/Publication: 2025-02-04 17:40:02 UTC

More information about shiny2docker at CRAN
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New package rmcmc with initial version 0.1.1
Package: rmcmc
Title: Robust Markov Chain Monte Carlo Methods
Version: 0.1.1
Description: Functions for simulating Markov chains using the Barker proposal to compute Markov chain Monte Carlo (MCMC) estimates of expectations with respect to a target distribution on a real-valued vector space. The Barker proposal, described in Livingstone and Zanella (2022) <doi:10.1111/rssb.12482>, is a gradient-based MCMC algorithm inspired by the Barker accept-reject rule. It combines the robustness of simpler MCMC schemes, such as random-walk Metropolis, with the efficiency of gradient-based methods, such as the Metropolis adjusted Langevin algorithm. The key function provided by the package is sample_chain(), which allows sampling a Markov chain with a specified target distribution as its stationary distribution. The chain is sampled by generating proposals and accepting or rejecting them using a Metropolis-Hasting acceptance rule. During an initial warm-up stage, the parameters of the proposal distribution can be adapted, with adapters available to both: tune the scale of the prop [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: bridgestan (>= 2.5.0), knitr, posterior, progress, ramcmc, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/UCL/rmcmc, http://github-pages.ucl.ac.uk/rmcmc/
BugReports: https://github.com/UCL/rmcmc/issues
Imports: Matrix, rlang, withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-04 16:29:30 UTC; matt
Author: Matthew M. Graham [aut, cre] , Samuel Livingstone [aut] , University College London [cph], Engineering and Physical Sciences Research Council [fnd]
Maintainer: Matthew M. Graham <m.graham@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2025-02-04 17:50:02 UTC

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New package MOsemiind with initial version 0.1.0
Package: MOsemiind
Title: Marshall-Olkin Shock Models with Semi-Independent Time
Version: 0.1.0
Description: Provides tools for analyzing Marshall-Olkin shock models semi-independent time. It includes interactive 'shiny' applications for exploring copula-based dependence structures, along with functions for modeling and visualization. The methods are based on Mijanovic and Popovic (2024, submitted) "An R package for Marshall-Olkin shock models with semi-independent times."
License: MIT + file LICENSE
Encoding: UTF-8
Imports: copula, graphics, pracma, shiny, stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-04 09:36:17 UTC; Andjela
Author: Andjela Mijanovic [aut, cre], Bozidar Popovic [aut]
Maintainer: Andjela Mijanovic <andjela.m@ucg.ac.me>
Repository: CRAN
Date/Publication: 2025-02-04 17:30:02 UTC

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New package kpiwidget with initial version 0.1.0
Package: kpiwidget
Title: KPI Widgets for Quarto Dashboards with Crosstalk
Version: 0.1.0
Description: Provides an easy way to create interactive KPI (key performance indicator) widgets for 'Quarto' dashboards using 'Crosstalk'. The package enables visualization of key metrics in a structured format, supporting interactive filtering and linking with other 'Crosstalk'-enabled components. Designed for use in 'Quarto' Dashboards.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: crosstalk, htmlwidgets
Suggests: dplyr, flexdashboard, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://arnold-kakas.github.io/kpiwidget/, https://github.com/Arnold-Kakas/kpiwidget
BugReports: https://github.com/Arnold-Kakas/kpiwidget/issues
NeedsCompilation: no
Packaged: 2025-02-04 16:40:27 UTC; Arnold
Author: Arnold Kakas [aut, cre, cph]
Maintainer: Arnold Kakas <kakasarnold@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-04 17:50:07 UTC

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Package gmoTree updated to version 1.4.0 with previous version 1.3.0 dated 2024-12-06

Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments. Import 'oTree' data and clean them by using functions that handle messy data, dropouts, and other problematic cases. Create IDs, calculate the time, transfer variables between app data frames, and delete sensitive information. Review your experimental data prior to running the experiment and automatically generate a detailed summary of the variables used in your 'oTree' code. Information on 'oTree' is found in Chen, D. L., Schonger, M., & Wickens, C. (2016) <doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>

Diff between gmoTree versions 1.3.0 dated 2024-12-06 and 1.4.0 dated 2025-02-04

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 gmoTree-1.4.0/gmoTree/DESCRIPTION                                                                  |   14 
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 gmoTree-1.4.0/gmoTree/R/assignv.R                                                                  |   19 
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 gmoTree-1.4.0/gmoTree/R/delete_duplicate.R                                                         |   15 
 gmoTree-1.4.0/gmoTree/R/delete_plabels.R                                                           |    5 
 gmoTree-1.4.0/gmoTree/R/delete_sessions.R                                                          |   47 
 gmoTree-1.4.0/gmoTree/R/extime.R                                                                   |   87 
 gmoTree-1.4.0/gmoTree/R/import_otree.R                                                             |  141 
 gmoTree-1.4.0/gmoTree/R/make_ids.R                                                                 |   76 
 gmoTree-1.4.0/gmoTree/R/messy_chat.R                                                               |    3 
 gmoTree-1.4.0/gmoTree/R/messy_time.R                                                               |    3 
 gmoTree-1.4.0/gmoTree/R/pagesec.R                                                                  |    7 
 gmoTree-1.4.0/gmoTree/R/show_constant.R                                                            |   19 
 gmoTree-1.4.0/gmoTree/R/show_dropouts.R                                                            |   12 
 gmoTree-1.4.0/gmoTree/README.md                                                                    |   14 
 gmoTree-1.4.0/gmoTree/inst/CITATION                                                                |    4 
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 gmoTree-1.4.0/gmoTree/man/codebook.Rd                                                              |   87 
 gmoTree-1.4.0/gmoTree/man/delete_cases.Rd                                                          |   80 
 gmoTree-1.4.0/gmoTree/man/delete_dropouts.Rd                                                       |   42 
 gmoTree-1.4.0/gmoTree/man/delete_duplicate.Rd                                                      |   15 
 gmoTree-1.4.0/gmoTree/man/delete_plabels.Rd                                                        |    6 
 gmoTree-1.4.0/gmoTree/man/delete_sessions.Rd                                                       |   49 
 gmoTree-1.4.0/gmoTree/man/extime.Rd                                                                |   38 
 gmoTree-1.4.0/gmoTree/man/import_otree.Rd                                                          |   28 
 gmoTree-1.4.0/gmoTree/man/make_ids.Rd                                                              |   15 
 gmoTree-1.4.0/gmoTree/man/messy_chat.Rd                                                            |    4 
 gmoTree-1.4.0/gmoTree/man/messy_time.Rd                                                            |    4 
 gmoTree-1.4.0/gmoTree/man/pagesec.Rd                                                               |    6 
 gmoTree-1.4.0/gmoTree/man/show_constant.Rd                                                         |   16 
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Package ggbreak updated to version 0.1.4 with previous version 0.1.3 dated 2025-01-08

Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggbreak versions 0.1.3 dated 2025-01-08 and 0.1.4 dated 2025-02-04

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Package rollupTree updated to version 0.2.0 with previous version 0.1.0 dated 2025-01-20

Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>

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Package joineRML updated to version 0.4.7 with previous version 0.4.6 dated 2023-01-19

Title: Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000) <doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple continuous longitudinal measures. The time-to-event data is modelled using a Cox proportional hazards regression model with time-varying covariates. The multiple longitudinal outcomes are modelled using a multivariate version of the Laird and Ware linear mixed model. The association is captured by a multivariate latent Gaussian process. The model is estimated using a Monte Carlo Expectation Maximization algorithm. This project was funded by the Medical Research Council (Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut] , Pete Philipson [aut] , Andrea Jorgensen [ctb] , Ruwanthi Kolamunnage-Dona [aut] , Paula Williamson [ctb] , Dimitris Rizopoulos [ctb, dtc] , Alessandro Gasparini [aut] , Medical Research Council [fnd]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>

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Package gstat updated to version 2.1-3 with previous version 2.1-2 dated 2024-09-05

Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] , Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package fbnet updated to version 1.0.4 with previous version 1.0.3 dated 2023-07-01

Title: Forensic Bayesian Networks
Description: Open-source package for computing likelihood ratios in kinship testing and human identification cases. It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals.
Author: Franco Marsico [aut, cre], Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>

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Package RSAGA updated to version 1.4.2 with previous version 1.4.0 dated 2022-12-09

Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] , Donovan Bangs [aut], Marc Becker [aut], Patrick Schratz [ctb] , Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>

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Package forensIT updated to version 1.1.1 with previous version 1.0.0 dated 2023-06-22

Title: Information Theory Tools for Forensic Analysis
Description: The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Author: Franco Marsico [aut, cre], Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>

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Package BMisc updated to version 1.4.8 with previous version 1.4.7 dated 2025-01-10

Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>

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Package ssifs updated to version 1.0.4 with previous version 1.0.2 dated 2023-05-12

Title: Stochastic Search Inconsistency Factor Selection
Description: Evaluating the consistency assumption of Network Meta-Analysis both globally and locally in the Bayesian framework. Inconsistencies are located by applying Bayesian variable selection to the inconsistency factors. The implementation of the method is described by Seitidis et al. (2023) <doi:10.1002/sim.9891>.
Author: Georgios Seitidis [aut, cre] , Stavros Nikolakopoulos [aut] , Ioannis Ntzoufras [aut] , Dimitris Mavridis [aut]
Maintainer: Georgios Seitidis <g.seitidis@uoi.gr>

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Package netmeta updated to version 3.1-0 with previous version 3.0-2 dated 2025-01-22

Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis": - frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>; - additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>; - network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>; - rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>; - ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] , Ulrike Krahn [aut], Jochem Koenig [aut] , Orestis Efthimiou [aut] , Annabel Davies [aut] , Theodoros Papakonstantinou [aut] , Theodoros Evrenoglou [ctb] , Krzysztof Ciomek [ctb] , Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>

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Package HVT updated to version 25.2.1 with previous version 24.9.1 dated 2024-09-11

Title: Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut], Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>

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More information about HVT at CRAN
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Package RoBMA updated to version 3.4.0 with previous version 3.3.0 dated 2025-01-15

Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic and meta-regression models (assuming either presence or absence of the effect, heterogeneity, publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to combine the competing meta-analytic models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect; Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022, <doi:10.1037/met0000405>). Users can define a wide range of prior distributions for + the effect size, heterogeneity, publication bias (including selection models and PET-PEESE), and moderator components. The package provides convenient functions for summary, visualizations, and fit diagnostics.
Author: Frantisek Bartos [aut, cre] , Maximilian Maier [aut] , Eric-Jan Wagenmakers [ths] , Joris Goosen [ctb], Matthew Denwood [cph] , Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>

Diff between RoBMA versions 3.3.0 dated 2025-01-15 and 3.4.0 dated 2025-02-04

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New package RFplus with initial version 1.2-2
Package: RFplus
Title: Progressive Bias Correction of Satellite Environmental Data
Version: 1.2-2
Encoding: UTF-8
Maintainer: Jonnathan Augusto Landi Bermeo <jonnathan.landi@outlook.com>
Description: Implements a bias correction method that combines Random Forest models with Quantile Mapping to improve the accuracy of satellite-derived environmental datasets. The model corrects biases in meteorological variables, such as precipitation and temperature, by integrating in situ measurements and a Digital Elevation Model (DEM).
License: GPL (>= 3)
Depends: R (>= 4.4.0)
Imports: terra, randomForest, data.table, dplyr, pbapply, qmap
URL: https://github.com/Jonnathan-Landi/RFplus
BugReports: https://github.com/Jonnathan-Landi/RFplus/issues
NeedsCompilation: no
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Packaged: 2025-02-03 23:36:34 UTC; Jonna
Author: Jonnathan Augusto Landi Bermeo [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-04 09:10:02 UTC

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Package maptiles updated to version 0.9.0 with previous version 0.8.0 dated 2024-10-22

Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and displays tiles from a large number of providers (e.g. 'OpenStreetMap', 'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] , Diego Hernangomez [ctb] , Robert J. Hijmans [ctb] , Hugh A. Graham [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>

Diff between maptiles versions 0.8.0 dated 2024-10-22 and 0.9.0 dated 2025-02-04

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Package primes updated to version 1.6.1 with previous version 1.6.0 dated 2024-01-08

Title: Fast Functions for Prime Numbers
Description: Fast functions for dealing with prime numbers, such as testing whether a number is prime and generating a sequence prime numbers. Additional functions include finding prime factors and Ruth-Aaron pairs, finding next and previous prime numbers in the series, finding or estimating the nth prime, estimating the number of primes less than or equal to an arbitrary number, computing primorials, prime k-tuples (e.g., twin primes), finding the greatest common divisor and smallest (least) common multiple, testing whether two numbers are coprime, and computing Euler's totient function. Most functions are vectorized for speed and convenience.
Author: Os Keyes [aut], Paul Egeler [aut, cre]
Maintainer: Paul Egeler <paulegeler@gmail.com>

Diff between primes versions 1.6.0 dated 2024-01-08 and 1.6.1 dated 2025-02-04

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New package nlpembeds with initial version 1.0.0
Package: nlpembeds
Title: Natural Language Processing Embeddings
Version: 1.0.0
Description: Provides efficient methods to compute co-occurrence matrices, pointwise mutual information (PMI) and singular value decomposition (SVD). In the biomedical and clinical settings, one challenge is the huge size of databases, e.g. when analyzing data of millions of patients over tens of years. To address this, this package provides functions to efficiently compute monthly co-occurrence matrices, which is the computational bottleneck of the analysis, by using the 'RcppAlgos' package and sparse matrices. Furthermore, the functions can be called on 'SQL' databases, enabling the computation of co-occurrence matrices of tens of gigabytes of data, representing millions of patients over tens of years. Partly based on Hong C. (2021) <doi:10.1038/s41746-021-00519-z>.
Imports: data.table, magrittr, Matrix, methods, parallel, RcppAlgos, reshape2, RSQLite, rsvd
Depends: R (>= 3.5.0)
Suggests: knitr, testthat
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
URL: https://gitlab.com/thomaschln/nlpembeds
BugReports: https://gitlab.com/thomaschln/nlpembeds/-/issues
NeedsCompilation: no
Packaged: 2025-02-03 20:02:33 UTC; root
Author: Thomas Charlon [aut, cre] , Doudou Zhou [ctb] , CELEHS [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Repository: CRAN
Date/Publication: 2025-02-04 08:30:01 UTC

More information about nlpembeds at CRAN
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New package fastQR with initial version 1.0.0
Package: fastQR
Title: Fast QR Decomposition and Update
Version: 1.0.0
Date: 2025-01-25
Author: Mauro Bernardi [aut, cre], Claudio Busatto [aut], Manuela Cattelan [aut]
Maintainer: Mauro Bernardi <mauro.bernardi@unipd.it>
Description: Efficient algorithms for performing, updating, and downdating the QR decomposition, R decomposition, or the inverse of the R decomposition of a matrix as rows or columns are added or removed. It also includes functions for solving linear systems of equations, normal equations for linear regression models, and normal equations for linear regression with a RIDGE penalty. For a detailed introduction to these methods, see the book by Golub and Van Loan (2013, <doi:10.1007/978-3-319-05089-8>) for complete introduction to the methods.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.10), RcppEigen, Rdpack
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
Encoding: UTF-8
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2025-02-03 22:19:19 UTC; maurobernardi
Repository: CRAN
Date/Publication: 2025-02-04 08:40:01 UTC

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Package singleRcapture updated to version 0.2.2 with previous version 0.2.1.4 dated 2025-01-07

Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, ctb] , Maciej Beresewicz [aut, cre]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>

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Mon, 03 Feb 2025

Package ForestTools updated to version 1.0.3 with previous version 1.0.2 dated 2024-04-28

Title: Tools for Analyzing Remote Sensing Forest Data
Description: Tools for analyzing remote sensing forest data, including functions for detecting treetops from canopy models, outlining tree crowns, and calculating textural metrics.
Author: Andrew Plowright [aut, cre], Jean-Romain Roussel [ctb]
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

Diff between ForestTools versions 1.0.2 dated 2024-04-28 and 1.0.3 dated 2025-02-03

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Package ggpca updated to version 0.1.3 with previous version 0.1.2 dated 2024-10-28

Title: Publication-Ready PCA, t-SNE, and UMAP Plots
Description: Provides tools for creating publication-ready dimensionality reduction plots, including Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP). This package helps visualize high-dimensional data with options for custom labels, density plots, and faceting, using the 'ggplot2' framework Wickham (2016) <doi:10.1007/978-3-319-24277-4>.
Author: Yaoxiang Li [cre, aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>

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Package dbi.table updated to version 1.0.3 with previous version 1.0.1 dated 2024-12-10

Title: Database Queries Using 'data.table' Syntax
Description: Query database tables over a 'DBI' connection using 'data.table' syntax. Attach database schemas to the search path. Automatically merge using foreign key constraints.
Author: Kjell P. Konis [aut, cre], Luis Rocha [ctb]
Maintainer: Kjell P. Konis <kjellk@gmail.com>

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Package cmhc updated to version 0.2.10 with previous version 0.2.9 dated 2024-11-05

Title: Access, Retrieve, and Work with CMHC Data
Description: Wrapper around the Canadian Mortgage and Housing Corporation (CMHC) web interface. It enables programmatic and reproducible access to a wide variety of housing data from CMHC.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>

Diff between cmhc versions 0.2.9 dated 2024-11-05 and 0.2.10 dated 2025-02-03

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Package areaplot updated to version 2.1.3 with previous version 2.1.2 dated 2024-01-14

Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add polygons to existing plots. A variety of input formats are supported, including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <thisisarni@gmail.com>

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Package teal.slice updated to version 0.6.0 with previous version 0.5.1 dated 2024-04-30

Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for interactive filtering of data stored in 'data.frame' and 'MultiAssayExperiment' objects. Also displays filtered and unfiltered observation counts.
Author: Dawid Kaledkowski [aut, cre] , Pawel Rucki [aut], Aleksander Chlebowski [aut] , Andre Verissimo [aut] , Kartikeya Kirar [aut], Marcin Kosinski [aut], Chendi Liao [rev], Dony Unardi [rev], Andrew Bates [aut], Mahmoud Hallal [aut], Nikolas Burkoff [aut [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package miceFast updated to version 0.8.5 with previous version 0.8.2 dated 2022-11-17

Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm. Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'. The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used. A single evaluation of a quantitative model for the multiple imputations is another major enhancement. A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

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Package strata updated to version 1.4.0 with previous version 1.0.1 dated 2024-11-27

Title: Simple Framework for Simple Automation
Description: Build a project framework for users with access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>

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Package tidyterra updated to version 0.7.0 with previous version 0.6.2 dated 2025-01-08

Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] , Dewey Dunnington [ctb] , ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

Diff between tidyterra versions 0.6.2 dated 2025-01-08 and 0.7.0 dated 2025-02-03

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New package shinyr with initial version 0.4.2
Package: shinyr
Title: Data Insights Through Inbuilt R Shiny App
Version: 0.4.2
Description: It builds dynamic R shiny based dashboards to analyze any CSV files. It provides simple dashboard design to subset the data, perform exploratory data analysis and preliminary machine learning (supervised and unsupervised). It also provides filters based on columns of interest.
Depends: R (>= 3.5.0),
Imports: dplyr, shiny, shinydashboard, tm, wordcloud, corrplot, randomForest, RColorBrewer, caret, nnet, plotly
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-03 14:15:51 UTC; RPUSH1
Author: Jayachandra N [aut, cre], Pushker Ravindra [aut]
Maintainer: Jayachandra N <itsjay510@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 19:30:02 UTC

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Package rgrass updated to version 0.5-1 with previous version 0.4-4 dated 2024-09-03

Title: Interface Between 'GRASS' Geographical Information System and 'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [aut] , Sebastian Jeworutzki [ctb] , Rainer Krug [ctb] , Robin Lovelace [ctb] , Markus Neteler [ctb] , Steven Pawley [cre, aut] , Floris Vanderhaeghe [ctb]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>

Diff between rgrass versions 0.4-4 dated 2024-09-03 and 0.5-1 dated 2025-02-03

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Package ordbetareg updated to version 0.8 with previous version 0.7.2 dated 2023-08-10

Title: Ordered Beta Regression Models with 'brms'
Description: Implements ordered beta regression models, which are for modeling continuous variables with upper and lower bounds, such as survey sliders, dose-response relationships and indexes. For more information, see Kubinec (2023) <doi:10.31235/osf.io/2sx6y>. The package is a front-end to the R package 'brms', which facilitates a range of regression specifications, including hierarchical, dynamic and multivariate modeling.
Author: Robert Kubinec [aut, cre]
Maintainer: Robert Kubinec <bobkubinec@gmail.com>

Diff between ordbetareg versions 0.7.2 dated 2023-08-10 and 0.8 dated 2025-02-03

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Package cgmanalysis updated to version 3.0.2 with previous version 3.0.1 dated 2025-02-01

Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom', 'iPro 2', 'Diasend', 'Libre', or 'Carelink' data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload. cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <timothy.vigers@cuanschutz.edu>

Diff between cgmanalysis versions 3.0.1 dated 2025-02-01 and 3.0.2 dated 2025-02-03

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New package tmap.cartogram with initial version 0.1
Package: tmap.cartogram
License: GPL-3
Title: Extension to 'tmap' for Creating Cartograms
Description: Provides new layer functions to 'tmap' for creating various types of cartograms. A cartogram is a type of thematic map in which geographic areas are resized or distorted based on a quantitative variable, such as population. The goal is to make the area sizes proportional to the selected variable while preserving geographic positions as much as possible.
Version: 0.1
Encoding: UTF-8
Depends: R (>= 3.5.0),
Imports: tmap (>= 4.0), sf, cartogram
Suggests: knitr
URL: https://github.com/r-tmap/tmap.cartogram, https://r-tmap.github.io/tmap.cartogram/
BugReports: https://github.com/r-tmap/tmap.cartogram/issues
NeedsCompilation: no
Packaged: 2025-02-03 16:19:33 UTC; mtes
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 18:20:02 UTC

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New package shinykanban with initial version 0.0.1
Package: shinykanban
Title: Create Kanban Board in Shiny Applications
Version: 0.0.1
Description: Provides an interactive Kanban board widget for 'shiny' applications. It allows users to manage tasks using a drag-and-drop interface and offers customizable styling options. 'shinykanban' is ideal for project management, task tracking, and agile workflows within 'shiny' apps.
License: MIT + file LICENSE
URL: https://github.com/ugurdar/shinykanban
BugReports: https://github.com/ugurdar/shinykanban/issues
Encoding: UTF-8
Imports: htmlwidgets, reactR, shiny, bsicons, htmltools
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-03 14:10:49 UTC; ugurdar
Author: Ugur Dar [aut, cre], Brian Pillmore [aut, cph]
Maintainer: Ugur Dar <ugurdarr@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 18:10:02 UTC

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New package authoritative with initial version 0.1.0
Package: authoritative
Title: Parse and Deduplicate Author Names
Version: 0.1.0
Description: Utilities to parse authors fields from DESCRIPTION files and general purpose functions to deduplicate names in database, beyond the specific case of R package authors.
License: MIT + file LICENSE
URL: https://github.com/epiverse-connect/authoritative
BugReports: https://github.com/epiverse-connect/authoritative/issues
Depends: R (>= 4.1.0)
Imports: stringi, utils
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-03 17:27:42 UTC; hugo
Author: Hugo Gruson [aut, cre, cph] , Chris Hartgerink [rev]
Maintainer: Hugo Gruson <hugo@data.org>
Repository: CRAN
Date/Publication: 2025-02-03 18:30:02 UTC

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Package SWMPr updated to version 2.5.2 with previous version 2.5.1 dated 2024-06-24

Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. These tools address common challenges associated with continuous time series data for environmental decision making.
Author: Marcus W. Beck [aut, cre], Kimberly Cressman [ctb]
Maintainer: Marcus W. Beck <mbeck@tbep.org>

Diff between SWMPr versions 2.5.1 dated 2024-06-24 and 2.5.2 dated 2025-02-03

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Package sommer updated to version 4.3.7 with previous version 4.3.6 dated 2024-10-20

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

Diff between sommer versions 4.3.6 dated 2024-10-20 and 4.3.7 dated 2025-02-03

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Package RcppAlgos updated to version 2.9.3 with previous version 2.9.1 dated 2025-01-27

Title: High Performance Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions and flexible iterators implemented in C++ for solving problems in combinatorics and computational mathematics. Handles various combinatorial objects including combinations, permutations, integer partitions and compositions, Cartesian products, unordered Cartesian products, and partition of groups. Utilizes the RMatrix class from 'RcppParallel' for thread safety. The combination and permutation functions contain constraint parameters that allow for generation of all results of a vector meeting specific criteria (e.g. finding all combinations such that the sum is between two bounds). Capable of ranking/unranking combinatorial objects efficiently (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are [...truncated...]
Author: Joseph Wood [aut, cre]
Maintainer: Joseph Wood <jwood000@gmail.com>

Diff between RcppAlgos versions 2.9.1 dated 2025-01-27 and 2.9.3 dated 2025-02-03

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New package raybevel with initial version 0.2.2
Package: raybevel
Title: Generates Polygon Straight Skeletons and 3D Bevels
Version: 0.2.2
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Description: Generates polygon straight skeletons and 3D models. Provides functions to create and visualize interior polygon offsets, 3D beveled polygons, and 3D roof models.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: progress, digest, decido, rayvertex (>= 0.11.4), sf, grid
LinkingTo: Rcpp, BH, RcppCGAL (>= 6.0.1), progress, RcppThread (>= 2.1.6)
Suggests: spData, rayrender (>= 0.38.3), testthat (>= 3.0.0), ggplot2, png
URL: https://www.raybevel.com, https://github.com/tylermorganwall/raybevel/, http://www.raybevel.com/
BugReports: https://github.com/tylermorganwall/raybevel/issues
NeedsCompilation: yes
Packaged: 2025-02-02 04:36:39 UTC; tyler
Author: Tyler Morgan-Wall [aut, cph, cre]
Repository: CRAN
Date/Publication: 2025-02-03 17:40:02 UTC

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New package lightAUC with initial version 0.1.1
Package: lightAUC
Title: Fast AUC Computation
Version: 0.1.1
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Description: Fast calculation of Area Under Curve (AUC) metric of a Receiver Operating Characteristic (ROC) curve, using the algorithm of Fawcett (2006) <doi:10.1016/j.patrec.2005.10.010>. Therefore it is appropriate for large-scale AUC metric calculations.
License: GPL-3
Imports: Rcpp (>= 1.0.13), RcppParallel (>= 5.1.9)
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Encoding: UTF-8
SystemRequirements: GNU make
Suggests: Rfast, Rfast2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr, rmarkdown
URL: https://github.com/cadam00/lightAUC, https://cadam00.github.io/lightAUC/
BugReports: https://github.com/cadam00/lightAUC/issues
NeedsCompilation: yes
Packaged: 2025-02-03 06:15:31 UTC; Administrator
Author: Christos Adam [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-03 18:00:01 UTC

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Package interfacer updated to version 0.3.3 with previous version 0.3.2 dated 2024-11-14

Title: Define and Enforce Contracts for Dataframes as Function Parameters
Description: A dataframe validation framework for package builders who use dataframes as function parameters. It performs checks on column names, coerces data-types, and checks grouping to make sure user inputs conform to a specification provided by the package author. It provides a mechanism for package authors to automatically document supported dataframe inputs and selectively dispatch to functions depending on the format of a dataframe much like S3 does for classes. It also contains some developer tools to make working with and documenting dataframe specifications easier. It helps package developers to improve their documentation and simplifies parameter validation where dataframes are used as function parameters.
Author: Robert Challen [aut, cre, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>

Diff between interfacer versions 0.3.2 dated 2024-11-14 and 0.3.3 dated 2025-02-03

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New package HetSeq with initial version 0.1.0
Package: HetSeq
Title: Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity
Version: 0.1.0
Author: Kevin Berg [aut, cre], Florian Erhard [aut] , Lygeri Sakellaridi [aut]
Maintainer: Kevin Berg <Kevin.Berg@informatik.uni-regensburg.de>
Description: Cellular responses to perturbations are highly heterogeneous and depend largely on the initial state of cells. Connecting post-perturbation cells via cellular trajectories to untreated cells (e.g. by leveraging metabolic labeling information) enables exploitation of intercellular heterogeneity as a combined knock-down and overexpression screen to identify pathway modulators, termed Heterogeneity-seq (see 'Berg et al' <doi:10.1101/2024.10.28.620481>). This package contains functions to generate cellular trajectories based on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) time courses, functions to identify pathway modulators and to visualize the results.
License: Apache License (>= 2)
URL: https://github.com/erhard-lab/HetSeq
BugReports: https://github.com/erhard-lab/HetSeq/issues
Depends: R (>= 4.1.0)
Imports: cowplot, doParallel, foreach, DoubleML, e1071, igraph, ggplot2, ggrastr, ggrepel, grandR, lpSolve, mlr3, pROC, reshape2, scales, Seurat, stats
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-03 11:36:32 UTC; berg
Repository: CRAN
Date/Publication: 2025-02-03 18:00:05 UTC

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Package aebdata updated to version 0.1.4 with previous version 0.1.3 dated 2025-01-12

Title: Access Data from the Atlas do Estado Brasileiro
Description: Facilitates access to the data from the Atlas do Estado Brasileiro (<https://www.ipea.gov.br/atlasestado/>), maintained by the Instituto de Pesquisa Econômica Aplicada (Ipea). It allows users to search for specific series, list series or themes, and download data when available.
Author: Hugo Macedo [aut, cre, cph]
Maintainer: Hugo Macedo <aebdata@hhmace.do>

Diff between aebdata versions 0.1.3 dated 2025-01-12 and 0.1.4 dated 2025-02-03

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Package torch updated to version 0.14.1 with previous version 0.14.0 dated 2025-01-30

Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph], Javier Luraschi [aut], Dmitriy Selivanov [ctb], Athos Damiani [ctb], Christophe Regouby [ctb], Krzysztof Joachimiak [ctb], Hamada S. Badr [ctb], Sebastian Fischer [ctb], Maximilian Pichler [ctb], RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>

Diff between torch versions 0.14.0 dated 2025-01-30 and 0.14.1 dated 2025-02-03

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Package smooth updated to version 4.1.1 with previous version 4.1.0 dated 2024-10-01

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>

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Package sgs updated to version 0.3.3 with previous version 0.3.2 dated 2024-11-28

Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>

Diff between sgs versions 0.3.2 dated 2024-11-28 and 0.3.3 dated 2025-02-03

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Package RegSDC updated to version 1.0.0 with previous version 0.7.0 dated 2022-08-19

Title: Information Preserving Regression-Based Tools for Statistical Disclosure Control
Description: Implementation of the methods described in the paper with the above title: Langsrud, Ø. (2019) <doi:10.1007/s11222-018-9848-9>. The package can be used to generate synthetic or hybrid continuous microdata, and the relationship to the original data can be controlled in several ways. A function for replacing suppressed tabular cell frequencies with decimal numbers is included.
Author: Oeyvind Langsrud [aut, cre]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>

Diff between RegSDC versions 0.7.0 dated 2022-08-19 and 1.0.0 dated 2025-02-03

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Package locfit updated to version 1.5-9.11 with previous version 1.5-9.10 dated 2024-06-24

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

Diff between locfit versions 1.5-9.10 dated 2024-06-24 and 1.5-9.11 dated 2025-02-03

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New package legion with initial version 0.2.1
Package: legion
Title: Forecasting Using Multivariate Models
Version: 0.2.1
Date: 2025-02-03
URL: https://github.com/config-i1/legion
BugReports: https://github.com/config-i1/legion/issues
Language: en-GB
Description: Functions implementing multivariate state space models for purposes of time series analysis and forecasting. The focus of the package is on multivariate models, such as Vector Exponential Smoothing, Vector ETS (Error-Trend-Seasonal model) etc. It currently includes Vector Exponential Smoothing (VES, de Silva et al., 2010, <doi:10.1177/1471082X0901000401>), Vector ETS (Svetunkov et al., 2023, <doi:10.1016/j.ejor.2022.04.040>) and simulation function for VES.
License: LGPL-2.1
Depends: R (>= 3.5.0), greybox (>= 1.0.4), smooth (>= 3.1.0)
Imports: Rcpp (>= 0.12.3), stats, generics (>= 0.1.2), graphics, grDevices, Matrix, nloptr, utils, zoo
LinkingTo: Rcpp, RcppArmadillo (>= 0.8.100.0.0)
Suggests: numDeriv, testthat, knitr, rmarkdown, doMC, doParallel, foreach
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-03 14:14:35 UTC; config
Author: Ivan Svetunkov [aut, cre] , Kandrika Fadhlan Pritularga [aut]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Repository: CRAN
Date/Publication: 2025-02-03 16:10:02 UTC

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Package dfr updated to version 0.1.3 with previous version 0.1.2 dated 2024-11-28

Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>

Diff between dfr versions 0.1.2 dated 2024-11-28 and 0.1.3 dated 2025-02-03

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Package mongolite updated to version 3.0.1 with previous version 3.0.0 dated 2025-01-27

Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] , MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

Diff between mongolite versions 3.0.0 dated 2025-01-27 and 3.0.1 dated 2025-02-03

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Package lessR updated to version 4.4.1 with previous version 4.4.0 dated 2025-01-12

Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>

Diff between lessR versions 4.4.0 dated 2025-01-12 and 4.4.1 dated 2025-02-03

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Package crew updated to version 1.0.0 with previous version 0.10.2 dated 2024-11-15

Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre] , Daniel Woodie [ctb], Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>

Diff between crew versions 0.10.2 dated 2024-11-15 and 1.0.0 dated 2025-02-03

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Package TSLSTMplus updated to version 1.0.6 with previous version 1.0.5 dated 2024-09-06

Title: Long-Short Term Memory for Time-Series Forecasting, Enhanced
Description: The LSTM (Long Short-Term Memory) model is a Recurrent Neural Network (RNN) based architecture that is widely used for time series forecasting. Customizable configurations for the model are allowed, improving the capabilities and usability of this model compared to other packages. This package is based on 'keras' and 'tensorflow' modules and the algorithm of Paul and Garai (2021) <doi:10.1007/s00500-021-06087-4>.
Author: Jaime Pizarroso Gonzalo [aut, ctb, cre], Antonio Munoz San Roque [aut]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>

Diff between TSLSTMplus versions 1.0.5 dated 2024-09-06 and 1.0.6 dated 2025-02-03

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Package optRF updated to version 1.1.0 with previous version 1.0.1 dated 2024-09-23

Title: Optimising Random Forest Stability by Determining the Optimal Number of Trees
Description: Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.
Author: Thomas Martin Lange [cre, aut] , Felix Heinrich [ctb]
Maintainer: Thomas Martin Lange <thomas.lange@uni-goettingen.de>

Diff between optRF versions 1.0.1 dated 2024-09-23 and 1.1.0 dated 2025-02-03

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Package openssl updated to version 2.3.2 with previous version 2.3.1 dated 2025-01-09

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] , Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

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Package SCDB updated to version 0.5.0 with previous version 0.4.1 dated 2024-10-03

Title: Easily Access and Maintain Time-Based Versioned Data (Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time. More specifically, the package facilitates type-2 history for data-warehouses and provides a number of Quality of life improvements for working on SQL databases with R. For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev] , Marcus Munch Gruenewald [aut] , Lasse Engbo Christiansen [rev] , Sofia Myrup Otero [rev], Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>

Diff between SCDB versions 0.4.1 dated 2024-10-03 and 0.5.0 dated 2025-02-03

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Package lcmm updated to version 2.2.0 with previous version 2.1.0 dated 2023-10-06

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent class mixed models, mixed models for curvilinear outcomes, mixed models for multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
Author: Cecile Proust-Lima [aut, cre], Viviane Philipps [aut], Amadou Diakite [ctb], Benoit Liquet [ctb], Alan Genz [ctb] , John Burkardt [ctb]
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

Diff between lcmm versions 2.1.0 dated 2023-10-06 and 2.2.0 dated 2025-02-03

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New package MplusLGM with initial version 1.0.0
Package: MplusLGM
Title: Automate Latent Growth Mixture Modelling in 'Mplus'
Version: 1.0.0
Description: Provide a suite of functions for conducting and automating Latent Growth Modeling (LGM) in 'Mplus', including Growth Curve Model (GCM), Growth-Based Trajectory Model (GBTM) and Latent Class Growth Analysis (LCGA). The package builds upon the capabilities of the 'MplusAutomation' package (Hallquist & Wiley, 2018) to streamline large-scale latent variable analyses. “MplusAutomation: An R Package for Facilitating Large-Scale Latent Variable Analyses in Mplus.” Structural Equation Modeling, 25(4), 621–638. <doi:10.1080/10705511.2017.1402334> The workflow implemented in this package follows the recommendations outlined in Van Der Nest et al. (2020). “An Overview of Mixture Modeling for Latent Evolutions in Longitudinal Data: Modeling Approaches, Fit Statistics, and Software.” Advances in Life Course Research, 43, Article 100323. <doi:10.1016/j.alcr.2019.100323>.
Depends: R (>= 4.1.0),
License: GPL (>= 3)
Imports: MplusAutomation, magrittr, tibble, dplyr, tidyr, tidyselect, stringr, purrr, ggplot2, glue, parallel
Encoding: UTF-8
URL: https://github.com/OlivierPDS/MplusLGM
BugReports: https://github.com/OlivierPDS/MplusLGM/issues
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-01 20:20:08 UTC; olivierpercie
Author: Olivier Percie du Sert [aut, cre, cph] , Joshua Unrau [aut]
Maintainer: Olivier Percie du Sert <olivier.perciedusert@mail.mcgill.ca>
Repository: CRAN
Date/Publication: 2025-02-03 12:20:02 UTC

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New package writer with initial version 0.1.0
Package: writer
Title: Write from Multiple Sources to a Database Table
Version: 0.1.0
Description: Provides unified syntax to write data from lazy 'dplyr' 'tbl' or 'dplyr' 'sql' query or a dataframe to a database table with modes such as create, append, insert, update, upsert, patch, delete, overwrite, overwrite_schema.
License: LGPL (>= 3)
Imports: DBI (>= 1.2.3), dplyr (>= 1.1.0), dbplyr (>= 2.3.1), glue (>= 1.5.1), cli (>= 3.4.0), rlang (>= 1.1.2)
Suggests: RSQLite, testthat (>= 3.0.0),
URL: https://github.com/talegari/writer
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-01-31 18:22:17 UTC; srikanth-ks1
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 11:40:02 UTC

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New package resumiR with initial version 1.0.2
Package: resumiR
Title: Medidas Resumen y Tablas de Frecuencia para Datos Numéricos / Summary Measures and Frequency Tables for Numerical Data
Version: 1.0.2
Maintainer: Juan Manuel Solis <juanmasolis@fca.unju.edu.ar>
URL: https://github.com/juanMaSolisJujuy/resumiR
Description: Permite obtener rápidamente una serie de medidas de resumen y gráficos para datos numéricos discretos o continuos en series simples. También permite obtener tablas de frecuencia clásicas y gráficos cuando se desea realizar un análisis de series agrupadas. Su objetivo es de aplicación didáctica para un curso introductorio de Bioestadística utilizando el software R, para las carreras de grado las carreras de grado y otras ofertas educativas de la Facultad de Ciencias Agrarias de la UNJu / It generates summary measures and graphs for discrete or continuous numerical data in simple series. It also enables the creation of classic frequency tables and graphs when analyzing grouped series. Its purpose is for educational application in an introductory Biostatistics course using the R software, aimed at undergraduate programs and other educational offerings of the Faculty of Agricultural Sciences at the National University of Jujuy (UNJu).
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Depends: R (>= 4.1.0)
Language: es
Imports: ggplot2, tibble
NeedsCompilation: no
Packaged: 2025-01-31 16:03:06 UTC; usuario
Author: Juan Manuel Solis [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-03 11:30:02 UTC

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New package OPL with initial version 1.0.0
Package: OPL
Title: Optimal Policy Learning
Version: 1.0.0
Author: Federico Brogi [aut, cre], Barbara Guardabascio [aut], Giovanni Cerulli [aut]
Maintainer: Federico Brogi <federicobrogi@gmail.com>
Description: Provides functions for optimal policy learning in socioeconomic applications helping users to learn the most effective policies based on data in order to maximize empirical welfare. Specifically, 'OPL' allows to find "treatment assignment rules" that maximize the overall welfare, defined as the sum of the policy effects estimated over all the policy beneficiaries. Documentation about 'OPL' is provided by several international articles via Athey et al (2021, <doi:10.3982/ECTA15732>), Kitagawa et al (2018, <doi:10.3982/ECTA13288>), Cerulli (2022, <doi:10.1080/13504851.2022.2032577>), the paper by Cerulli (201, <doi:10.1080/13504851.2020.1820939>) and the book by Gareth et al (2013, <doi:10.1007/978-1-4614-7138-7>).
License: GPL-3
Encoding: UTF-8
Imports: stats, dplyr, ggplot2, pander, randomForest, tidyr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-31 20:54:44 UTC; UTENTE
Repository: CRAN
Date/Publication: 2025-02-03 12:00:05 UTC

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New package gimap with initial version 1.0.1
Package: gimap
Title: Calculate Genetic Interactions for Paired CRISPR Targets
Version: 1.0.1
Description: Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.
License: GPL-3
URL: https://github.com/FredHutch/gimap
BugReports: https://github.com/FredHutch/gimap/issues
Imports: readr, dplyr, tidyr, rmarkdown, vroom, ggplot2, magrittr, pheatmap, purrr, janitor, broom, utils, stats, stringr, httr, jsonlite, openssl
Suggests: testthat (>= 3.0.0), roxygen2, kableExtra, knitr
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-01-31 19:15:48 UTC; candacesavonen
Author: Candace Savonen [aut, cre], Phoebe Parrish [aut], Kate Isaac [aut], Howard Baek [aut], Daniel Grosso [aut], Siobhan O'Brien [aut], Alice Berger [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-03 11:50:03 UTC

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New package autoimport with initial version 0.1.1
Package: autoimport
Version: 0.1.1
Title: Automatic Generation of @importFrom Tags
Description: A toolbox to read all R files inside a package and automatically generate @importFrom 'roxygen2' tags in the right place. Includes a 'shiny' application to review the changes before applying them.
License: GPL-3
URL: https://github.com/DanChaltiel/autoimport, https://danchaltiel.github.io/autoimport/
BugReports: https://github.com/DanChaltiel/autoimport/issues
Depends: R (>= 3.6.0)
Imports: cli, desc, diffviewer, digest, dplyr, fs, glue, purrr, readr, rlang, shiny, stringr, tibble, tidyr, utils
Suggests: callr, covr, devtools, knitr, pkgload, rstudioapi, testthat (>= 3.0.0), tidyverse
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-01 09:31:57 UTC; Dan
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 12:00:02 UTC

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New package timeplyr with initial version 1.0.0
Package: timeplyr
Title: Fast Tidy Tools for Date and Date-Time Manipulation
Version: 1.0.0
Description: A set of fast tidy functions for wrangling, completing and summarising date and date-time data. It combines 'tidyverse' syntax with the efficiency of 'data.table' and speed of 'collapse'.
License: GPL (>= 2)
BugReports: https://github.com/NicChr/timeplyr/issues
Depends: R (>= 4.0.0)
Imports: cheapr (>= 1.0.0), cli, collapse (>= 2.0.0), cppdoubles (>= 0.2.0), data.table (>= 1.14.8), dplyr (>= 1.1.0), fastplyr (>= 0.5.0), ggplot2 (>= 3.4.0), lifecycle, lubridate (>= 1.9.0), pillar (>= 1.7.0), rlang (>= 1.0.0), scales, stringr (>= 1.4.0), tidyselect (>= 1.2.0), timechange (>= 0.2.0), vctrs (>= 0.6.0)
Suggests: bench, knitr, nycflights13, outbreaks, rmarkdown, testthat (>= 3.0.0), tidyr, zoo
LinkingTo: cpp11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-01 11:00:22 UTC; Nmc5
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-03 09:10:02 UTC

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Package RStoolbox updated to version 1.0.2.1 with previous version 1.0.1 dated 2025-02-01

Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] , Ned Horning [aut], Jakob Schwalb-Willmann [aut] , Robert J. Hijmans [ctb] , Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>

Diff between RStoolbox versions 1.0.1 dated 2025-02-01 and 1.0.2.1 dated 2025-02-03

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 RStoolbox-1.0.2.1/RStoolbox/R/spectralIndices.R                   |    7 
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 9 files changed, 214 insertions(+), 55 deletions(-)

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Package poweRlaw updated to version 1.0.0 with previous version 0.80.0 dated 2024-01-25

Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>

Diff between poweRlaw versions 0.80.0 dated 2024-01-25 and 1.0.0 dated 2025-02-03

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 tests/testthat/test_get_sims.R              |    8 +-
 tests/testthat/test_plot.R                  |   36 ++++++------
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Package mltest updated to version 1.0.3 with previous version 1.0.2 dated 2025-02-02

Title: Classification Evaluation Metrics
Description: A fast, robust and easy-to-use calculation of multi-class classification evaluation metrics based on confusion matrix.
Author: G. Dudnik [aut, cre, cph]
Maintainer: G. Dudnik <gl.dudnik@gmail.com>

Diff between mltest versions 1.0.2 dated 2025-02-02 and 1.0.3 dated 2025-02-03

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Package datacutr updated to version 0.2.3 with previous version 0.2.2 dated 2025-01-10

Title: SDTM Datacut
Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM), as part of the analysis of specific points in time of the data, normally as part of investigation into clinical trials. The functions support different approaches of cutting to the different domains of SDTM normally observed.
Author: Tim Barnett [cph, aut, cre], Nathan Rees [aut], Alana Harris [aut], Cara Andrews [aut]
Maintainer: Tim Barnett <timothy.barnett@roche.com>

Diff between datacutr versions 0.2.2 dated 2025-01-10 and 0.2.3 dated 2025-02-03

 DESCRIPTION                |    6 +++---
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 NEWS.md                    |    5 +++++
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Package rayvertex updated to version 0.12.0 with previous version 0.11.4 dated 2024-07-22

Title: 3D Software Rasterizer
Description: Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Author: Tyler Morgan-Wall [aut, cph, cre] , Syoyo Fujita [ctb, cph], Vilya Harvey [ctb, cph], G-Truc Creation [ctb, cph], Sean Barrett [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

Diff between rayvertex versions 0.11.4 dated 2024-07-22 and 0.12.0 dated 2025-02-03

 DESCRIPTION               |   14 ++---
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Package petersenlab updated to version 1.1.0 with previous version 1.0.0 dated 2024-04-30

Title: A Collection of R Functions by the Petersen Lab
Description: A collection of R functions that are widely used by the Petersen Lab. Included are functions for various purposes, including evaluating the accuracy of judgments and predictions, performing scoring of assessments, generating correlation matrices, conversion of data between various types, data management, psychometric evaluation, extensions related to latent variable modeling, various plotting capabilities, and other miscellaneous useful functions. By making the package available, we hope to make our methods reproducible and replicable by others and to help others perform their data processing and analysis methods more easily and efficiently. The codebase is provided in Petersen (2024) <doi:10.5281/zenodo.7602890> and on CRAN: <doi: 10.32614/CRAN.package.petersenlab>. The package is described in "Principles of Psychological Assessment: With Applied Examples in R" (Petersen, 2024, 2025) <doi:10.1201/9781003357421>, <doi:10.25820/work.007199>, <doi:10.5281/zenod [...truncated...]
Author: Isaac T. Petersen [aut, cre] , Developmental Psychopathology Lab at the University of Iowa [ctb], Angela D. Staples [ctb] , Johanna Caskey [ctb] , Philipp Doebler [ctb] , Loreen Sabel [ctb]
Maintainer: Isaac T. Petersen <isaac-t-petersen@uiowa.edu>

Diff between petersenlab versions 1.0.0 dated 2024-04-30 and 1.1.0 dated 2025-02-03

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 65 files changed, 754 insertions(+), 443 deletions(-)

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