Wed, 19 Feb 2025

Package mxfda updated to version 0.2.2-1 with previous version 0.2.2 dated 2024-10-07

Title: A Functional Data Analysis Package for Spatial Single Cell Data
Description: Methods and tools for deriving spatial summary functions from single-cell imaging data and performing functional data analyses. Functions can be applied to other single-cell technologies such as spatial transcriptomics. Functional regression and functional principal component analysis methods are in the 'refund' package <https://cran.r-project.org/package=refund> while calculation of the spatial summary functions are from the 'spatstat' package <https://spatstat.org/>.
Author: Julia Wrobel [aut] , Alex Soupir [aut, cre]
Maintainer: Alex Soupir <alex.soupir@moffitt.org>

Diff between mxfda versions 0.2.2 dated 2024-10-07 and 0.2.2-1 dated 2025-02-19

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Package sfhotspot updated to version 0.9.1 with previous version 0.9.0 dated 2025-02-10

Title: Hot-Spot Analysis with Simple Features
Description: Identify and understand clusters of points (typically representing the locations of places or events) stored in simple-features (SF) objects. This is useful for analysing, for example, hot-spots of crime events. The package emphasises producing results from point SF data in a single step using reasonable default values for all other arguments, to aid rapid data analysis by users who are starting out. Functions available include kernel density estimation (for details, see Yip (2020) <doi:10.22224/gistbok/2020.1.12>), analysis of spatial association (Getis and Ord (1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>) and hot-spot classification (Chainey (2020) ISBN:158948584X).
Author: Matt Ashby [aut, cre]
Maintainer: Matt Ashby <matthew.ashby@ucl.ac.uk>

Diff between sfhotspot versions 0.9.0 dated 2025-02-10 and 0.9.1 dated 2025-02-19

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Package wdiEF updated to version 1.0.3 with previous version 1.0.2 dated 2024-12-02

Title: Calculation of the Water Deficit Index (WDI) and the Evaporative Fraction (EF) on Rasters
Description: Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data, such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA). Terms like "raster", "CRS" are part of standard geospatial terminology.
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>

Diff between wdiEF versions 1.0.2 dated 2024-12-02 and 1.0.3 dated 2025-02-19

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Package tinytex updated to version 0.55 with previous version 0.54 dated 2024-11-01

Title: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] , Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] , Devon Ryan [ctb] , Ethan Heinzen [ctb], Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between tinytex versions 0.54 dated 2024-11-01 and 0.55 dated 2025-02-19

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Package coneproj updated to version 1.20 with previous version 1.19 dated 2024-06-11

Title: Primal or Dual Cone Projections with Routines for Constrained Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer [aut], Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>

Diff between coneproj versions 1.19 dated 2024-06-11 and 1.20 dated 2025-02-19

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Package circlus updated to version 0.0.2 with previous version 0.0.1 dated 2024-10-17

Title: Clustering and Simulation of Spherical Cauchy and PKBD Models
Description: Provides tools for estimation and clustering of spherical data, seamlessly integrated with the 'flexmix' package. Includes the necessary M-step implementations for both Poisson Kernel-Based Distribution (PKBD) and spherical Cauchy distribution. Additionally, the package provides random number generators for PKBD and spherical Cauchy distribution. Methods are based on Golzy M., Markatou M. (2020) <doi:10.1080/10618600.2020.1740713>, Kato S., McCullagh P. (2020) <doi:10.3150/20-bej1222> and Sablica L., Hornik K., Leydold J. (2023) <doi:10.1214/23-ejs2149>.
Author: Lukas Sablica [aut, cre] , Kurt Hornik [aut] , Bettina Gruen [aut] , Josef Leydold [aut]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>

Diff between circlus versions 0.0.1 dated 2024-10-17 and 0.0.2 dated 2025-02-19

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Package aftables updated to version 1.0.2 with previous version 1.0.1 dated 2025-02-19

Title: Create Spreadsheet Publications Following Best Practice
Description: Generate spreadsheet publications that follow best practice guidance from the UK government's Analysis Function, available at <https://analysisfunction.civilservice.gov.uk/policy-store/releasing-statistics-in-spreadsheets/>, with a focus on accessibility. See also the 'Python' package 'gptables'.
Author: Matt Dray [aut], Tim Taylor [ctb], Matt Kerlogue [ctb], Crown Copyright [cph], Olivia Box Power [cre, ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>

Diff between aftables versions 1.0.1 dated 2025-02-19 and 1.0.2 dated 2025-02-19

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Package xfun updated to version 0.51 with previous version 0.50 dated 2025-01-07

Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] , Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brueggemann [ctb] , Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package metricminer updated to version 1.0.0 with previous version 0.5.1 dated 2024-02-02

Title: Mine Metrics from Common Places on the Web
Description: Mine metrics on common places on the web through the power of their APIs (application programming interfaces). It also helps make the data in a format that is easily used for a dashboard or other purposes. There is an associated dashboard template and tutorials that are underdevelopment that help you fully utilize 'metricminer'.
Author: Candace Savonen [aut, cre], Howard Baek [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>

Diff between metricminer versions 0.5.1 dated 2024-02-02 and 1.0.0 dated 2025-02-19

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Package lares updated to version 5.2.13 with previous version 5.2.12 dated 2025-02-19

Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>

Diff between lares versions 5.2.12 dated 2025-02-19 and 5.2.13 dated 2025-02-19

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Package kerntools updated to version 1.2.0 with previous version 1.1.0 dated 2024-10-25

Title: Kernel Functions and Tools for Machine Learning Applications
Description: Kernel functions for diverse types of data (including, but not restricted to: nonnegative and real vectors, real matrices, categorical and ordinal variables, sets, strings), plus other utilities like kernel similarity, kernel Principal Components Analysis (PCA) and features' importance for Support Vector Machines (SVMs), which expand other 'R' packages like 'kernlab'.
Author: Elies Ramon [aut, cre, cph]
Maintainer: Elies Ramon <eramon@everlyrusher.com>

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Package jsonlite updated to version 1.9.0 with previous version 1.8.9 dated 2024-09-20

Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] , Duncan Temple Lang [ctb], Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

Diff between jsonlite versions 1.8.9 dated 2024-09-20 and 1.9.0 dated 2025-02-19

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Package viralmodels updated to version 1.3.3 with previous version 1.3.1 dated 2024-10-18

Title: Viral Load and CD4 Lymphocytes Regression Models
Description: Provides a comprehensive framework for building, evaluating, and visualizing regression models for analyzing viral load and CD4 (Cluster of Differentiation 4) lymphocytes data. It leverages the principles of the tidymodels ecosystem of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org> to offer a user-friendly experience in model development. This package includes functions for data preprocessing, feature engineering, model training, tuning, and evaluation, along with visualization tools to enhance the interpretation of model results. It is specifically designed for researchers in biostatistics, computational biology, and HIV research who aim to perform reproducible and rigorous analyses to gain insights into disease dynamics. The main focus is on improving the understanding of the relationships between viral load, CD4 lymphocytes, and other relevant covariates to contribute to HIV research and the visibility of vulnerable seropositive populations.
Author: Juan Pablo Acuna Gonzalez [aut, cre]
Maintainer: Juan Pablo Acuna Gonzalez <acua6307@gmail.com>

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Package watson updated to version 0.6 with previous version 0.5 dated 2024-11-19

Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions. The random sampling scheme of the package offers two sampling algorithms that are based of the results of Sablica, Hornik and Leydold (2022) <doi:10.1080/10618600.2024.2416521>. What is more, the package offers a smart tool to combine these two methods, and based on the selected parameters, it approximates the relative sampling speed for both methods and picks the faster one. In addition, the package offers a fitting function for the mixtures of Watson distribution, that uses the expectation-maximization (EM) algorithm. Special features are the possibility to use multiple variants of the E-step and M-step, sparse matrices for the data representation and state of the art methods for numerical evaluation of needed special functions using the results of Sablica and Hornik (2022) <doi:10.1090/mcom/3690> and Sablica and Hornik (2024) <doi:10.1016/j.jmaa.2024.128262>.
Author: Lukas Sablica [aut, cre] , Kurt Hornik [aut] , Josef Leydold [aut] , Gerard Jungman [ctb, cph] , Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>

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Package Rrepest updated to version 1.5.4 with previous version 1.5.3 dated 2025-02-17

Title: An Analyzer of International Large Scale Assessments in Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre], Francesco Avvisati [aut], Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>

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Package psborrow updated to version 0.2.2 with previous version 0.2.1 dated 2023-03-03

Title: Bayesian Dynamic Borrowing with Propensity Score
Description: A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.
Author: Isaac Gravestock [cre, ctb], Craig Gower-Page [aut], Matt Secrest [ctb], Yichen Lu [aut], Aijing Lin [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>

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Package MiscMetabar updated to version 0.14.1 with previous version 0.12.1 dated 2025-01-29

Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>

Diff between MiscMetabar versions 0.12.1 dated 2025-01-29 and 0.14.1 dated 2025-02-19

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 man/adonis_pq.Rd                                                       |    2 
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 man/ggbetween_pq.Rd                                                    |    2 
 man/ggscatt_pq.Rd                                                      |    2 
 man/glmutli_pq.Rd                                                      |    2 
 man/hill_curves_pq.Rd                                                  |    2 
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 man/lulu_pq.Rd                                                         |    2 
 man/multipatt_pq.Rd                                                    |    2 
 man/plot_LCBD_pq.Rd                                                    |    2 
 man/plot_SCBD_pq.Rd                                                    |    2 
 man/plot_tsne_pq.Rd                                                    |    2 
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 man/read_pq.Rd                                                         |    2 
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 man/track_wkflow.Rd                                                    |    2 
 man/treemap_pq.Rd                                                      |    2 
 man/tsne_pq.Rd                                                         |    2 
 man/umap_pq.Rd                                                         |    2 
 man/upset_pq.Rd                                                        |    2 
 man/upset_test_pq.Rd                                                   |    2 
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 man/write_pq.Rd                                                        |    2 
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Package maestro updated to version 0.5.1 with previous version 0.5.0 dated 2025-01-07

Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] , Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>

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Package RapidoPGS updated to version 2.3.1 with previous version 2.3.0 dated 2023-10-13

Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] , Chris Wallace [aut] , Olly Burren [ctb]
Maintainer: Guillermo Reales <gr440@cam.ac.uk>

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Package lares updated to version 5.2.12 with previous version 5.2.11 dated 2025-01-09

Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>

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Package tclust updated to version 2.1-0 with previous version 2.0-5 dated 2024-10-15

Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12>, Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Valentin Todorov [aut, cre] , Luis Angel Garcia Escudero [aut], Agustin Mayo Iscar [aut], Javier Crespo Guerrero [aut], Heinrich Fritz [aut]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

Diff between tclust versions 2.0-5 dated 2024-10-15 and 2.1-0 dated 2025-02-19

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Package CodelistGenerator updated to version 3.4.0 with previous version 3.3.2 dated 2025-01-28

Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] , Marti Catala [ctb] , Xihang Chen [aut] , Nuria Mercade-Besora [aut] , Mike Du [ctb] , Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

Diff between CodelistGenerator versions 3.3.2 dated 2025-01-28 and 3.4.0 dated 2025-02-19

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Package NewmanOmics updated to version 1.0.13 with previous version 1.0.11 dated 2024-04-28

Title: Extending the Newman Studentized Range Statistic to Transcriptomics
Description: Extends the classical Newman studentized range statistic in various ways that can be applied to genome-scale transcriptomic or other expression data.
Author: Zachary B. Abrams [aut], Greg Gershkowitz [aut], Anoushka Joglekar [aut], Chao Liu [aut], Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>

Diff between NewmanOmics versions 1.0.11 dated 2024-04-28 and 1.0.13 dated 2025-02-19

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Package jsmodule updated to version 1.6.3 with previous version 1.6.1 dated 2025-01-08

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd], Hyunki Lee [aut], Changwoo Lim [aut], Jinhwan Kim [aut] , Yoonkyoung Jeon [aut], Jaewoong Heo [aut], Youngsun Park [aut] , Hyungwoo Jo [aut], Jeongmin Seo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jsmodule versions 1.6.1 dated 2025-01-08 and 1.6.3 dated 2025-02-19

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Package easy.utils updated to version 0.1.0 with previous version 0.0.5 dated 2024-09-24

Title: Frequently Used Functions for Easy R Programming
Description: Some utility functions for validation and data manipulation. These functions can be helpful to reduce internal codes everywhere in package development.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <ycli1995@outlook.com>

Diff between easy.utils versions 0.0.5 dated 2024-09-24 and 0.1.0 dated 2025-02-19

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Package BioM2 updated to version 1.1.1 with previous version 1.1.0 dated 2024-09-20

Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang [aut, cre], Junfang Chen [aut]
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>

Diff between BioM2 versions 1.1.0 dated 2024-09-20 and 1.1.1 dated 2025-02-19

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Package tm updated to version 0.7-16 with previous version 0.7-15 dated 2024-11-18

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] , Kurt Hornik [aut, cre] , Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between tm versions 0.7-15 dated 2024-11-18 and 0.7-16 dated 2025-02-19

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Package relations updated to version 0.6-15 with previous version 0.6-14 dated 2024-11-13

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: David Meyer [aut] , Kurt Hornik [aut, cre] , Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between relations versions 0.6-14 dated 2024-11-13 and 0.6-15 dated 2025-02-19

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Package mappeR updated to version 2.0.1 with previous version 2.0.0 dated 2025-02-16

Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that uses techniques from topology to analyze high-dimensional data. Here we implement Mapper, an algorithm from this area developed by Singh, Mémoli and Carlsson (2007) which generalizes the concept of a Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>

Diff between mappeR versions 2.0.0 dated 2025-02-16 and 2.0.1 dated 2025-02-19

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Package cgam updated to version 1.23 with previous version 1.22 dated 2025-02-17

Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut], Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>

Diff between cgam versions 1.22 dated 2025-02-17 and 1.23 dated 2025-02-19

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Package BGmisc updated to version 1.3.3 with previous version 1.3.2 dated 2024-06-18

Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>], calculation of relatedness coefficients using path-tracing methods [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview, see Garrison et al. (2025) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] , Michael D. Hunter [aut] , Xuanyu Lyu [aut] , Rachel N. Good [ctb], Jonathan D. Trattner [aut] , S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>

Diff between BGmisc versions 1.3.2 dated 2024-06-18 and 1.3.3 dated 2025-02-19

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Package gpboost updated to version 1.5.6 with previous version 1.5.5.1 dated 2025-01-20

Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre], Tim Gyger [aut], Pascal Kuendig [aut], Benoit Jacob [cph], Gael Guennebaud [cph], Nicolas Carre [cph], Pierre Zoppitelli [cph], Gauthier Brun [cph], Jean Ceccato [cph], Jitse Niesen [cph], Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>

Diff between gpboost versions 1.5.5.1 dated 2025-01-20 and 1.5.6 dated 2025-02-19

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Package curl updated to version 6.2.1 with previous version 6.2.0 dated 2025-01-23

Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] , Hadley Wickham [ctb], Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

Diff between curl versions 6.2.0 dated 2025-01-23 and 6.2.1 dated 2025-02-19

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Package plumber updated to version 1.3.0 with previous version 1.2.2 dated 2024-03-25

Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.
Author: Barret Schloerke [cre, aut] , Jeff Allen [aut, ccp], Bruno Tremblay [ctb], Frans van Dunne [ctb], Sebastiaan Vandewoude [ctb], Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>

Diff between plumber versions 1.2.2 dated 2024-03-25 and 1.3.0 dated 2025-02-19

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Package PL94171 updated to version 1.1.3 with previous version 1.1.2 dated 2022-09-11

Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files produced by the United States Census Bureau pursuant to P.L. 94-171. These files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre], Christopher T. Kenny [aut]
Maintainer: Cory McCartan <mccartan@psu.edu>

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Tue, 18 Feb 2025

Package workflows updated to version 1.2.0 with previous version 1.1.4 dated 2024-02-19

Title: Modeling Workflows
Description: Managing both a 'parsnip' model and its data preparation steps, such as a model formula or recipe from 'recipes', can often be challenging. The goal of 'workflows' is to streamline this process by bundling the model with its data preparation, all within the same object.
Author: Davis Vaughan [aut], Simon Couch [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>

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Package RcppDE updated to version 0.1.8 with previous version 0.1.7 dated 2022-12-20

Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim' function which performs global optimization by differential evolution. Its creation was motivated by trying to see if the old approximation "easier, shorter, faster: pick any two" could in fact be extended to achieving all three goals while moving the code from plain old C to modern C++. The initial version did in fact do so, but a good part of the gain was due to an implicit code review which eliminated a few inefficiencies which have since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel [aut, cre] , David Ardia [aut] , Katharine Mullen [aut] , Brian Peterson [aut] , Joshua Ulrich [aut] , Kris Boudt [ctb] , Rainer Storn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package nlmixr2est updated to version 3.0.4 with previous version 3.0.3 dated 2025-01-18

Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] , Yuan Xiong [aut], Rik Schoemaker [aut] , Justin Wilkins [aut] , Wenping Wang [aut], Robert Leary [ctb], Mason McComb [ctb] , Vipul Mann [aut], Mirjam Trame [ctb], Mahmoud Abdelwahab [ctb], Teun Post [ctb], Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

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Package NaileR updated to version 1.2.2 with previous version 1.2.1 dated 2024-11-11

Title: Interpreting Latent Variables with AI
Description: A small package designed for interpreting continuous and categorical latent variables. You provide a data set with a latent variable you want to understand and some other explanatory variables. It provides a description of the latent variable based on the explanatory variables. It also provides a name to the latent variable.
Author: Nel Herve [aut], Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>

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Package mvgam updated to version 1.1.4 with previous version 1.1.3 dated 2024-09-03

Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] , Sarah Heaps [ctb] , Scott Pease [ctb] , Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>

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Package conquestr updated to version 1.4.5 with previous version 1.3.4 dated 2024-07-24

Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions designed to improve graphical outputs and help with advanced analysis (e.g., differential item functioning). Allows R users to call 'ACER ConQuest' from within R and read 'ACER ConQuest' System Files (generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>). Requires 'ACER ConQuest' version 5.40 or later. A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] , Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>

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Package SimTOST updated to version 1.0.2 with previous version 1.0.1 dated 2025-02-18

Title: Sample Size Estimation for Bio-Equivalence Trials Through Simulation
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints. Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability, and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987) <doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022) <doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>. Comprehensive documentation and vignettes guid [...truncated...]
Author: Thomas Debray [aut, cre] , Johanna Munoz [aut], Dewi Amaliah [ctb], Wei Wei [ctb], Marian Mitroiu [ctb], Scott McDonald [ctb], Biogen Inc [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>

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Package RRPP updated to version 2.1.2 with previous version 2.1.1 dated 2025-02-09

Title: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
Description: Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] , Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>

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Package r2dii.plot updated to version 0.5.1 with previous version 0.5.0 dated 2025-02-12

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

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Package ps updated to version 1.9.0 with previous version 1.8.1 dated 2024-10-28

Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gabor Csardi [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

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Package plmmr updated to version 4.2.0 with previous version 4.1.0 dated 2024-10-23

Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for unobserved confounding factors. 'plmmr' infers and corrects for the presence of unobserved confounding effects such as population stratification and environmental heterogeneity. It then fits a linear model via penalized maximum likelihood. Originally designed for the multivariate analysis of single nucleotide polymorphisms (SNPs) measured in a genome-wide association study (GWAS), 'plmmr' eliminates the need for subpopulation-specific analyses and post-analysis p-value adjustments. Functions for the appropriate processing of 'PLINK' files are also supplied. For examples, see the package homepage. <https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] , Anna C. Reisetter [aut] , Patrick J. Breheny [aut, cre] , Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>

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Package mlr3cluster updated to version 0.1.11 with previous version 0.1.10 dated 2024-10-03

Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] , Damir Pulatov [aut], Michel Lang [aut] , Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>

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Package MixedPsy updated to version 1.2.0 with previous version 1.1.0 dated 2021-11-08

Title: Statistical Tools for the Analysis of Psychophysical Data
Description: Tools for the analysis of psychophysical data in R. This package allows to estimate the Point of Subjective Equivalence (PSE) and the Just Noticeable Difference (JND), either from a psychometric function or from a Generalized Linear Mixed Model (GLMM). Additionally, the package allows plotting the fitted models and the response data, simulating psychometric functions of different shapes, and simulating data sets. For a description of the use of GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012).
Author: Alessandro Moscatelli [aut, cre] , Priscilla Balestrucci [aut]
Maintainer: Alessandro Moscatelli <moskante@gmail.com>

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Package metaGE updated to version 1.2.0 with previous version 1.1.0 dated 2024-07-31

Title: Meta-Analysis for Detecting Genotype x Environment Associations
Description: Provides functions to perform all steps of genome-wide association meta-analysis for studying Genotype x Environment interactions, from collecting the data to the manhattan plot. The procedure accounts for the potential correlation between studies. In addition to the Fixed and Random models, one can investigate the relationship between QTL effects and some qualitative or quantitative covariate via the test of contrast and the meta-regression, respectively. The methodology is available from: (De Walsche, A., et al. (2023) \doi{10.1101/2023.03.01.530237}).
Author: Annaig De Walsche [aut, cre] , Tristan Mary-Huard [aut]
Maintainer: Annaig De Walsche <annaig.de-walsche@inrae.fr>

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Package logrx updated to version 0.3.2 with previous version 0.3.1 dated 2024-04-11

Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre], Thomas Bermudez [aut], Ben Straub [aut], Michael Rimler [aut], Nicholas Masel [aut], Sam Parmar [aut], GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>

Diff between logrx versions 0.3.1 dated 2024-04-11 and 0.3.2 dated 2025-02-18

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Package gimap updated to version 1.0.2 with previous version 1.0.1 dated 2025-02-03

Title: Calculate Genetic Interactions for Paired CRISPR Targets
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>.
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>

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Package Benchmarking updated to version 0.33 with previous version 0.32 dated 2024-03-13

Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.
Author: Peter Bogetoft [aut], Lars Otto [aut, cre]
Maintainer: Lars Otto <larsot23@gmail.com>

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Package r2dii.analysis updated to version 0.5.1 with previous version 0.5.0 dated 2025-02-13

Title: Measure Climate Scenario Alignment of Corporate Loans
Description: These tools help you to assess if a corporate lending portfolio aligns with climate goals. They summarize key climate indicators attributed to the portfolio (e.g. production, emission factors), and calculate alignment targets based on climate scenarios. They implement in R the last step of the free software 'PACTA' (Paris Agreement Capital Transition Assessment; <https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals.
Author: Jacob Kastl [aut, cre, ctr] , Alex Axthelm [aut, ctr] , Jackson Hoffart [aut, ctr] , Mauro Lepore [aut, ctr] , Klaus Hogedorn [aut], Nicky Halterman [aut], RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>

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Package enderecobr updated to version 0.4.1 with previous version 0.4.0 dated 2025-01-14

Title: Padronizador de Endereços Brasileiros (Brazilian Addresses Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes critérios. Os métodos de padronização incluem apenas manipulações básicas de strings, não oferecendo suporte a correspondências probabilísticas entre strings. (Standardizes brazilian addresses using different criteria. Standardization methods include only basic string manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] , Rafael H. M. Pereira [aut] , Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>

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Package AID updated to version 3.1 with previous version 3.0 dated 2024-11-22

Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Muhammed Ali Yilmaz [aut], Ozgur Asar [ctb], Ozlem Ilk [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>

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Package calidad updated to version 0.7.0 with previous version 0.6.0 dated 2024-10-16

Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs, following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>) and by Economic Commission for Latin America and Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Author: Klaus Lehmann [aut, cre], Ricardo Pizarro [aut], Ignacio Agloni [ctb], Andrea Lopez [ctb], Javiera Preuss [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>

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Package spiro updated to version 0.2.3 with previous version 0.2.1 dated 2023-08-14

Title: Manage Data from Cardiopulmonary Exercise Testing
Description: Import, process, summarize and visualize raw data from metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Author: Simon Nolte [aut, cre] , Manuel Ramon [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/541>), James Hunter [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/541>)
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>

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Package ursa updated to version 3.11.3 with previous version 3.11.2 dated 2025-01-14

Title: Non-Interactive Spatial Tools for Raster Processing and Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sev-in.ru>

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Package ProtE updated to version 1.0.3 with previous version 1.0.2 dated 2025-02-17

Title: Processing Proteomics Data, Statistical Analysis and Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>

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Package clarabel updated to version 0.10.0 with previous version 0.9.0.1 dated 2024-09-03

Title: Interior Point Conic Optimization Solver
Description: A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Author: Balasubramanian Narasimhan [aut, cre], Paul Goulart [aut, cph], Yuwen Chen [aut], Hiroaki Yutani [ctb] , David Zimmermann-Kollenda [ctb] , Hiroaki Yutani [ctb] , The authors of the dependency Rust crates [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>

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Package XLConnect updated to version 1.2.0 with previous version 1.1.0 dated 2024-08-22

Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] , Graph Builder [ctb, cph] , Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>

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Package TransProR updated to version 1.0.3 with previous version 1.0.2 dated 2025-02-14

Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>

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Package sae.projection updated to version 0.1.2 with previous version 0.1.1 dated 2025-02-15

Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut] , Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>

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Package dartRverse updated to version 1.0.6 with previous version 1.0.2 dated 2024-05-24

Title: Install and Load the 'dartRverse' Suits of Packages
Description: Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [aut], Oliver Berry [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

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Package cardx updated to version 0.2.3 with previous version 0.2.2 dated 2024-11-27

Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] , Abinaya Yogasekaram [aut], Emily de la Rua [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package iNEXT.3D updated to version 1.0.8 with previous version 1.0.7 dated 2025-01-22

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

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Mon, 17 Feb 2025

Package RConics updated to version 1.1.2 with previous version 1.1.1 dated 2022-03-11

Title: Computations on Conics
Description: Solve some conic related problems (intersection of conics with lines and conics, arc length of an ellipse, polar lines, etc.).
Author: Emanuel Huber [aut, cre]
Maintainer: Emanuel Huber <emanuel.huber@pm.me>

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Package cata updated to version 0.1.0.26 with previous version 0.1.0.7 dated 2024-10-08

Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Package contains functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis are provided; for details, see Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis, then evaluated using various measures; for details, see Castura, Meyners, Varela & Næs (2022) <doi:10.1016/j.foodqual.2022.104564>. Methods are adapted to cluster consumers based on their product-related hedonic responses; for details, see Castura, Meyners, Pohjanheimo, Varela & Næs (2023) <doi:10.1111/joss.12860>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>

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Package UAHDataScienceUC updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-17

Title: Learn Clustering Techniques Through Examples and Code
Description: A comprehensive educational package combining clustering algorithms with detailed step-by-step explanations. Provides implementations of both traditional (hierarchical, k-means) and modern (Density-Based Spatial Clustering of Applications with Noise (DBSCAN), Gaussian Mixture Models (GMM), genetic k-means) clustering methods as described in Ezugwu et. al., (2022) <doi:10.1016/j.engappai.2022.104743>. Includes educational datasets highlighting different clustering challenges, based on 'scikit-learn' examples (Pedregosa et al., 2011) <https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html>. Features detailed algorithm explanations, visualizations, and weighted distance calculations for enhanced learning.
Author: Eduardo Ruiz Sabajanes [aut], Roberto Alcantara [aut], Juan Jose Cuadrado Gallego [aut] , Andriy Protsak Protsak [aut, cre], Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>

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Package geocodebr updated to version 0.1.1 with previous version 0.1.0 dated 2025-02-12

Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O pacote é baseado em conjuntos de dados espaciais abertos de endereços brasileiros, utilizando principalmente o Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia do Brasil. (A simple and efficient method for geolocating data in Brazil. The package is based on open spatial datasets of Brazilian addresses, primarily using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE), published by the Instituto Brasileiro de Geografia e Estatística (IBGE), Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] , Daniel Herszenhut [aut] , Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>

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Package fdasrvf updated to version 2.3.6 with previous version 2.3.5 dated 2025-02-11

Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] , Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>

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Package cards updated to version 0.5.0 with previous version 0.4.0 dated 2024-11-27

Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] , Becca Krouse [aut], Emily de la Rua [aut], F. Hoffmann-La Roche AG [cph, fnd], GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package blocklength updated to version 0.2.0 with previous version 0.1.5 dated 2022-03-02

Title: Select an Optimal Block-Length to Bootstrap Dependent Data (Block Bootstrap)
Description: A set of functions to select the optimal block-length for a dependent bootstrap (block-bootstrap). Includes the Hall, Horowitz, and Jing (1995) <doi:10.1093/biomet/82.3.561> subsampling-based cross-validation method, the Politis and White (2004) <doi:10.1081/ETC-120028836> Spectral Density Plug-in method, including the Patton, Politis, and White (2009) <doi:10.1080/07474930802459016> correction, and the Lahiri, Furukawa, and Lee (2007) <doi:10.1016/j.stamet.2006.08.002> nonparametric plug-in method, with a corresponding set of S3 plot methods.
Author: Alec Stashevsky [aut, cre] , Sergio Armella [ctb]
Maintainer: Alec Stashevsky <alec@alecstashevsky.com>

Diff between blocklength versions 0.1.5 dated 2022-03-02 and 0.2.0 dated 2025-02-17

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Package BaseSet updated to version 1.0.0 with previous version 0.9.0 dated 2023-08-22

Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets, doing intersection, union, complementary sets, power sets, cartesian product and other set operations in a "tidy" way. These set operations are available for both classical sets and fuzzy sets. Import sets from several formats or from other several data structures.
Author: Lluis Revilla Sancho [aut, cre, cph] , Zebulun Arendsee [rev], Jennifer Chang [rev]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>

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Package sgboost updated to version 0.2.0 with previous version 0.1.3 dated 2024-05-19

Title: Sparse-Group Boosting
Description: Sparse-group boosting to be used in conjunction with the 'mboost' for modeling grouped data. Applicable to all sparse-group lasso type problems where within-group and between-group sparsity is desired. Interprets and visualizes individual variables and groups.
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>

Diff between sgboost versions 0.1.3 dated 2024-05-19 and 0.2.0 dated 2025-02-17

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Package NNS updated to version 11.1 with previous version 11.0 dated 2025-01-10

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre], Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Permanent link

Package MLE updated to version 1.4 with previous version 1.3 dated 2024-12-16

Title: Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre], Sofia Piperaki [aut], Muhammad Imran [ctb], Rafail Vargiakakis [aut], Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package cgam updated to version 1.22 with previous version 1.21 dated 2023-08-10

Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut], Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>

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Package readsparse updated to version 0.1.5-8 with previous version 0.1.5-6 dated 2023-11-27

Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM' Formats
Description: Read and write labelled sparse matrices in text format as used by software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM', and others. Supports labelled data for regression, classification (binary, multi-class, multi-label), and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes [aut, cre, cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package ProtE updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-15

Title: Processing Proteomics Data, Statistical Analysis and Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>

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Package pxmake updated to version 0.15.1 with previous version 0.14.2 dated 2025-01-22

Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones. Includes a function for every PX keyword, making metadata manipulation simple and human-readable.
Author: Johan Ejstrud [cre, aut], Lars Pedersen [aut], Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>

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Package OPL updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-03

Title: Optimal Policy Learning
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 (2021, <doi:10.1080/13504851.2020.1820939>) and the book by Gareth et al (2013, <doi:10.1007/978-1-4614-7138-7>).
Author: Federico Brogi [aut, cre], Barbara Guardabascio [aut], Giovanni Cerulli [aut]
Maintainer: Federico Brogi <federicobrogi@gmail.com>

Diff between OPL versions 1.0.0 dated 2025-02-03 and 1.0.1 dated 2025-02-17

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Package Rrepest updated to version 1.5.3 with previous version 1.5.2 dated 2025-02-10

Title: An Analyzer of International Large Scale Assessments in Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre], Francesco Avvisati [aut], Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>

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Package pathfindR updated to version 2.4.2 with previous version 2.4.1 dated 2024-05-04

Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] , Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>

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Package gdverse updated to version 1.3-2 with previous version 1.3-1 dated 2024-12-14

Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] , Yangyang Lei [aut] , Fangmei Liu [aut] , Jianwu Yan [aut] , Yongze Song [aut] , Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>

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Package survivalSL updated to version 0.97.1 with previous version 0.97 dated 2025-01-29

Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] , Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>

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Package rstanemax updated to version 0.1.9 with previous version 0.1.8 dated 2025-02-05

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>

Diff between rstanemax versions 0.1.8 dated 2025-02-05 and 0.1.9 dated 2025-02-17

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Package FLORAL updated to version 0.4.0 with previous version 0.3.0 dated 2024-08-20

Title: Fit Log-Ratio Lasso Regression for Compositional Data
Description: Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.
Author: Teng Fei [aut, cre, cph] , Tyler Funnell [aut] , Nicholas Waters [aut] , Sandeep Raj [aut]
Maintainer: Teng Fei <feit1@mskcc.org>

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Package nlmixr2extra updated to version 3.0.2 with previous version 3.0.1 dated 2024-10-29

Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.
Author: Matthew Fidler [aut, cre] , Vipul Mann [aut], Vishal Sarsani [aut] , Christian Bartels [ctb], Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

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Sun, 16 Feb 2025

Package waywiser updated to version 0.6.1 with previous version 0.6.0 dated 2024-06-27

Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be challenging, both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors, with "hot spots" of higher than expected error clustered geographically due to spatial structure in the underlying data. Methods are provided for assessing models fit to spatial data, including approaches for measuring the spatial structure of model errors, assessing model predictions at multiple spatial scales, and evaluating where predictions can be made safely. Methods are particularly useful for models fit using the 'tidymodels' framework. Methods include Moran's I ('Moran' (1950) <doi:10.2307/2332142>), Geary's C ('Geary' (1954) <doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from 'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement m [...truncated...]
Author: Michael Mahoney [aut, cre] , Lucas Johnson [ctb] , Virgilio Gomez-Rubio [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571>), Jakub Nowosad [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>

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Package EFAfactors updated to version 1.2.1 with previous version 1.2.0 dated 2025-01-07

Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor Analysis (EFA), making it easier to determine the number of factors. Traditional methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>, Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis (PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA are readily available. This package also implements several newer methods, such as the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017) <doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012) <doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011) <doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like Comparison Data Forest (CDF) by Goretzko and Ruscio (2024) <doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph] , Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>

Diff between EFAfactors versions 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-02-16

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Package rsparse updated to version 0.5.3 with previous version 0.5.2 dated 2024-06-28

Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on sparse matrices - matrix factorizations, matrix completion, elastic net regressions, factorization machines. Also 'rsparse' enhances 'Matrix' package by providing methods for multithreaded <sparse, dense> matrix products and native slicing of the sparse matrices in Compressed Sparse Row (CSR) format. List of the algorithms for regression problems: 1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL) Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>) 2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>) List of algorithms for matrix factorization and matrix completion: 1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>) 2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro (2005, <doi:10.1145/110 [...truncated...]
Author: Dmitriy Selivanov [aut, cre, cph] , David Cortes [ctb], Drew Schmidt [ctb] , Wei-Chen Chen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>

Diff between rsparse versions 0.5.2 dated 2024-06-28 and 0.5.3 dated 2025-02-16

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Package pqrBayes updated to version 1.1.0 with previous version 1.0.5 dated 2025-02-05

Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable selection and statistical inference. In this package, we have implemented robust Bayesian variable selection with spike-and-slab priors under high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular, valid robust Bayesian inferences under both models in the presence of heavy-tailed errors can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut], Cen Wu [aut, cre], Jie Ren [aut], Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>

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Package modEvA updated to version 3.29 with previous version 3.23 dated 2024-11-24

Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre], Jennifer A. Brown [aut], Alberto Jimenez-Valverde [aut], Raimundo Real [aut], Oswald van Ginkel [ctb], Jurica Levatic [ctb], Victoria Formoso-Freire [ctb], Andres Baselga [ctb], Carola Gomez-Rodriguez [ctb], Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>

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Package mappeR updated to version 2.0.0 with previous version 1.3.0 dated 2024-10-30

Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that uses techniques from topology to analyze high-dimensional data. Here we implement Mapper, an algorithm from this area developed by Singh, Mémoli and Carlsson (2007) which generalizes the concept of a Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>

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Package jmvReadWrite updated to version 0.4.10 with previous version 0.4.9 dated 2025-01-16

Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (<https://www.jamovi.org>) aims to make statistical analyses easy and intuitive. 'jamovi' produces syntax that can directly be used in R (in connection with the R-package 'jmv'). Having import / export routines for the data files 'jamovi' produces ('.omv') permits an easy transfer of data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>

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Package CCAMLRGIS updated to version 4.2.1 with previous version 4.2.0 dated 2024-10-15

Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources. Provides two categories of functions: load functions and create functions. Load functions are used to import existing spatial layers from the online CCAMLR GIS such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.
Author: Stephane Thanassekos [aut, cre], Keith Reid [aut], Lucy Robinson [aut], Michael D. Sumner [ctb], Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>

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Package assessor updated to version 1.1.1 with previous version 1.1.0 dated 2024-04-03

Title: Assessment Tools for Regression Models with Discrete and Semicontinuous Outcomes
Description: Provides assessment tools for regression models with discrete and semicontinuous outcomes proposed in Yang (2023) <doi:10.48550/arXiv.2308.15596>. It calculates the double probability integral transform (DPIT) residuals, constructs QQ plots of residuals and the ordered curve for assessing mean structures.
Author: Lu Yang [aut], Jeonghwan Lee [cre, aut]
Maintainer: Jeonghwan Lee <lee03938@umn.edu>

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Package asremlPlus updated to version 4.4.46 with previous version 4.4.43 dated 2024-12-10

Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

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Package PhenotypeR updated to version 0.1.3 with previous version 0.1.2 dated 2025-02-05

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 nanonext updated to version 1.5.1 with previous version 1.5.0 dated 2025-01-27

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

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Package rjaf updated to version 0.1.2 with previous version 0.1.1 dated 2024-12-08

Title: Regularized Joint Assignment Forest with Treatment Arm Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] , Xinyi Zhang [aut, cre, cph] , Jann Spiess [aut, cph] , Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>

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Package urlshorteneR updated to version 1.6.0 with previous version 1.5.7 dated 2022-08-22

Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening Services
Description: Allows using two URL shortening services, which also provide expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).
Author: John Malc [aut, cre] , Andrea Dodet [ctb] , Stephen Synchronicity [ctb]
Maintainer: John Malc <cincenko@outlook.com>

Diff between urlshorteneR versions 1.5.7 dated 2022-08-22 and 1.6.0 dated 2025-02-16

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Package subincomeR updated to version 0.3.0 with previous version 0.2.2 dated 2024-12-19

Title: Access to Global Sub-National Income Data
Description: Provides access to granular sub-national income data from the MCC-PIK Database Of Sub-national Economic Output (DOSE). The package downloads and processes the data from its open repository on 'Zenodo' (<https://zenodo.org/records/13773040>). Functions are provided to fetch data at multiple geographic levels, match coordinates to administrative regions, and access associated geometries.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>

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Package CohortConstructor updated to version 0.3.5 with previous version 0.3.4 dated 2025-01-17

Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] , Marti Catala [aut] , Nuria Mercade-Besora [aut] , Marta Alcalde-Herraiz [aut] , Mike Du [aut] , Yuchen Guo [aut] , Xihang Chen [aut] , Kim Lopez-Guell [aut] , Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

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Package nda updated to version 0.2.4 with previous version 0.1.15 dated 2024-10-14

Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre], Marcell T. Kurbucz [aut], Attila I. Katona [aut], Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>

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Package gibasa updated to version 1.1.2 with previous version 1.1.1 dated 2024-07-05

Title: An Alternative 'Rcpp' Wrapper of 'MeCab'
Description: A plain 'Rcpp' wrapper for 'MeCab' that can segment Chinese, Japanese, and Korean text into tokens. The main goal of this package is to provide an alternative to 'tidytext' using morphological analysis.
Author: Akiru Kato [aut, cre], Shogo Ichinose [aut], Taku Kudo [aut], Jorge Nocedal [ctb], Nippon Telegraph and Telephone Corporation [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>

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

Title: Access Colombia's Public Data via 'API-Colombia'
Description: Provides a seamless interface to access diverse public data about Colombia through the 'API-Colombia', a RESTful API. The package enables users to explore various aspects of Colombia, including general information, geography, and cultural insights. It includes five API-related functions to retrieve data on topics such as Colombia's general information, airports, departments, regions, and presidents. Additionally, 'ColombiAPI' offers a built-in function to view the datasets available within the package. The package also includes curated datasets covering Bogota air stations, business and holiday dates, public schools, Colombian coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota, making it a comprehensive tool for exploring Colombia's data. For more details on the 'API-Colombia', see <https://api-colombia.com/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>

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Sat, 15 Feb 2025

Package divo updated to version 1.0.2 with previous version 1.0.1 dated 2019-12-16

Title: Tools for Analysis of Diversity and Similarity in Biological Systems
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in a population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Christoph Sadee [aut], Maciej Pietrzak [aut, cre], Michal Seweryn [aut], Cankun Wang [aut], Grzegorz Rempala [aut]
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>

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Package fixr updated to version 0.2.0 with previous version 0.1.0 dated 2023-04-20

Title: Fixing Data Made Easy for Statistical Analysis
Description: A set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.
Author: Ambu Vijayan [aut, cre] , J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>

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Package aqp updated to version 2.2 with previous version 2.1.0 dated 2024-10-19

Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

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Package deBif updated to version 0.1.9 with previous version 0.1.8 dated 2023-12-04

Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary differential equations. The package allows for computation of equilibrium curves as a function of a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along these curves, and computation of curves representing these transcritical, saddle-node and hopf bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995; ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>

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Package TDAvec updated to version 0.1.4 with previous version 0.1.3 dated 2022-10-31

Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency, all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut], Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>

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Package openxlsx2 updated to version 1.13 with previous version 1.12 dated 2024-12-19

Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.
Author: Jordan Mark Barbone [aut] , Jan Marvin Garbuszus [aut, cre], Olivier Roy [ctb], openxlsx authors [cph] , Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>

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Package patterncausality updated to version 0.2.1 with previous version 0.2.0 dated 2025-01-09

Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut] , Athanasios Pantelous [aut] , Hui Wang [aut, cre]
Maintainer: Hui Wang <huiw1128@gmail.com>

Diff between patterncausality versions 0.2.0 dated 2025-01-09 and 0.2.1 dated 2025-02-15

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Package sae.projection updated to version 0.1.1 with previous version 0.1.0 dated 2024-12-19

Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut] , Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>

Diff between sae.projection versions 0.1.0 dated 2024-12-19 and 0.1.1 dated 2025-02-15

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Package rix updated to version 0.15.2 with previous version 0.14.4 dated 2025-01-21

Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] , Philipp Baumann [aut] , David Watkins [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/625>), Jacob Wujiciak-Jens [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>

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Package dtreg updated to version 1.1.1 with previous version 1.1.0 dated 2024-12-02

Title: Interact with Data Type Registries and Create Machine-Readable Data
Description: You can load a schema from a DTR (data type registry) as an R object. Use this schema to write your data in JSON-LD (JavaScript Object Notation for Linked Data) format to make it machine readable.
Author: Olga Lezhnina [aut, cre] , Manuel Prinz [aut] , Markus Stocker [aut] , Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Olga Lezhnina <olga.lezhnina@tib.eu>

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Package rolog updated to version 0.9.20 with previous version 0.9.18 dated 2024-07-09

Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] , European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>

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Package IceSat2R updated to version 1.0.7 with previous version 1.0.6 dated 2024-08-17

Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] , OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package flexsurvcure updated to version 1.3.3 with previous version 1.3.1 dated 2022-11-01

Title: Flexible Parametric Cure Models
Description: Flexible parametric mixture and non-mixture cure models for time-to-event data.
Author: Jordan Amdahl [aut, cre]
Maintainer: Jordan Amdahl <jrdnmdhl@gmail.com>

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Package MapperAlgo updated to version 1.0.2 with previous version 1.0.1 dated 2024-12-08

Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl], Paul Pearson [ctb], Daniel Muellner [ctb], Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>

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Package r2redux updated to version 1.0.18 with previous version 1.0.17 dated 2023-11-28

Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph], Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>

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Package oneinfl updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-06

Title: Estimates OIPP and OIZTNB Regression Models
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>.
Author: Ryan T. Godwin [aut, cre]
Maintainer: Ryan T. Godwin <ryan.godwin@umanitoba.ca>

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Fri, 14 Feb 2025

Package ife updated to version 0.1.12 with previous version 0.1.0 dated 2024-11-08

Title: Influence Function Based Estimate Objects
Description: Implements an S7 class for estimates based on influence functions. Standard arithmetic operations are defined for the class.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>

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Package R6 updated to version 2.6.1 with previous version 2.6.0 dated 2025-02-12

Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Winston Chang <winston@posit.co>

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Package nlive updated to version 0.7.0 with previous version 0.6.0 dated 2024-05-26

Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] , Ana W. Capuano [aut], Emmanuelle Comets [ctb]
Maintainer: Maude Wagner <maude_wagner@rush.edu>

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Package PhylogeneticEM updated to version 1.8.0 with previous version 1.7.0 dated 2024-01-31

Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>

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Package nhdplusTools updated to version 1.3.1 with previous version 1.3.0 dated 2024-12-18

Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] , Mike Johnson [aut] , Marc Weber [ctb] , Josh Erickson [ctb], Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package torch updated to version 0.14.2 with previous version 0.14.1 dated 2025-02-03

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>

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Package TapeS updated to version 0.13.3 with previous version 0.13.2 dated 2025-01-22

Title: Tree Taper Curves and Sorting Based on 'TapeR'
Description: Providing new german-wide 'TapeR' Models and functions for their evaluation. Included are the most common tree species in Germany (Norway spruce, Scots pine, European larch, Douglas fir, Silver fir as well as European beech, Common/Sessile oak and Red oak). Many other species are mapped to them so that 36 tree species / groups can be processed. Single trees are defined by species code, one or multiple diameters in arbitrary measuring height and tree height. The functions then provide information on diameters along the stem, bark thickness, height of diameters, volume of the total or parts of the trunk and total and component above-ground biomass. It is also possible to calculate assortments from the taper curves. Uncertainty information is provided for diameter, volume and component biomass estimation.
Author: Christian Vonderach [aut, cre], Edgar Kublin [aut], Gerald Kaendler [aut]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>

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Package solvebio updated to version 2.15.1 with previous version 2.15.0 dated 2024-08-16

Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs.
Author: Tobi Guennel [aut, cre]
Maintainer: Tobi Guennel <tobi.guennel@precisionformedicine.com>

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Package jobqueue updated to version 1.3.1 with previous version 1.3.0 dated 2025-02-13

Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>

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Package bootStateSpace updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-22

Title: Bootstrap for State Space Models
Description: Provides a streamlined and user-friendly framework for bootstrapping in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>

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Package BayesChange updated to version 1.1.1 with previous version 1.1.0 dated 2025-02-13

Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] , Riccardo Corradin [aut], Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>

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Package simStateSpace updated to version 1.2.9 with previous version 1.2.8 dated 2025-01-23

Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework for simulating data in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>

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Package rKIN updated to version 1.0.3 with previous version 1.0.2 dated 2023-10-02

Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but instead of geospatial coordinates, we use isotopic coordinates. The estimation methods include: 1) 2-dimensional bivariate normal kernel utilization density estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon estimator, all applied to stable isotope data. Additionally, functions to determine niche area, polygon overlap between groups and levels (confidence contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>

Diff between rKIN versions 1.0.2 dated 2023-10-02 and 1.0.3 dated 2025-02-14

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Package censored updated to version 0.3.3 with previous version 0.3.2 dated 2024-06-11

Title: 'parsnip' Engines for Survival Models
Description: Engines for survival models from the 'parsnip' package. These include parametric models (e.g., Jackson (2016) <doi:10.18637/jss.v070.i08>), semi-parametric (e.g., Simon et al (2011) <doi:10.18637/jss.v039.i05>), and tree-based models (e.g., Buehlmann and Hothorn (2007) <doi:10.1214/07-STS242>).
Author: Emil Hvitfeldt [aut] , Hannah Frick [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>

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Package epm updated to version 1.1.4 with previous version 1.1.3 dated 2024-09-13

Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] , Donald Swiderski [aut], Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>

Diff between epm versions 1.1.3 dated 2024-09-13 and 1.1.4 dated 2025-02-14

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Package transltr updated to version 0.1.0 with previous version 0.0.1 dated 2025-01-24

Title: Support Many Languages in R
Description: An object model for source text and translations. Find and extract translatable strings. Provide translations and seamlessly retrieve them at runtime.
Author: Jean-Mathieu Potvin [aut, cre, cph], Jerome Lavoue [ctb, fnd, rev]
Maintainer: Jean-Mathieu Potvin <jeanmathieupotvin@ununoctium.dev>

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Package spant updated to version 3.2.0 with previous version 3.1.0 dated 2024-12-17

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] , Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

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Package rxode2 updated to version 3.0.4 with previous version 3.0.3 dated 2024-12-15

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] , Wenping Wang [aut], Alan Hindmarsh [ctb], Arun Srinivasan [ctb], Awad H. Al-Mohy [ctb], Bill Denney [ctb] , Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Ernst Hairer [ctb], Gabriel Staples [ctb], Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>

Diff between rxode2 versions 3.0.3 dated 2024-12-15 and 3.0.4 dated 2025-02-14

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More information about rxode2 at CRAN
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Package overturemapsr updated to version 0.1.0 with previous version 0.0.4 dated 2024-06-24

Title: Download Overture Maps Data in R
Description: Overture Maps offers free and open geospatial map data sourced from various providers and standardized to a common schema. This tool allows you to download Overture Maps data for a specific region of interest and convert it to several different file formats. For more information, visit <https://overturemaps.org/download/>.
Author: Dennis Irorere [aut, cre, cph]
Maintainer: Dennis Irorere <denironyx@gmail.com>

Diff between overturemapsr versions 0.0.4 dated 2024-06-24 and 0.1.0 dated 2025-02-14

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Package EmpiricalCalibration updated to version 3.1.4 with previous version 3.1.3 dated 2024-09-30

Title: Routines for Performing Empirical Calibration of Observational Study Estimates
Description: Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account. A similar approach can be used to calibrate confidence intervals, using both negative and positive controls. For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] , Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between EmpiricalCalibration versions 3.1.3 dated 2024-09-30 and 3.1.4 dated 2025-02-14

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Package SaturnCoefficient updated to version 1.4 with previous version 1.3 dated 2024-12-17

Title: Statistical Evaluation of UMAP Dimensionality Reductions
Description: A metric expressing the quality of a UMAP layout. This is a package that contains the Saturn_coefficient() function that reads an input matrix, its dimensionality reduction produced by UMAP, and evaluates the quality of this dimensionality reduction by producing a real value in the [0; 1] interval. We call this real value Saturn coefficient. A higher value means better dimensionality reduction; a lower value means worse dimensionality reduction. Reference: Davide Chicco et al. "The Saturn coefficient for evaluating the quality of UMAP dimensionality reduction results" (2025, in preparation).
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>

Diff between SaturnCoefficient versions 1.3 dated 2024-12-17 and 1.4 dated 2025-02-14

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Package r2dii.match updated to version 0.4.0 with previous version 0.3.0 dated 2024-12-04

Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software 'PACTA' (Paris Agreement Capital Transition Assessment), which is a free tool that calculates the alignment between financial portfolios and climate scenarios (<https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals. This package matches data from corporate lending portfolios to asset level data from market-intelligence databases (e.g. power plant capacities, emission factors, etc.). This is the first step to assess if a financial portfolio aligns with climate goals.
Author: Jacob Kastl [aut, cre, ctr] , Alex Axthelm [aut, ctr] , Jackson Hoffart [aut, ctr] , Mauro Lepore [aut, ctr] , Klaus Hagedorn [aut], Florence Palandri [aut], Evgeny Petrovsky [aut], RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>

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Package nlmixr2plot updated to version 3.0.1 with previous version 3.0.0 dated 2024-09-18

Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] , Bill Denney [ctb] , Wenping Wang [aut], Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

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Package pysparklyr updated to version 0.1.6 with previous version 0.1.5 dated 2024-06-24

Title: Provides a 'PySpark' Back-End for the 'sparklyr' Package
Description: It enables 'sparklyr' to integrate with 'Spark Connect', and 'Databricks Connect' by providing a wrapper over the 'PySpark' 'python' library.
Author: Edgar Ruiz [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>

Diff between pysparklyr versions 0.1.5 dated 2024-06-24 and 0.1.6 dated 2025-02-14

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Package ade4 updated to version 1.7-23 with previous version 1.7-22 dated 2023-02-06

Title: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray [aut] , Anne-Beatrice Dufour [aut] , Jean Thioulouse [aut] , Daniel Chessel [ant], Thibaut Jombart [ctb], Sandrine Pavoine [ctb], Jean R. Lobry [ctb], Sebastien Ollier [ctb], Daniel Borcard [ctb], Pierre Legendre [ctb], Stephanie Bougea [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Permanent link

Package BAwiR updated to version 1.3.4 with previous version 1.3.3 dated 2025-01-21

Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>, <https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions of their respectives robots.txt files, when available. Box score data are available for the three leagues. Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games, maps of nationalities, combinations of lineups, possessions-related variables, timeouts, performance by periods, personal fouls and offensive rebounds. Please see Vinue (2020) <doi:10.1089/big.2018.0124> and Vinue (2024) [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>

Diff between BAwiR versions 1.3.3 dated 2025-01-21 and 1.3.4 dated 2025-02-14

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Package antaresEditObject updated to version 0.9.0 with previous version 0.7.1 dated 2024-09-27

Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Tatiana Vargas [aut, cre], Frederic Breant [ctb], Victor Perrier [ctb], Baptiste Seguinot [ctb], Benoit Thieurmel [ctb], Titouan Robert [ctb], Jalal-Edine Zawam [ctb], Etienne Sanchez [ctb], Janus De Bondt [ctb], Assil Mansouri [ctb], Abdallah Mahoud [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>

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Package adelie updated to version 1.0.6 with previous version 1.0.2 dated 2024-09-03

Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package 'glmnet' in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver, a wide range of matrix classes that can exploit special structure to allow large-scale inputs, and an assortment of generalized linear model classes for fitting various types of data. The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph], Trevor Hastie [aut, cph, cre], Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between adelie versions 1.0.2 dated 2024-09-03 and 1.0.6 dated 2025-02-14

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 adelie-1.0.6/adelie/DESCRIPTION                                                                            |   16 
 adelie-1.0.6/adelie/MD5                                                                                    |  388 ++-
 adelie-1.0.6/adelie/NAMESPACE                                                                              |   13 
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 adelie-1.0.6/adelie/inst/adelie/adelie/io.py                                                               |   10 
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Package teal.logger updated to version 0.3.2 with previous version 0.3.1 dated 2025-01-22

Title: Logging Setup for the 'teal' Family of Packages
Description: Utilizing the 'logger' framework to record events within a package, specific to 'teal' family of packages. Supports logging namespaces, hierarchical logging, various log destinations, vectorization, and more.
Author: Dawid Kaledkowski [aut, cre], Konrad Pagacz [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package teal.code updated to version 0.6.1 with previous version 0.6.0 dated 2025-01-27

Title: Code Storage and Execution Class for 'teal' Applications
Description: Introduction of 'qenv' S4 class, that facilitates code execution and reproducibility in 'teal' applications.
Author: Dawid Kaledkowski [aut, cre], Aleksander Chlebowski [aut], Marcin Kosinski [aut], Pawel Rucki [aut], Nikolas Burkoff [aut], Mahmoud Hallal [aut], Maciej Nasinski [aut], Konrad Pagacz [aut], Junlue Zhao [aut], Chendi Liao [rev], Dony Unardi [rev], F. [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package rgrass updated to version 0.5-2 with previous version 0.5-1 dated 2025-02-03

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>

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Thu, 13 Feb 2025

Package parsnip updated to version 1.3.0 with previous version 1.2.1 dated 2024-03-22

Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', 'H2O', etc).
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], Emil Hvitfeldt [ctb], Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>

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Package omopgenerics updated to version 1.0.0 with previous version 0.4.1 dated 2024-12-05

Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.
Author: Marti Catala [aut, cre] , Edward Burn [aut] , Mike Du [ctb] , Yuchen Guo [ctb] , Adam Black [ctb] , Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>

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Package epiomics updated to version 1.2.0 with previous version 1.1.0 dated 2024-02-26

Title: Analysis of Omics Data in Observational Studies
Description: A collection of fast and flexible functions for analyzing omics data in observational studies. Multiple different approaches for integrating multiple environmental/genetic factors, omics data, and/or phenotype data are implemented. This includes functions for performing omics wide association studies with one or more variables of interest as the exposure or outcome; a function for performing a meet in the middle analysis for linking exposures, omics, and outcomes (as described by Chadeau-Hyam et al., (2010) <doi:10.3109/1354750X.2010.533285>); and a function for performing a mixtures analysis across all omics features using quantile-based g-Computation (as described by Keil et al., (2019) <doi:10.1289/EHP5838>).
Author: Jesse Goodrich [aut, cre]
Maintainer: Jesse Goodrich <jagoodri@usc.edu>

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Package r2dii.analysis updated to version 0.5.0 with previous version 0.4.0 dated 2024-03-26

Title: Measure Climate Scenario Alignment of Corporate Loans
Description: These tools help you to assess if a corporate lending portfolio aligns with climate goals. They summarize key climate indicators attributed to the portfolio (e.g. production, emission factors), and calculate alignment targets based on climate scenarios. They implement in R the last step of the free software 'PACTA' (Paris Agreement Capital Transition Assessment; <https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals.
Author: Jacob Kastl [aut, cre, ctr] , Alex Axthelm [aut, ctr] , Jackson Hoffart [aut, ctr] , Mauro Lepore [aut, ctr] , Klaus Hogedorn [aut], Nicky Halterman [aut], RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>

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Package mkin updated to version 1.2.9 with previous version 1.2.6 dated 2023-10-14

Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph] , Katrin Lindenberger [ctb] ), Rene Lehmann [ctb] and invilr), Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <johannes.ranke@jrwb.de>

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Package automap updated to version 1.1-16 with previous version 1.1-12 dated 2024-09-03

Title: Automatic Interpolation Package
Description: An automatic interpolation is done by automatically estimating the variogram and then calling gstat. An overview is given by Hiemstra et al (2008) <doi:10.1016/j.cageo.2008.10.011>.
Author: Paul Hiemstra [aut], Jon Olav Skoien [aut, cre]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>

Diff between automap versions 1.1-12 dated 2024-09-03 and 1.1-16 dated 2025-02-13

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Permanent link

Package micromapST updated to version 3.1.0 with previous version 3.0.4 dated 2024-10-26

Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create linked micromap plots for a collection of geographic areas. Linked micromap plots are visualizations of geo-referenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the 'micromapST' function. Contained in this package are border group datasets to support creating linked micromap plots for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph], Dan Carr [aut, cph], Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>

Diff between micromapST versions 3.0.4 dated 2024-10-26 and 3.1.0 dated 2025-02-13

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Package lightgbm updated to version 4.6.0 with previous version 4.5.0 dated 2024-07-26

Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks. 'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>. This package offers an R interface to work with it. It is designed to be distributed and efficient with the following advantages: 1. Faster training speed and higher efficiency. 2. Lower memory usage. 3. Better accuracy. 4. Parallel learning supported. 5. Capable of handling large-scale data. In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions. Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple m [...truncated...]
Author: Yu Shi [aut], Guolin Ke [aut], Damien Soukhavong [aut], James Lamb [aut, cre], Qi Meng [aut], Thomas Finley [aut], Taifeng Wang [aut], Wei Chen [aut], Weidong Ma [aut], Qiwei Ye [aut], Tie-Yan Liu [aut], Nikita Titov [aut], Yachen Yan [ctb], Microsof [...truncated...]
Maintainer: James Lamb <jaylamb20@gmail.com>

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Package CASMI updated to version 2.0.0 with previous version 1.2.2 dated 2024-02-16

Title: 'CASMI'-Based Functions
Description: Contains Coverage Adjusted Standardized Mutual Information ('CASMI')-based functions. 'CASMI' is a fundamental concept of a series of methods. For more information about 'CASMI' and 'CASMI'-related methods, please refer to the corresponding publications (e.g., a feature selection method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.3390/e21121179>, and a dataset quality measurement method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.1109/ICHI.2019.8904553>) or contact the package author for the latest updates.
Author: Jingyi Shi [aut, cre, cph, ctb], Shirli Arndt [aut], Jialin Zhang [ctb]
Maintainer: Jingyi (Catherine) Shi <jshi@math.msstate.edu>

Diff between CASMI versions 1.2.2 dated 2024-02-16 and 2.0.0 dated 2025-02-13

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Package wikkitidy updated to version 0.1.14 with previous version 0.1.13 dated 2024-08-17

Title: Tidy Analysis of Wikipedia
Description: Access 'Wikipedia' through the several 'MediaWiki' APIs (<https://www.mediawiki.org/wiki/API>), as well as through the 'XTools' API (<https://www.mediawiki.org/wiki/XTools/API>). Ensure your API calls are correct, and receive results in tidy tibbles.
Author: Michael Falk [aut, cre, cph]
Maintainer: Michael Falk <michaelgfalk@gmail.com>

Diff between wikkitidy versions 0.1.13 dated 2024-08-17 and 0.1.14 dated 2025-02-13

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Package reveneraR updated to version 1.0.0 with previous version 0.1.2 dated 2022-08-06

Title: Connect to Your 'Revenera' (Formerly 'Revulytics') Data
Description: Facilitates making a connection to the 'Revenera' API and executing various queries. You can use it to get event data and metadata. The 'Revenera' documentation is available at <https://rui-api.redoc.ly/>. This package is not supported by 'Flexera' (owner of the software).
Author: Chris Umphlett [aut, cre], Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>

Diff between reveneraR versions 0.1.2 dated 2022-08-06 and 1.0.0 dated 2025-02-13

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Package IsoplotRgui updated to version 6.5 with previous version 6.4 dated 2024-10-19

Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre], Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotRgui versions 6.4 dated 2024-10-19 and 6.5 dated 2025-02-13

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Package rtpcr updated to version 2.0.1 with previous version 2.0.0 dated 2024-07-07

Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>

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Package rcompanion updated to version 2.5.0 with previous version 2.4.36 dated 2024-05-27

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support Summary and Analysis of Extension Program Evaluation in R, and An R Companion for the Handbook of Biological Statistics. Vignettes are available at <https://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

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Package Colossus updated to version 1.2 with previous version 1.1.4.2 dated 2024-10-21

Title: "Risk Model Regression and Analysis with Complex Non-Linear Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] , Amir Bahadori [ctb] , Dan Andresen [ctb], Linda Walsh [ctb] , Benjamin French [ctb] , Lawrence Dauer [ctb], John Boice Jr [ctb] , Kansas State University [cph], NASA [fnd], NCRP [fnd], NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>

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Package statConfR updated to version 0.2.0 with previous version 0.1.1 dated 2024-04-25

Title: Models of Decision Confidence and Measures of Metacognition
Description: Provides fitting functions and other tools for decision confidence and metacognition researchers, including meta-d'/d', often considered to be the gold standard to measure metacognitive efficiency, and information-theoretic measures of metacognition. Also allows to fit several static models of decision making and confidence.
Author: Manuel Rausch [aut, cre] , Sascha Meyen [aut] , Sebastian Hellmann [aut]
Maintainer: Manuel Rausch <manuel.rausch@hochschule-rhein-waal.de>

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Package groqR updated to version 0.0.3 with previous version 0.0.1 dated 2024-09-20

Title: A Coding Assistant using the Fast AI Inference 'Groq'
Description: A comprehensive suite of functions and 'RStudio' Add-ins leveraging the capabilities of open-source Large Language Models (LLMs) to support R developers. These functions offer a range of utilities, including text rewriting, translation, and general query capabilities. Additionally, the programming-focused functions provide assistance with debugging, translating, commenting, documenting, and unit testing code, as well as suggesting variable and function names, thereby streamlining the development process.
Author: Gabriel Kaiser [aut, cre]
Maintainer: Gabriel Kaiser <quantresearch.gk@gmail.com>

Diff between groqR versions 0.0.1 dated 2024-09-20 and 0.0.3 dated 2025-02-13

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Package dawaR updated to version 0.3.0 with previous version 0.2.7 dated 2024-12-07

Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of the official 'Danish Address Web API' (also known as 'DAWA') <https://api.dataforsyningen.dk>. The development of this package is completely independent from the government agency, Klimadatastyrelsen, who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] , Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>

Diff between dawaR versions 0.2.7 dated 2024-12-07 and 0.3.0 dated 2025-02-13

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 dawaR-0.3.0/dawaR/DESCRIPTION                                                                           |   10 
 dawaR-0.3.0/dawaR/MD5                                                                                   |  103 
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 dawaR-0.3.0/dawaR/R/utils.R                                                                             |    7 
 dawaR-0.3.0/dawaR/inst/doc/dawaR.R                                                                      |   40 
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 dawaR-0.3.0/dawaR/inst/doc/status.html                                                                  |    5 
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 dawaR-0.3.0/dawaR/tests/fixtures/regioner_get_data.yml                                                  |   24 
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 dawaR-0.3.0/dawaR/tests/testthat/_snaps/autocomplete.md                                                 |   14 
 dawaR-0.3.0/dawaR/tests/testthat/_snaps/base_api.md                                                     |   28 
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 dawaR-0.3.0/dawaR/tests/testthat/test-status_check.R                                                    |    1 
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Package spacetime updated to version 1.3-3 with previous version 1.3-2 dated 2024-09-04

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [aut, cre] , Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between spacetime versions 1.3-2 dated 2024-09-04 and 1.3-3 dated 2025-02-13

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Package phenopix updated to version 2.4.5 with previous version 2.4.4 dated 2024-01-19

Title: Process Digital Images of a Vegetation Cover
Description: A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.
Author: Gianluca Filippa [aut, cre], Edoardo Cremonese [aut], Mirco Migliavacca [aut], Marta Galvagno [aut], Matthias Folker [aut], Andrew D. Richardson [aut], Enrico Tomelleri [aut]
Maintainer: Gianluca Filippa <gian.filippa@gmail.com>

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Package fluxible updated to version 1.0.0 with previous version 0.0.1 dated 2024-08-27

Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Processes the raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Functions provided include different models (exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and linear) to estimate the fluxes from the raw data, quality assessment, plotting for visual check and calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...).
Author: Joseph Gaudard [aut, cre] , Paul Efren Santos-Andrade [aut], Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>

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Package mlr3torch updated to version 0.2.1 with previous version 0.2.0 dated 2025-02-07

Title: Deep Learning with 'mlr3'
Description: Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.
Author: Sebastian Fischer [cre, aut] , Bernd Bischl [ctb] , Lukas Burk [ctb] , Martin Binder [aut], Florian Pfisterer [ctb] , Carson Zhang [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>

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Package mnet updated to version 0.1.4 with previous version 0.1.2 dated 2023-06-07

Title: Modeling Group Differences and Moderation Effects in Statistical Network Models
Description: A toolbox for modeling manifest and latent group differences and moderation effects in various statistical network models.
Author: Jonas Haslbeck [aut, cre]
Maintainer: Jonas Haslbeck <jonashaslbeck@protonmail.com>

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Package collegeScorecard updated to version 0.2.0 with previous version 0.1.0 dated 2024-07-29

Title: US College Scorecard Data
Description: Provides a tidied subset of the US College Scorecard dataset, containing institutional characteristics, enrollment, student aid, costs, and student outcomes at institutions of higher education in the United States.
Author: Garrick Aden-Buie [aut, cre, cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>

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Package webdav updated to version 0.1.4 with previous version 0.1.3 dated 2025-01-08

Title: A Simple Interface for Interacting with 'WebDAV' Servers
Description: An easy-to-use interface for interacting with 'WebDAV' servers, including 'OwnCloud'. It simplifies the use of 'WebDAV' methods such as COPY, MKCOL, MOVE, and others. With built-in authentication and request handling, it allows for easy management of files and directories over the 'WebDAV' protocol.
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>

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Package CvmortalityMult updated to version 1.0.9 with previous version 1.0.8 dated 2025-02-06

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 RQdeltaCT updated to version 1.3.2 with previous version 1.3.0 dated 2024-04-17

Title: Relative Quantification of Gene Expression using Delta Ct Methods
Description: The commonly used methods for relative quantification of gene expression levels obtained in real-time PCR (Polymerase Chain Reaction) experiments are the delta Ct methods, encompassing 2^-dCt and 2^-ddCt methods, originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) <doi:10.1006/meth.2001.1262>. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that cover both methods for comparison of either independent groups of samples or groups with paired samples, together with importing expression datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment of the standard workflow with additional useful analyses (correlation analysis, Receiver Op [...truncated...]
Author: Daniel Zalewski [aut, cre]
Maintainer: Daniel Zalewski <daniel.piotr.zalewski@gmail.com>

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Package fitPoly updated to version 4.0.0 with previous version 3.0.0 dated 2018-03-16

Title: Genotype Calling for Bi-Allelic Marker Assays
Description: Genotyping assays for bi-allelic markers (e.g. SNPs) produce signal intensities for the two alleles. 'fitPoly' assigns genotypes (allele dosages) to a collection of polyploid samples based on these signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011) <doi:10.1186/1471-2105-12-172>. New functions added on conversion of data from SNP array software formats, drawing of XY-scatterplots with or without genotype colors, checking against expected F1 segregation patterns, comparing results from two different assays (probes) for the same SNP, recovery from a saveMarkerModels() crash.
Author: Roeland E. Voorrips [aut], Gerrit Gort [aut], Alejandro Therese Navarro [aut], Giorgio Tumino [aut, cre]
Maintainer: Giorgio Tumino <giorgio.tumino@wur.nl>

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Package IsoplotR updated to version 6.5 with previous version 6.4 dated 2024-10-19

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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Package dials updated to version 1.4.0 with previous version 1.3.0 dated 2024-07-30

Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
Author: Max Kuhn [aut], Hannah Frick [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>

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Package tourr updated to version 1.2.4 with previous version 1.2.0 dated 2024-04-19

Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Author: Hadley Wickham [aut, ctb] , Dianne Cook [aut, cre] , Nick Spyrison [ctb] , Ursula Laa [ctb] , H. Sherry Zhang [ctb] , Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>

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Package singleRcapture updated to version 0.2.3 with previous version 0.2.2 dated 2025-02-04

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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Package rqPen updated to version 4.1.3 with previous version 4.1.2 dated 2024-10-29

Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. In addition, offers a group penalty that provides consistent variable selection across quantiles. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre], Shaobo Li [aut], Adam Maidman [aut]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>

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Package jobqueue updated to version 1.3.0 with previous version 1.0.1 dated 2025-01-30

Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>

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Package tidyquant updated to version 1.0.11 with previous version 1.0.10 dated 2025-01-08

Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

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Package NEONiso updated to version 0.7.2 with previous version 0.7.1 dated 2025-01-08

Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
Description: Functions for downloading, calibrating, and analyzing atmospheric isotope data bundled into the eddy covariance data products of the National Ecological Observatory Network (NEON) <https://www.neonscience.org>. Calibration tools are provided for carbon and water isotope products. Carbon isotope calibration details are found in Fiorella et al. (2021) <doi:10.1029/2020JG005862>, and the readme file at <https://github.com/lanl/NEONiso>. Tools for calibrating water isotope products have been added as of 0.6.0, but have known deficiencies and should be considered experimental and unsupported.
Author: Rich Fiorella [aut, cre]
Maintainer: Rich Fiorella <rfiorella@lanl.gov>

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Package hbamr updated to version 2.4.1 with previous version 2.4.0 dated 2025-01-26

Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological positions of survey respondents and political actors on a common scale using positional survey data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform other versions both in terms of yielding meaningful posterior distributions for respondent positions and in terms of recovering true respondent positions in simulations. The package contains functions for preparing data, fitting models, extracting estimates, plotting key results, and comparing models using cross-validation. The original version of the default model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>

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Package cli updated to version 3.6.4 with previous version 3.6.3 dated 2024-06-21

Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Author: Gabor Csardi [aut, cre], Hadley Wickham [ctb], Kirill Mueller [ctb], Salim Brueggemann [ctb] , Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <gabor@posit.co>

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Package acepack updated to version 1.6.1 with previous version 1.5.2 dated 2025-01-27

Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided. The first, Alternating Conditional Expectations (ACE), is an algorithm to find the fixed point of maximal correlation, i.e. it finds a set of transformed response variables that maximizes R^2 using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations for Multiple Regression and Correlation". Journal of the American Statistical Association. 80:580-598. <doi:10.1080/01621459.1985.10478157>]. Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when correlation is low [see Tibshirani, R. 1986. "Estimating Transformations for Regression via Additivity and Variance Stabilization". Journal of the American Statistical Association. 83:394-405. <doi:10.1080/01621459.1988.10478610>]. A good introduction to these two methods is in chapter 16 of Frank Harrell's "Regression Modeling Strategies" in the Springer Serie [...truncated...]
Author: Phil Spector [aut], Jerome Friedman [aut], Robert Tibshirani [aut], Thomas Lumley [aut], Shawn Garbett [cre, aut] , Jonathan Baron [aut], Bernhard Klar [aut], Scott Chasalow [aut]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>

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Wed, 12 Feb 2025

Package dsem updated to version 1.5.0 with previous version 1.4.1 dated 2025-02-01

Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data with generic and simplified specification for simultaneous and lagged effects. Methods are described in Thorson et al. (2024) "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms."
Author: James Thorson [aut, cre] , Maurice Goodman [ctb] , Wouter van der Bijl [ctb]
Maintainer: James Thorson <James.Thorson@noaa.gov>

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Package Argentum updated to version 1.0.0 with previous version 0.5.1 dated 2024-09-30

Title: Access and Import WMS and WFS Data from Argentine Organizations
Description: Provides functions to retrieve information from Web Feature Service (WFS) and Web Map Service (WMS) layers from various Argentine organizations and import them into R for further analysis. WFS and WMS are standardized protocols for serving georeferenced map data over the internet. For more information on these services, see <https://www.ogc.org/publications/standard/wfs/> and <https://www.ogc.org/publications/standard/wms/>.
Author: Thomas Artopoulos [aut, cre]
Maintainer: Thomas Artopoulos <thomas.artopoulos@gmail.com>

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More information about Argentum at CRAN
Permanent link

Package PhySortR updated to version 1.0.9 with previous version 1.0.8 dated 2018-08-06

Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non- Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] , Debashish Bhattacharya [aut], Mark Ragan [aut], Cheong Xin Chan [aut, cph]
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>

Diff between PhySortR versions 1.0.8 dated 2018-08-06 and 1.0.9 dated 2025-02-12

 DESCRIPTION      |   14 ++++-----
 MD5              |   10 +++---
 NAMESPACE        |    1 
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More information about PhySortR at CRAN
Permanent link

Package sits updated to version 1.5.2 with previous version 1.5.1 dated 2024-08-19

Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
Description: An end-to-end toolkit for land use and land cover classification using big Earth observation data. Builds satellite image data cubes from cloud collections. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps and to reduce training samples imbalance. Provides machine learning algorithms including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolution neural networks, and temporal attention encoders. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference. Enables best practices for estimating area and assessing accuracy of land change. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
Author: Rolf Simoes [aut], Gilberto Camara [aut, cre, ths], Felipe Souza [aut], Felipe Carlos [aut], Lorena Santos [ctb], Karine Ferreira [ctb, ths], Charlotte Pelletier [ctb], Pedro Andrade [ctb], Alber Sanchez [ctb], Estefania Pizarro [ctb], Gilberto Queir [...truncated...]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>

Diff between sits versions 1.5.1 dated 2024-08-19 and 1.5.2 dated 2025-02-12

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 sits-1.5.2/sits/R/RcppExports.R                                    |   16 
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 sits-1.5.2/sits/R/api_colors.R                                     |   24 
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 sits-1.5.2/sits/R/api_conf.R                                       |   78 
 sits-1.5.2/sits/R/api_crop.R                                       |   74 
 sits-1.5.2/sits/R/api_csv.R                                        |   45 
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 sits-1.5.2/sits/R/api_ml_model.R                                   |   30 
 sits-1.5.2/sits/R/api_mosaic.R                                     |   19 
 sits-1.5.2/sits/R/api_plot_raster.R                                |  330 +--
 sits-1.5.2/sits/R/api_plot_time_series.R                           |    4 
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 sits-1.5.2/sits/R/api_request_httr2.R                              |   13 
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 sits-1.5.2/sits/R/api_ts.R                                         |   14 
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 sits-1.5.2/sits/R/api_view.R                                       | 1003 +++++-----
 sits-1.5.2/sits/R/sits_accuracy.R                                  |   44 
 sits-1.5.2/sits/R/sits_add_base_cube.R                             |    2 
 sits-1.5.2/sits/R/sits_apply.R                                     |   24 
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More information about sits at CRAN
Permanent link

Package saros updated to version 1.5.1 with previous version 1.5.0 dated 2025-01-10

Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many (and bivariate combinations of) variables, typically from survey data. Contains interactive 'ggiraph'-based (<https://CRAN.R-project.org/package=ggiraph>) plotting functions and data frame-based summary tables (bivariate significance tests, frequencies/proportions, unique open ended responses, etc) with many arguments for customization, and extensions possible. Uses a global options() system for neatly reducing redundant code. Also contains tools for immediate saving of objects and returning a hashed link to the object, useful for creating download links to high resolution images upon rendering in 'Quarto'. Suitable for highly customized reports, primarily intended for survey research.
Author: Stephan Daus [aut, cre, cph] , Julia Silge [ctb] , David Robinson [ctb] , Nordic Institute for The Studies of Innovation, Research and Education [fnd], Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>

Diff between saros versions 1.5.0 dated 2025-01-10 and 1.5.1 dated 2025-02-12

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More information about saros at CRAN
Permanent link

Package PSweight updated to version 2.1.0 with previous version 1.2.0 dated 2024-03-29

Title: Propensity Score Weighting for Causal Inference with Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut], Guangyu Tong [aut], Fan Li [aut], Laine Thomas [aut], Fan Li [aut], Yukang Zeng [cre]
Maintainer: Yukang Zeng <yukang.zeng@yale.edu>

Diff between PSweight versions 1.2.0 dated 2024-03-29 and 2.1.0 dated 2025-02-12

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 PSweight-2.1.0/PSweight/R/SumStat_SW.R                         |only
 PSweight-2.1.0/PSweight/R/SumStat_cl.R                         |   19 +--
 PSweight-2.1.0/PSweight/R/bin_est.R                            |    3 
 PSweight-2.1.0/PSweight/R/bin_est_SW.R                         |only
 PSweight-2.1.0/PSweight/R/plot_SumStat_SW.R                    |only
 PSweight-2.1.0/PSweight/R/psdata_bin_prospective_fp.R          |only
 PSweight-2.1.0/PSweight/R/psdata_bin_prospective_sp.R          |only
 PSweight-2.1.0/PSweight/R/psdata_bin_retrospective_fp.R        |only
 PSweight-2.1.0/PSweight/R/psdata_bin_retrospective_sp.R        |only
 PSweight-2.1.0/PSweight/R/pt_est_SW.R                          |only
 PSweight-2.1.0/PSweight/R/sand_var_SW.R                        |only
 PSweight-2.1.0/PSweight/README.md                              |   56 ++++------
 PSweight-2.1.0/PSweight/build/vignette.rds                     |binary
 PSweight-2.1.0/PSweight/data/psdata_bin_prospective_fp.RData   |only
 PSweight-2.1.0/PSweight/data/psdata_bin_prospective_sp.RData   |only
 PSweight-2.1.0/PSweight/data/psdata_bin_retrospective_fp.RData |only
 PSweight-2.1.0/PSweight/data/psdata_bin_retrospective_sp.RData |only
 PSweight-2.1.0/PSweight/inst/doc/Software_vig.Rmd              |    3 
 PSweight-2.1.0/PSweight/inst/doc/Software_vig.pdf              |binary
 PSweight-2.1.0/PSweight/man/OUTmethod_SW.Rd                    |only
 PSweight-2.1.0/PSweight/man/PSmethod_SW.Rd                     |only
 PSweight-2.1.0/PSweight/man/PStrim_SW.Rd                       |only
 PSweight-2.1.0/PSweight/man/PSweight_SW.Rd                     |only
 PSweight-2.1.0/PSweight/man/SumStat_SW.Rd                      |only
 PSweight-2.1.0/PSweight/man/SumStat_cl.Rd                      |    9 -
 PSweight-2.1.0/PSweight/man/plot.SumStat_SW.Rd                 |only
 PSweight-2.1.0/PSweight/man/psdata_bin_prospective_fp.Rd       |only
 PSweight-2.1.0/PSweight/man/psdata_bin_prospective_sp.Rd       |only
 PSweight-2.1.0/PSweight/man/psdata_bin_retrospective_fp.Rd     |only
 PSweight-2.1.0/PSweight/man/psdata_bin_retrospective_sp.Rd     |only
 PSweight-2.1.0/PSweight/vignettes/Software_vig.Rmd             |    3 
 41 files changed, 109 insertions(+), 95 deletions(-)

More information about PSweight at CRAN
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