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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 man/robyn_modelselector.Rd |  174 +-
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 man/rtistry_sphere.Rd      |   36 
 man/scale_x_comma.Rd       |  208 +--
 man/scrabble.Rd            |  318 ++--
 man/sentimentBreakdown.Rd  |  110 -
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 man/textFeats.Rd           |  134 +-
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 man/weighted_value.Rd      |  102 -
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 man/winsorize.Rd           |   64 
 man/wordle.Rd              |  156 +-
 man/x2y.Rd                 |  256 +--
 man/year_month.Rd          |  110 -
 man/zerovar.Rd             |   98 -
 262 files changed, 35209 insertions(+), 35182 deletions(-)

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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>

Diff between kerntools versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-02-19

 DESCRIPTION                            |    6 
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 NAMESPACE                              |    4 
 NEWS.md                                |   15 
 R/importancies.R                       |   74 ++++
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 R/kernel_study.R                       |   22 -
 README.md                              |    7 
 inst/WORDLIST                          |   18 +
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 man/Chi2.Rd                            |only
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 man/aggregate_imp.Rd                   |only
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 man/heatK.Rd                           |    3 
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 vignettes/Kernel-functions.Rmd         |  131 +++++++-
 vignettes/kerntools.Rmd                |   26 +
 27 files changed, 1240 insertions(+), 339 deletions(-)

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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

 jsonlite-1.8.9/jsonlite/src/modp_stdint.h               |only
 jsonlite-1.9.0/jsonlite/DESCRIPTION                     |    6 ++---
 jsonlite-1.9.0/jsonlite/MD5                             |   17 +++++++---------
 jsonlite-1.9.0/jsonlite/NEWS                            |    3 ++
 jsonlite-1.9.0/jsonlite/build/vignette.rds              |binary
 jsonlite-1.9.0/jsonlite/inst/doc/json-aaquickstart.html |   10 ++++-----
 jsonlite-1.9.0/jsonlite/inst/doc/json-mapping.pdf       |binary
 jsonlite-1.9.0/jsonlite/man/stream_in.Rd                |    2 -
 jsonlite-1.9.0/jsonlite/src/modp_numtoa.c               |    5 ++--
 jsonlite-1.9.0/jsonlite/src/modp_numtoa.h               |    4 ++-
 10 files changed, 26 insertions(+), 21 deletions(-)

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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>

Diff between viralmodels versions 1.3.1 dated 2024-10-18 and 1.3.3 dated 2025-02-19

 DESCRIPTION                       |    6 +-
 MD5                               |   32 ++++++-------
 NAMESPACE                         |    1 
 NEWS.md                           |   12 ++++-
 R/viralmodel.R                    |   64 +++++++++++++--------------
 R/viralpreds.R                    |   88 +++++++++++++++++++++++++++++--------
 R/viraltab.R                      |   89 ++++++++++++++++++++++----------------
 R/viralvis.R                      |   60 ++++++++++++-------------
 man/viralmodel.Rd                 |    2 
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 man/viraltab.Rd                   |   11 +++-
 man/viralvis.Rd                   |    2 
 tests/testthat/_snaps/viraltab.md |    2 
 tests/testthat/test-viralmodel.R  |    2 
 tests/testthat/test-viralpreds.R  |    2 
 tests/testthat/test-viraltab.R    |    4 -
 tests/testthat/test-viralvis.R    |    3 -
 17 files changed, 247 insertions(+), 157 deletions(-)

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New package SDModels with initial version 1.0.4
Package: SDModels
Title: Spectrally Deconfounded Models
Version: 1.0.4
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).
License: GPL-3
Imports: data.tree, DiagrammeR, doParallel, ggplot2, GPUmatrix, gridExtra, locatexec, parallel, pbapply, Rdpack, tidyr, fda, grplasso, rlang
Suggests: plotly, datasets, rpart, knitr, rmarkdown, ranger, HDclassif, qpdf, igraph, testthat (>= 3.0.0)
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://markusul.github.io/SDModels/
BugReports: https://github.com/markusul/SDModels/issues
NeedsCompilation: no
Packaged: 2025-02-18 10:55:30 UTC; maulmer
Author: Markus Ulmer [aut, cre, cph] , Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Repository: CRAN
Date/Publication: 2025-02-19 14:30:08 UTC

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New package popsom7 with initial version 7.0.0
Package: popsom7
Version: 7.0.0
Title: A User-Friendly Implementation of Self-Organizing Maps
Maintainer: Lutz Hamel <lutzhamel@uri.edu>
Description: Self-organizing maps with a number of distinguishing features: (1) Automatic centroid detection and cluster visualization using starbursts, for more details see the paper "Improved Interpretability of the Unified Distance Matrix with Connected Components" by Hamel and Brown (2011) in <ISBN:1-60132-168-6>. (2) Two models of the data: (a) a self organizing map model, (b) a centroid based clustering model. (3) A number of easily accessible quality metrics, Hamel (2016) <doi:10.1007/978-3-319-28518-4_4>.
License: GPL-3
URL: https://github.com/lutzhamel/popsom7
BugReports: https://github.com/lutzhamel/popsom7/issues
Imports: fields, graphics, ggplot2, hash, stats, som, grDevices
Suggests: testthat (>= 3.0.0)
Repository: CRAN
NeedsCompilation: no
Packaged: 2025-02-18 14:21:56 UTC; lutz
Author: Lutz Hamel [aut, cre], Benjamin Ott [aut], Gregory Breard [aut], Robert Tatoian [aut], Michael Eiger [aut], Vishakh Gopu [aut]
Date/Publication: 2025-02-19 15:00:02 UTC

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New package nplr with initial version 0.1-8
Package: nplr
Title: N-Parameter Logistic Regression
Version: 0.1-8
Maintainer: Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>
Depends: methods
Imports: stats,graphics,utils
Suggests: RUnit,knitr
VignetteBuilder: knitr
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. Can also be applied to proliferation analyses.
License: GPL
URL: https://github.com/mini-pw/nplr
NeedsCompilation: no
Packaged: 2025-02-18 00:03:29 UTC; tymot
Author: Frederic Commo [aut], Brian M. Bot [aut], Tymoteusz Kwiecinski [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-19 14:10:01 UTC

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New package netknitr with initial version 0.2.1
Package: netknitr
Title: Knit Network Map for any Dataset
Version: 0.2.1
Description: Designed to create interactive and visually compelling network maps using R Shiny. It allows users to quickly analyze CSV files and visualize complex relationships, structures, and connections within data by leveraging powerful network analysis libraries and dynamic web interfaces.
Depends: R (>= 3.1.0),
Imports: openxlsx, utils, shiny, shinydashboard, dplyr, visNetwork
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-18 07:05:48 UTC; RPUSH1
Author: Jayachandra N [aut, cre], Pushker Ravindra [aut]
Maintainer: Jayachandra N <itsjay510@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-19 14:30:05 UTC

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New package MSCA with initial version 1.0
Package: MSCA
Title: Clustering of Multiple Censored Time-to-Event Endpoints
Version: 1.0
Description: Provides basic tools for computing clusters of instances described by multiple time-to-event censored endpoints. From long-format datasets, where one instance is described by one or more records of events, a procedure is used to compute state matrices. Then, from state matrices, a procedure provides optimised computation of the Jaccard distance between instances. The library is currently in development, and more options and tools allowing graphical representation of typologies are expected. For methodological details, see our methodological paper: Delord M, Douiri A (2025) <doi:10.1186/s12874-025-02476-7>.
License: GPL-3
Imports: dplyr, Matrix, Rcpp, RcppParallel, rlang, stats, tibble, utils
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-18 10:44:32 UTC; marc
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-19 14:30:13 UTC

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New package gander with initial version 0.1.0
Package: gander
Title: High Performance, Low Friction Large Language Model Chat
Version: 0.1.0
Description: Introduces a 'Copilot'-like completion experience, but it knows how to talk to the objects in your R environment. 'ellmer' chats are integrated directly into your 'RStudio' and 'Positron' sessions, automatically incorporating relevant context from surrounding lines of code and your global environment (like data frame columns and types). Open the package dialog box with a keyboard shortcut, type your request, and the assistant will stream its response directly into your documents.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/simonpcouch/gander, https://simonpcouch.github.io/gander/
BugReports: https://github.com/simonpcouch/gander/issues
Depends: R (>= 4.3.0)
Imports: cli (>= 3.6.3), glue (>= 1.8.0), ellmer (>= 0.1.0), miniUI (>= 0.1.1.1), rlang (>= 1.1.4), rstudioapi (>= 0.17.1), shiny (>= 1.9.1), streamy, treesitter, treesitter.r
Suggests: gt, knitr, rmarkdown, testthat (>= 3.0.0), tibble, withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-18 15:20:37 UTC; simoncouch
Author: Simon Couch [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Repository: CRAN
Date/Publication: 2025-02-19 15:00:05 UTC

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New package epigrowthfit with initial version 0.15.4
Package: epigrowthfit
Version: 0.15.4
Date: 2025-02-14
License: GPL-3
Encoding: UTF-8
URL: https://github.com/davidearn/epigrowthfit
BugReports: https://github.com/davidearn/epigrowthfit/issues
Title: Nonlinear Mixed Effects Models of Epidemic Growth
Description: Maximum likelihood estimation of nonlinear mixed effects models of epidemic growth using Template Model Builder ('TMB'). Enables joint estimation for collections of disease incidence time series, including time series that describe multiple epidemic waves. Supports a set of widely used phenomenological models: exponential, logistic, Richards (generalized logistic), subexponential, and Gompertz. Provides methods for interrogating model objects and several auxiliary functions, including one for computing basic reproduction numbers from fitted values of the initial exponential growth rate. Preliminary versions of this software were applied in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.
Depends: R (>= 4.3)
LinkingTo: RcppEigen (>= 0.3.4.0.0), TMB
Imports: Matrix (>= 1.6-2), TMB, grDevices, graphics, methods, nlme, stats, utils
LazyData: true
NeedsCompilation: yes
Packaged: 2025-02-18 13:50:46 UTC; mikael
Author: Mikael Jagan [aut, cre] , Ben Bolker [aut] , Jonathan Dushoff [ctb] , David Earn [ctb] , Junling Ma [ctb]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Repository: CRAN
Date/Publication: 2025-02-19 14:50:02 UTC

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New package ctablerseh with initial version 1.1.2
Package: ctablerseh
Title: Processing Survey Data with Confidence Intervals Like 'SPSS' Software
Version: 1.1.2
Description: Processes survey data and displays estimation results along with the relative standard error in a table, including the number of samples and also uses a t-distribution approach to compute confidence intervals, similar to 'SPSS' (Statistical Package for the Social Sciences) software.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Author: Asy-Syaja'ul Haqqul Amin [aut, cre]
Maintainer: Asy-Syaja'ul Haqqul Amin <haqqul.amin06@gmail.com>
Depends: R (>= 2.10)
Imports: survey
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-18 11:45:24 UTC; Haqqul Amin
Repository: CRAN
Date/Publication: 2025-02-19 14:40:02 UTC

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New package ASML with initial version 1.0.0
Package: ASML
Title: Algorithm Portfolio Selection with Machine Learning
Version: 1.0.0
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
License: GPL-3
Language: en-US
Encoding: UTF-8
LazyData: true
Imports: caret, ggplot2, dplyr, purrr, tibble, tidyr, reshape2, Polychrome, scales, rlang
Suggests: snow
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2025-02-18 13:01:46 UTC; brais
Author: Brais Gonzalez-Rodriguez [aut, cre] , Ignacio Gomez-Casares [aut] , Beatriz Pateiro-Lopez [aut] , Julio Gonzalez-Diaz [aut] , Maria Caseiro-Arias [ctb], Antonio Farina-Elorza [ctb], Manuel Timiraos-Lopez [ctb]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>
Repository: CRAN
Date/Publication: 2025-02-19 14:40:05 UTC

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New package aftables with initial version 1.0.1
Package: aftables
Title: Create Spreadsheet Publications Following Best Practice
Version: 1.0.1
Description: Generate spreadsheet publications that follow best practice guidance from the UK government's Analysis Function, with a focus on accessibility. Based on 'openxlsx'. See also the Python package 'gptables'.
License: MIT + file LICENSE
URL: https://best-practice-and-impact.github.io/aftables/, https://github.com/best-practice-and-impact/aftables
BugReports: https://github.com/best-practice-and-impact/aftables/issues
Depends: R (>= 3.5)
Imports: openxlsx, pillar
Suggests: covr, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), tibble
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-18 14:57:06 UTC; OBoxPower
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>
Repository: CRAN
Date/Publication: 2025-02-19 15:00:09 UTC

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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>

Diff between watson versions 0.5 dated 2024-11-19 and 0.6 dated 2025-02-19

 DESCRIPTION     |   13 ++++++++-----
 MD5             |   10 +++++-----
 NEWS.md         |    6 ++++++
 R/RcppExports.R |    4 ++--
 man/rmwat.Rd    |    4 ++--
 src/rwat.cpp    |    8 ++++----
 6 files changed, 27 insertions(+), 18 deletions(-)

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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>

Diff between Rrepest versions 1.5.3 dated 2025-02-17 and 1.5.4 dated 2025-02-19

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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>

Diff between psborrow versions 0.2.1 dated 2023-03-03 and 0.2.2 dated 2025-02-19

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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/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 
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 man/plot_SCBD_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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New package oglcnac with initial version 0.1.5
Package: oglcnac
Title: Processing and Analysis of 'O-GlcNAcAtlas' Data
Version: 0.1.5
Description: Provides tools for processing and analyzing data from the 'O-GlcNAcAtlas' database <https://oglcnac.org/>, as described in Ma (2021) <doi:10.1093/glycob/cwab003>. It integrates 'UniProt' <https://www.uniprot.org/> API calls to retrieve additional information. It is specifically designed for research workflows involving 'O-GlcNAcAtlas' data, providing a flexible and user-friendly interface for customizing and downloading processed results. Interactive elements allow users to easily adjust parameters and handle various biological datasets.
License: GPL-3
Encoding: UTF-8
Imports: cli, httr, jsonlite, shiny, DT, bslib, readxl, glue
Suggests: testthat (>= 3.0.0), tibble, curl
NeedsCompilation: no
Packaged: 2025-02-19 06:16:16 UTC; Bach
Author: Yaoxiang Li [aut, cre]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Repository: CRAN
Date/Publication: 2025-02-19 09:30:02 UTC

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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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New package unigd with initial version 0.1.3
Package: unigd
Title: Universal Graphics Device
Version: 0.1.3
Description: A unified R graphics backend. Render R graphics fast and easy to many common file formats. Provides a thread safe 'C' interface for asynchronous rendering of R graphics.
License: GPL (>= 2)
Depends: R (>= 3.2.0)
Imports: systemfonts (>= 1.0.0)
LinkingTo: cpp11 (>= 0.2.4), systemfonts
Encoding: UTF-8
SystemRequirements: libpng, cairo, freetype2, fontconfig
URL: https://github.com/nx10/unigd, https://nx10.github.io/unigd/
BugReports: https://github.com/nx10/unigd/issues
Suggests: testthat (>= 3.0.0), xml2 (>= 1.0.0), fontquiver (>= 0.2.0), covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-18 23:21:43 UTC; floru
Author: Florian Rupprecht [aut, cre] , Kun Ren [ctb], Tatsuya Shima [ctb], Jeroen Ooms [ctb] , Hadley Wickham [cph] , Lionel Henry [cph] , Thomas Lin Pedersen [cph] , T Jake Luciani [cph] , Matthieu Decorde [cph] , Vaudor Lise [cph] , Tony Plate [cph] , Davi [...truncated...]
Maintainer: Florian Rupprecht <floruppr@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-19 08:20:02 UTC

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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>

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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>

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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>

Diff between PL94171 versions 1.1.2 dated 2022-09-11 and 1.1.3 dated 2025-02-19

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Package Pandora (with last version 24.2.0) was removed from CRAN

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

2024-02-26 24.2.0
2023-12-19 23.12.0

Permanent link
Package DATAstudio (with last version 1.1) was removed from CRAN

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

2022-04-28 1.1
2022-04-13 1.0

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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>

Diff between RcppDE versions 0.1.7 dated 2022-12-20 and 0.1.8 dated 2025-02-18

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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>

Diff between NaileR versions 1.2.1 dated 2024-11-11 and 1.2.2 dated 2025-02-18

 DESCRIPTION                 |   12 +-
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 R/nail_catdes.R             |  100 +++++++++++++++++-
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 man/quality.Rd              |    5 
 man/rorschach.Rd            |   12 --
 man/waste.Rd                |    2 
 23 files changed, 285 insertions(+), 214 deletions(-)

More information about NaileR at CRAN
Permanent link

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>

Diff between mvgam versions 1.1.3 dated 2024-09-03 and 1.1.4 dated 2025-02-18

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More information about mvgam at CRAN
Permanent link

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>

Diff between conquestr versions 1.3.4 dated 2024-07-24 and 1.4.5 dated 2025-02-18

 DESCRIPTION                                        |   17 
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 NEWS.md                                            |   33 
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New package WMWssp with initial version 0.5.3
Package: WMWssp
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Version: 0.5.3
Date: 2025-02-18
Maintainer: Martin Happ <statistics@happ.co.at>
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test that is needed for a given power and two sided type I error rate. The method works for metric data with and without ties, count data, ordered categorical data, and even dichotomous data. But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect. See Happ et al. (2019, <doi:10.1002/sim.7983>) for details.
Depends: R (>= 3.4.0)
License: GPL-3
URL: https://github.com/happma/WMWssp
BugReports: https://github.com/happma/WMWssp/issues
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-02-18 16:36:45 UTC; happma
Author: Arne C. Bathke [aut], Edgar Brunner [aut], Martin Happ [aut, cre] , Frank Konietschke [aut]
Repository: CRAN
Date/Publication: 2025-02-18 23:40:05 UTC

More information about WMWssp at CRAN
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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>

Diff between gimap versions 1.0.1 dated 2025-02-03 and 1.0.2 dated 2025-02-18

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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>

Diff between Benchmarking versions 0.32 dated 2024-03-13 and 0.33 dated 2025-02-18

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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>

Diff between r2dii.analysis versions 0.5.0 dated 2025-02-13 and 0.5.1 dated 2025-02-18

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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>

Diff between enderecobr versions 0.4.0 dated 2025-01-14 and 0.4.1 dated 2025-02-18

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 8 files changed, 90 insertions(+), 13 deletions(-)

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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>

Diff between AID versions 3.0 dated 2024-11-22 and 3.1 dated 2025-02-18

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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>

Diff between calidad versions 0.6.0 dated 2024-10-16 and 0.7.0 dated 2025-02-18

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New package UAHDataScienceSF with initial version 1.0.0
Package: UAHDataScienceSF
Version: 1.0.0
Title: Interactive Statistical Learning Functions
Description: An educational toolkit for learning statistical concepts through interactive exploration. Provides functions for basic statistics (mean, variance, etc.) and probability distributions with step-by-step explanations and interactive learning modes. Each function can be used for simple calculations, detailed learning with explanations, or interactive practice with feedback.
License: MIT + file LICENSE
Imports: stats, magick (>= 2.7.3), crayon (>= 1.3.4)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-17 15:31:07 UTC; andriy
Author: Carlos Javier Hellin Asensio [aut], Jose Manuel Gomez Caceres [aut], Dennis Monheimius [aut], Eduardo Benito [aut], Juan Jose Cuadrado [aut], Andriy Protsak Protsak [aut, cre], Universidad de Alcala de Henares [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Repository: CRAN
Date/Publication: 2025-02-18 11:10:07 UTC

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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>

Diff between spiro versions 0.2.1 dated 2023-08-14 and 0.2.3 dated 2025-02-18

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New package musicXML with initial version 1.0.1
Package: musicXML
Title: Data Sonification using 'musicXML'
Version: 1.0.1
Description: A set of tools to facilitate data sonification and handle the 'musicXML' format <https://usermanuals.musicxml.com/MusicXML/Content/XS-MusicXML.htm>. Several classes are defined for basic musical objects such as note pitch, note duration, note, measure and score. Moreover, sonification utilities functions are provided, e.g. to map data into musical attributes such as pitch, loudness or duration. A typical sonification workflow hence looks like: get data; map them to musical attributes; create and write the 'musicXML' score, which can then be further processed using specialized music software (e.g. 'MuseScore', 'GuitarPro', etc.). Examples can be found in the blog <https://globxblog.github.io/>, the presentation by Renard and Le Bescond (2022, <https://hal.science/hal-03710340v1>) or the poster by Renard et al. (2023, <https://hal.inrae.fr/hal-04388845v1>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: xml2
Suggests: knitr, rmarkdown, tidyr, gganimate, av
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-17 18:07:18 UTC; brenard
Author: Benjamin Renard [aut, cre, cph] , INRAE [fnd], European Commission [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Repository: CRAN
Date/Publication: 2025-02-18 11:10:02 UTC

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New package fishgrowth with initial version 1.0.1
Package: fishgrowth
Version: 1.0.1
Date: 2025-02-18
Title: Fit Growth Curves to Fish Data
Depends: R (>= 2.10), RTMB
Suggests: areaplot
LazyData: yes
Description: Fit growth models to otoliths and/or tagging data, using the 'RTMB' package and maximum likelihood. The otoliths (or similar measurements of age) provide direct observed coordinates of age and length. The tagging data provide information about the observed length at release and length at recapture at a later time, where the age at release is unknown and estimated as a vector of parameters. The growth models provided by this package can be fitted to otoliths only, tagging data only, or a combination of the two. Growth variability can be modelled as constant or increasing with length.
License: GPL-3
URL: https://github.com/arni-magnusson/fishgrowth
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-18 03:53:41 UTC; arnim
Author: Arni Magnusson [aut, cre], Mark Maunder [aut]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-18 11:20:02 UTC

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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>

Diff between ursa versions 3.11.2 dated 2025-01-14 and 3.11.3 dated 2025-02-18

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New package SimTOST with initial version 1.0.1
Package: SimTOST
Title: Sample Size Estimation for Bio-Equivalence Trials Through Simulation
Version: 1.0.1
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...]
License: Apache License (>= 2)
Encoding: UTF-8
Imports: MASS, Rcpp (>= 1.0.13), data.table, matrixcalc, parallel
Suggests: PowerTOST, ggplot2, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0), tibble, tinytest
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
URL: https://smartdata-analysis-and-statistics.github.io/SimTOST/
NeedsCompilation: yes
Packaged: 2025-02-17 11:37:16 UTC; Thomas
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>
Repository: CRAN
Date/Publication: 2025-02-18 10:10:14 UTC

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New package rb3 with initial version 0.0.12
Package: rb3
Title: Download and Parse Public Data Released by B3 Exchange
Description: Download and parse public files released by B3 and convert them into useful formats and data structures common to data analysis practitioners.
Version: 0.0.12
License: MIT + file LICENSE
Depends: R (>= 4.1.0),
Imports: bizdays, stringr, proto, cli, readr, dplyr, rvest, httr, jsonlite, purrr, ascii, rlang, methods, yaml, digest, base64enc, XML, readxl, tidyr
Suggests: testthat, knitr, DT, miniUI, shiny, xtable, rmarkdown, ggplot2, covr, scales, magrittr, tibble, withr, vcr (>= 0.6.0)
BugReports: https://github.com/ropensci/rb3/issues
URL: https://github.com/ropensci/rb3, http://ropensci.github.io/rb3/
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-16 18:57:35 UTC; root
Author: Wilson Freitas [aut, cre], Marcelo Perlin [aut]
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-18 10:10:02 UTC

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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>

Diff between ProtE versions 1.0.2 dated 2025-02-17 and 1.0.3 dated 2025-02-18

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New package logos with initial version 0.1.0
Package: logos
Title: Access to the Hebrew, Greek, and English Version of the Bible
Version: 0.1.0
Maintainer: JP Monteagudo <jpmonteagudo2014@gmail.com>
Description: Access to the Greek New Testament (27 books) and the Old Testament (39 books) and allow users to do textual analysis on the data. The New and Old Testament have been provided in their original languages, Greek and Hebrew, respectively. Additionally, the Revised American Standard Bible is also provided for users who'd rather use a word–for–word modern English translation.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/jpmonteagudo28/logos
BugReports: https://github.com/jpmonteagudo28/logos/issues
LazyData: true
Depends: R (>= 4.1)
Suggests: testthat (>= 3.0.0)
Imports: dplyr
NeedsCompilation: no
Packaged: 2025-02-17 13:25:23 UTC; jpmonteagudo
Author: JP Monteagudo [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-18 10:10:06 UTC

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New package datamedios with initial version 1.1.0
Package: datamedios
Title: Scraping Chilean Media
Version: 1.1.0
Maintainer: Exequiel Trujillo <exequiel.trujillo@ug.uchile.cl>
Description: A system for extracting news from Chilean media, specifically through Web Scapping from Chilean media. The package allows for news searches using search phrases and date filters, and returns the results in a structured format, ready for analysis. Additionally, it includes functions to clean the extracted data, visualize it, and store it in databases. All of this can be done automatically, facilitating the collection and analysis of relevant information from Chilean media.
License: MIT + file LICENSE
Encoding: UTF-8
Language: es-ES
Depends: R (>= 4.1)
Suggests: rcmdcheck
Imports: dplyr, httr, magrittr, jsonlite, utils, tidyverse, wordcloud2, tidytext, lubridate, rvest, stringr, xml2, purrr, DT, ggplot2
NeedsCompilation: no
Packaged: 2025-02-16 21:20:50 UTC; ismae
Author: Exequiel Trujillo [aut, cre, cph, fnd], Ismael Aguayo [aut, fnd], Klaus Lehmann [aut, fnd]
Repository: CRAN
Date/Publication: 2025-02-18 10:10:10 UTC

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New package correlatio with initial version 0.1.0
Package: correlatio
Title: Visualize Details Behind Pearson's Correlation Coefficient
Version: 0.1.0
Description: Helps visualizing what is summarized in Pearson's correlation coefficient. That is, it visualizes its main constituent, namely the distances of the single values to their respective mean. The visualization thereby shows what the etymology of the word correlation contains: In pairwise combination, bringing back (see package Vignette for more details). I hope that the 'correlatio' package may benefit some people in understanding and critically evaluating what Pearson's correlation coefficient summarizes in a single number, i.e., to what degree and why Pearson's correlation coefficient may (or may not) be warranted as a measure of association.
License: MIT + file LICENSE
Repository: CRAN
URL: https://github.com/mmiche/correlatio
Encoding: UTF-8
Imports: Rdpack, stats, ggplot2, tibble
Depends: R (>= 4.0.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/mmiche/correlatio/issues
NeedsCompilation: no
Packaged: 2025-02-17 14:51:36 UTC; mmiche
Author: Marcel Miche [aut, cre]
Maintainer: Marcel Miche <marcel.miche.predictme@gmail.com>
Date/Publication: 2025-02-18 10:20:10 UTC

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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>

Diff between clarabel versions 0.9.0.1 dated 2024-09-03 and 0.10.0 dated 2025-02-18

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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>

Diff between XLConnect versions 1.1.0 dated 2024-08-22 and 1.2.0 dated 2025-02-18

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New package PiC with initial version 1.0.3
Package: PiC
Title: Pointcloud Interactive Computation for Forest Structure Analysis
Version: 1.0.3
Description: Provides advanced algorithms for analyzing pointcloud data in forestry applications. Key features include fast voxelization of large datasets; segmentation of point clouds into forest floor, understorey, canopy, and wood components. The package enables efficient processing of large-scale forest pointcloud data, offering insights into forest structure, connectivity, and fire risk assessment. Algorithms to analyze pointcloud data (.xyz input file). For more details, see Ferrara & Arrizza (2025) <https://hdl.handle.net/20.500.14243/533471>. For single tree segmentation details, see Ferrara et al. (2018) <doi:10.1016/j.agrformet.2018.04.008>.
License: GPL (>= 3)
Depends: R (>= 4.3)
Imports: collapse, data.table, dbscan, dplyr, foreach, magrittr, stats, tictoc
Suggests: ggplot2, testthat (>= 3.0.0), withr
Encoding: UTF-8
URL: https://github.com/rupppy/PiC
BugReports: https://github.com/rupppy/PiC/issues
NeedsCompilation: no
Packaged: 2025-02-17 09:39:57 UTC; robertoferrara
Author: Roberto Ferrara [aut, cre] , Stefano Arrizza [aut]
Maintainer: Roberto Ferrara <roberto.ferrara@cnr.it>
Repository: CRAN
Date/Publication: 2025-02-18 10:00:02 UTC

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New package Dogoftest with initial version 0.1
Package: Dogoftest
Title: Distributed Online Goodness-of-Fit Tests for Distributed Datasets
Date: 2025-02-15
Version: 0.1
Description: Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-15 09:53:56 UTC; ASUS
Author: Guangbao Guo [aut, cre] , Di Chang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-18 10:00:05 UTC

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New package decompML with initial version 0.1.1
Package: decompML
Title: Decomposition Based Machine Learning Model
Version: 0.1.1
Maintainer: Kapil Choudhary <kapiliasri@gmail.com>
Description: The hybrid model is a highly effective forecasting approach that integrates decomposition techniques with machine learning to enhance time series prediction accuracy. Each decomposition technique breaks down a time series into multiple intrinsic mode functions (IMFs), which are then individually modeled and forecasted using machine learning algorithms. The final forecast is obtained by aggregating the predictions of all IMFs, producing an ensemble output for the time series. The performance of the developed models is evaluated using international monthly maize price data, assessed through metrics such as root mean squared error (RMSE), mean absolute percentage error (MAPE), and mean absolute error (MAE). For method details see Choudhary, K. et al. (2023). <https://ssca.org.in/media/14_SA44052022_R3_SA_21032023_Girish_Jha_FINAL_Finally.pdf>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: forecast, nnfor, Rlibeemd, VMDecomp
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2025-02-12 10:43:18 UTC; kapil
Author: Girish Kumar Jha [aut, ctb], Kapil Choudhary [aut, cre], Rajender Parsad [ctb], Ronit Jaiswal [ctb], Rajeev Ranjan Kumar [ctb], P Venkatesh [ctb], Dwijesh Chandra Mishra [ctb]
Repository: CRAN
Date/Publication: 2025-02-18 09:40:02 UTC

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Package fastQR (with last version 1.0.0) was removed from CRAN

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

2025-02-04 1.0.0

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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>

Diff between TransProR versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-02-18

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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>

Diff between sae.projection versions 0.1.1 dated 2025-02-15 and 0.1.2 dated 2025-02-18

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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>

Diff between dartRverse versions 1.0.2 dated 2024-05-24 and 1.0.6 dated 2025-02-18

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New package dartR.captive with initial version 1.0.2
Package: dartR.captive
Title: Analysing 'SNP' Data to Support Captive Breeding
Version: 1.0.2
Date: 2025-02-17
Description: Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), dartR.base, dartR.data, dartR.sim
Imports: methods, utils, crayon, ggplot2, patchwork, stringr, data.table
Suggests: SIBER, gplots, fields, igraph, reshape2, rrBLUP, scales, spelling
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2025-02-17 22:50:08 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb], Sam Amini [ctb]
URL: https://green-striped-gecko.github.io/dartR/
BugReports: https://groups.google.com/g/dartr?pli=1
Language: en-US
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2025-02-18 08:20:05 UTC

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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>

Diff between cardx versions 0.2.2 dated 2024-11-27 and 0.2.3 dated 2025-02-18

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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>

Diff between iNEXT.3D versions 1.0.7 dated 2025-01-22 and 1.0.8 dated 2025-02-18

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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>

Diff between RConics versions 1.1.1 dated 2022-03-11 and 1.1.2 dated 2025-02-17

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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>

Diff between cata versions 0.1.0.7 dated 2024-10-08 and 0.1.0.26 dated 2025-02-17

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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>

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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>

Diff between NNS versions 11.0 dated 2025-01-10 and 11.1 dated 2025-02-17

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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>

Diff between MLE versions 1.3 dated 2024-12-16 and 1.4 dated 2025-02-17

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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>

Diff between cgam versions 1.21 dated 2023-08-10 and 1.22 dated 2025-02-17

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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>

Diff between readsparse versions 0.1.5-6 dated 2023-11-27 and 0.1.5-8 dated 2025-02-17

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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>

Diff between ProtE versions 1.0.1 dated 2025-01-15 and 1.0.2 dated 2025-02-17

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New package nimbleAPT with initial version 1.0.7
Package: nimbleAPT
Title: Adaptive Parallel Tempering for 'NIMBLE'
Version: 1.0.7
Encoding: UTF-8
Date: 2025-02-17
Maintainer: David Pleydell <david.pleydell@inrae.fr>
URL: https://github.com/DRJP/nimbleAPT
Description: Functions for adaptive parallel tempering (APT) with NIMBLE models. Adapted from 'Lacki' & 'Miasojedow' (2016) <DOI:10.1007/s11222-015-9579-0> and 'Miasojedow, Moulines and Vihola' (2013) <DOI:10.1080/10618600.2013.778779>.
License: BSD_3_clause + file LICENSE
Copyright: See COPYRIGHTS file.
Depends: R (>= 3.1.2), nimble
Imports: methods
Suggests: knitr, rmarkdown, coda
VignetteBuilder: knitr
Note: The APT samplers within this package were adapted from MCMC samplers provided in the NIMBLE package (https://github.com/nimble-dev/nimble) and developed by the cited members of the NIMBLE Development Team. The adaptations for APT included in this package were the work of the package developer. Many thanks to the NIMBLE Development Team for their support during the development of this package.
NeedsCompilation: no
Packaged: 2025-02-17 11:08:02 UTC; pleydell
Author: David Pleydell [aut, cre, cph] , Daniel Turek [cph] , Perry de Valpine [cph] , Christopher Paciorek [cph] , Nick Michaud [cph]
Repository: CRAN
Date/Publication: 2025-02-17 13:10:02 UTC

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New package UAHDataScienceUC with initial version 1.0.0
Package: UAHDataScienceUC
Title: Learn Clustering Techniques Through Examples and Code
Version: 1.0.0
Description: A comprehensive educational package combining clustering algorithms with detailed step-by-step explanations. Provides implementations of both traditional (hierarchical, k-means) and modern (DBSCAN, 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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: proxy (>= 0.4-27), cli (>= 3.6.1)
Suggests: deldir (>= 1.0-9), knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-14 18:35:25 UTC; andriy
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>
Repository: CRAN
Date/Publication: 2025-02-17 12:20:02 UTC

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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>

Diff between pxmake versions 0.14.2 dated 2025-01-22 and 0.15.1 dated 2025-02-17

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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

 DESCRIPTION  |    8 -
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New package MissCP with initial version 0.1.1
Package: MissCP
Title: Change Point Detection with Missing Values
Version: 0.1.1
Author: Yanxi Liu [aut, cre], Abolfazl Safikhani [aut]
Maintainer: Yanxi Liu <liuyanxi@ufl.edu>
Description: A four step change point detection method that can detect break points with the presence of missing values proposed by Liu and Safikhani (2023) <https://drive.google.com/file/d/1a8sV3RJ8VofLWikTDTQ7W4XJ76cEj4Fg/view?usp=drive_link>.
License: GPL-2
Encoding: UTF-8
Imports: stats, graphics, mvtnorm, factoextra, Rcpp, ggplot2, glmnet
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-17 11:48:51 UTC; yanxiliu
Repository: CRAN
Date/Publication: 2025-02-17 12:30:07 UTC

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New package fishstat with initial version 2024.1.0.1
Package: fishstat
Version: 2024.1.0.1
Date: 2025-02-14
Title: Global Fishery and Aquaculture Statistics
Depends: R (>= 3.5.0)
Suggests: areaplot
LazyData: yes
Description: The Food and Agriculture Organization of the United Nations (FAO) FishStat database is the leading source of global fishery and aquaculture statistics and provides unique information for sector analysis and monitoring. This package provides the global production data from all fisheries and aquaculture in R format, ready for analysis.
License: CC BY-NC-SA 4.0
URL: https://www.fao.org/fishery/en/fishstat, https://github.com/sofia-taf/fishstat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-14 07:13:54 UTC; arnim
Author: Arni Magnusson [aut, cre], Rishi Sharma [aut], FAO [cph]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-17 12:50:02 UTC

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New package chatRater with initial version 1.0.0
Package: chatRater
Title: Rating Text Using Large Language Models
Version: 1.0.0
Date: 2025-02-14
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Description: Generates ratings for textual stimuli using large language models. It allows users to evaluate idioms and similar texts by combining context, prompts, and stimulus inputs. The package supports both 'OpenAI' and 'DeepSeek' APIs by enabling users to switch models simply by specifying the model parameter. It implements methods for constructing the request payload and parsing numeric ratings from the model outputs.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tidyverse, openai, httr, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-02-14 16:08:28 UTC; admin
Author: Shiyang Zheng [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-17 12:10:01 UTC

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New package UAHDataScienceSC with initial version 1.0.0
Package: UAHDataScienceSC
Title: Learn Supervised Classification Methods Through Examples and Code
Version: 1.0.0
Description: Supervised classification methods, which (if asked) can provide step-by-step explanations of the algorithms used, as described in PK Josephine et. al., (2021) <doi:10.59176/kjcs.v1i1.1259>; and datasets to test them on, which highlight the strengths and weaknesses of each technique.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.3.0)
Imports: cli (>= 3.6.1)
Suggests: knitr, rmarkdown
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2025-02-14 15:13:26 UTC; andriy
Author: Victor Amador Padilla [aut], Juan Jose Cuadrado Gallego [ctb] , Andriy Protsak Protsak [aut, cre], Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:09 UTC

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New package simqi with initial version 0.1.0
Package: simqi
Title: Simulate Quantities of Interest from Regression Models
Version: 0.1.0
Depends: R (>= 3.5.0)
Maintainer: Steve Miller <steve@svmiller.com>
Description: This is an all-encompassing suite to facilitate the simulation of so-called quantities of interest by way of a multivariate normal distribution of the regression model's coefficients and variance-covariance matrix.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stevemisc, tibble, methods
NeedsCompilation: no
Packaged: 2025-02-14 14:48:22 UTC; steve
Author: Steve Miller [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-17 12:00:02 UTC

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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>

Diff between Rrepest versions 1.5.2 dated 2025-02-10 and 1.5.3 dated 2025-02-17

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New package rpcss with initial version 0.1.0
Package: rpcss
Title: Constitution of Core Collections by Principal Component Scoring Strategy
Version: 0.1.0
Description: Generate a Core Collection with Principal Component Scoring Strategy (PCSS) using qualitative and/or quantitative trait data according to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>, Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003) <https://www.documentation.ird.fr/hor/fdi:010031886>.
License: GPL-2 | GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
BuildManual: TRUE
Imports: dplyr, FactoMineR, ggplot2, ggrepel, gslnls, mathjaxr, methods, Rdpack, stats, tidyr, utils
Suggests: EvaluateCore, factoextra, knitr, rmarkdown, pander
Copyright: 2024-2025, ICAR-NBPGR
URL: https://github.com/aravind-j/rpcss, https://aravind-j.github.io/rpcss/
BugReports: https://github.com/aravind-j/rpcss/issues
NeedsCompilation: no
Packaged: 2025-02-14 04:37:22 UTC; Aravind-DGC
Author: J. Aravind [aut, cre] , ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Repository: CRAN
Date/Publication: 2025-02-17 11:50:02 UTC

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New package indexr with initial version 0.2.2
Package: indexr
Title: A Thoughtful Saver of Results
Version: 0.2.2
Date: 2025-02-14
Description: Helps with the thoughtful saving, reading, and management of result files (using 'rds' files). The core functions take a list of parameters that are used to generate a unique hash to save results under. Then, the same parameter list can be used to read those results back in. This is helpful to avoid clunky file naming when running a large number of simulations. Additionally, helper functions are available for compiling a flat file of parameters of saved results, monitoring result usage, and cleaning up unwanted or unused results. For more information, visit the 'indexr' homepage <https://lharris421.github.io/indexr/>.
BugReports: https://github.com/lharris421/indexr/issues
License: GPL-3
URL: https://lharris421.github.io/indexr/, https://github.com/lharris421/indexr
Encoding: UTF-8
Imports: stringr, readr, dplyr, digest, glue, methods
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-14 15:01:45 UTC; loganharris
Author: Logan Harris [aut, cre]
Maintainer: Logan Harris <logan-harris@uiowa.edu>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:05 UTC

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New package flint with initial version 0.0.1
Package: flint
Version: 0.0.1
VersionNote: sync configure.ac
Date: 2025-02-14
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for number theory. 'FLINT' extends GNU 'MP' <https://gmplib.org/> and GNU 'MPFR' <https://www.mpfr.org/> with support for arithmetic in standard rings (the integers, the integers modulo n, the rational, p-adic, real, and complex numbers) as well as vectors, matrices, polynomials, and power series over rings. 'FLINT' implements midpoint-radius interval arithmetic, also known as ball arithmetic, in the real and complex numbers, enabling computation in arbitrary precision with rigorous propagation of errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>. Finally, 'FLINT' provides ball arithmetic implementations of many special mathematical functions, with high coverage of reference works such as the NIST Digital Library of Mathematical Functions <https://dlmf.nist.gov/>. The R interface defines S4 classes, generic functions, and methods for representation and basic operations as well as p [...truncated...]
License: GPL (>= 2)
URL: https://github.com/jaganmn/flint
BugReports: https://github.com/jaganmn/flint/issues
Depends: R (>= 4.3), methods
Imports: stats
SystemRequirements: gmp, mpfr (>= 3.1), flint (>= 3)
SystemRequirementsNote: purely informational as we use configure tests
NeedsCompilation: yes
Packaged: 2025-02-13 22:34:03 UTC; mikael
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Repository: CRAN
Date/Publication: 2025-02-17 11:30:03 UTC

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New package changepointGA with initial version 0.1.0
Package: changepointGA
Title: Changepoint Detection via Modified Genetic Algorithm
Version: 0.1.0
Date: 2025-01-21
Description: The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package [...truncated...]
License: MIT + file LICENSE
Depends: R (>= 4.3.0)
Imports: foreach, doParallel, Rcpp, RcppArmadillo, clue, stats
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/mli171/changepointGA
BugReports: https://github.com/mli171/changepointGA/issues
Suggests: knitr, rmarkdown
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-13 21:49:58 UTC; mo
Author: Mo Li [aut, cre]
Maintainer: Mo Li <mo.li@louisiana.edu>
Repository: CRAN
Date/Publication: 2025-02-17 11:30:16 UTC

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New package BigDataPE with initial version 0.0.95
Package: BigDataPE
Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Version: 0.0.95
Date: 2025-02-13
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr, tibble, httr2
URL: <https://github.com/StrategicProjects/bigdatape>
NeedsCompilation: no
Packaged: 2025-02-14 13:36:49 UTC; leite
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:12 UTC

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New package BaHZING with initial version 1.0.0
Package: BaHZING
Title: Bayesian Hierarchical Zero-Inflated Negative Binomial Regression with G-Computation
Version: 1.0.0
Description: A Bayesian model for examining the association between environmental mixtures and all Taxa measured in a hierarchical microbiome dataset in a single integrated analysis. Compared with analyzing the associations of environmental mixtures with each Taxa individually, 'BaHZING' controls Type 1 error rates and provides more stable effect estimates when dealing with small sample sizes.
License: GPL (>= 3)
Depends: R (>= 4.1.0), rjags (>= 4.0.0)
Imports: bayestestR, dplyr, magrittr, phyloseq, pscl, R2jags, stats, stringr, tidyr
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
SystemRequirements: JAGS 4.x.y (http://mcmc-jags.sourceforge.net)
NeedsCompilation: no
Packaged: 2025-02-13 20:53:48 UTC; jagoodri
Author: Hailey Hampson [aut], Jesse Goodrich [aut, cre] , Hongxu Wang [aut], Tanya Alderete [ctb], Shardul Nazirkar [ctb], David Conti [aut]
Maintainer: Jesse Goodrich <jagoodri@usc.edu>
Repository: CRAN
Date/Publication: 2025-02-17 11:20:07 UTC

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New package polykde with initial version 1.0.0
Package: polykde
Title: Polyspherical Kernel Density Estimation
Version: 1.0.0
Date: 2025-02-13
Description: Kernel density estimation on the polysphere, hypersphere, and circle. Includes functions for density estimation, regression estimation, ridge estimation, bandwidth selection, kernels, samplers, and homogeneity tests. Companion package to García-Portugués and Meilán-Vila (2024) <doi:10.48550/arXiv.2411.04166> and García-Portugués and Meilán-Vila (2023) <doi:10.1007/978-3-031-32729-2_4>.
License: GPL-3
Imports: abind, doFuture, foreach, future, gsl, movMF, progressr, Rcpp (>= 1.0.8.3), RcppProgress, rotasym, sphunif
Suggests: alphashape3d, DirStats, FixedPoint, ks, manipulate, numDeriv, optimParallel, testthat, viridis, rgl, scatterplot3d, sdetorus, smacof
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
URL: https://github.com/egarpor/polykde
BugReports: https://github.com/egarpor/polykde/issues
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-13 19:14:03 UTC; Eduardo
Author: Eduardo Garcia-Portugues [aut, cre] , Andrea Meilan-Vila [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Repository: CRAN
Date/Publication: 2025-02-17 11:00:01 UTC

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Package DDoutlier (with last version 0.1.0) was removed from CRAN

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

2018-05-30 0.1.0

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Package PvSTATEM (with last version 0.2.1) was removed from CRAN

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

2025-01-27 0.2.1
2025-01-08 0.1.3
2024-11-08 0.1.2
2024-11-02 0.1.1
2024-10-03 0.0.4

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Package figpatch (with last version 0.2) was removed from CRAN

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

2022-05-03 0.2
2021-07-09 0.1.0.1

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Package nplr (with last version 0.1-7) was removed from CRAN

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

2016-12-28 0.1-7
2016-11-20 0.1-6
2016-09-04 0.1-5
2015-08-01 0.1-4
2015-07-11 0.1-3
2015-07-08 0.1-2
2014-05-13 0.1-1
2014-05-04 0.1

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Package squat (with last version 0.3.0) was removed from CRAN

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

2024-01-10 0.3.0
2023-07-09 0.2.1
2023-06-04 0.2.0

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Package Statsomat (with last version 1.1.0) was removed from CRAN

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

2021-11-17 1.1.0
2021-09-16 1.0

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Package OwenQ (with last version 1.0.7) was removed from CRAN

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

2023-04-11 1.0.7
2023-01-27 1.0.6
2022-01-05 1.0.5
2021-09-20 1.0.4
2020-01-08 1.0.3
2019-08-30 1.0.1
2019-08-30 1.0.2
2019-08-28 1.0.0

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Package TwitterAutomatedTrading (with last version 0.1.0) was removed from CRAN

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2020-05-31 0.1.0

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Package MALDIcellassay (with last version 0.4.47) was removed from CRAN

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

2024-08-29 0.4.47

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Package twitteR (with last version 1.1.9) was removed from CRAN

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

2015-07-28 1.1.9
2015-02-10 1.1.8
2013-07-09 1.1.7
2013-04-29 1.1.6
2013-03-02 1.1.0
2012-02-20 0.99.19
2012-02-08 0.99.18
2012-01-18 0.99.17
2011-12-02 0.99.15
2011-11-17 0.99.14
2011-11-15 0.99.13
2011-11-09 0.99.12
2011-11-04 0.99.11
2011-06-15 0.99.9
2011-06-07 0.99.8
2011-06-04 0.99.7
2011-04-24 0.99.6
2011-04-14 0.99.4
2011-04-12 0.99.2
2011-03-31 0.99.0
2011-03-07 0.9.3
2010-12-08 0.9.2
2010-09-29 0.9.1
2010-09-09 0.9.0
2010-05-19 0.1.6
2009-12-14 0.1.5
2009-11-13 0.1.3
2009-10-20 0.1.2
2009-07-24 0.1.0

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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>

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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>

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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>

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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>

Diff between mappeR versions 1.3.0 dated 2024-10-30 and 2.0.0 dated 2025-02-16

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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>

Diff between jmvReadWrite versions 0.4.9 dated 2025-01-16 and 0.4.10 dated 2025-02-16

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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>

Diff between assessor versions 1.1.0 dated 2024-04-03 and 1.1.1 dated 2025-02-16

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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>

Diff between PhenotypeR versions 0.1.2 dated 2025-02-05 and 0.1.3 dated 2025-02-16

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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>

Diff between rjaf versions 0.1.1 dated 2024-12-08 and 0.1.2 dated 2025-02-16

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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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New package TransProR with initial version 1.0.2
Package: TransProR
Title: Analysis and Visualization of Multi-Omics Data
Version: 1.0.2
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
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...]
Imports: magrittr, stats, dplyr, rlang, tibble, sva, DESeq2, utils, edgeR, limma, ggplot2, ggVennDiagram, ggdensity, ggpubr, ggtree, hrbrthemes, grid, ggraph, tidygraph, tidyr, stringr, geomtextpath, ggalt, ggnewscale, ggtreeExtra, Hmisc, circlize, graphics, spiralize, ComplexHeatmap, grDevices
Suggests: prettydoc, knitr, rmarkdown
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/SSSYDYSSS/TransProRBook
BugReports: https://github.com/SSSYDYSSS/TransProR/issues
LazyData: true
Depends: R (>= 4.3.0)
NeedsCompilation: no
Packaged: 2025-02-14 16:18:34 UTC; Yu
Author: Dongyue Yu [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-14 23:00:10 UTC

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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>

Diff between jobqueue versions 1.3.0 dated 2025-02-13 and 1.3.1 dated 2025-02-14

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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>

Diff between bootStateSpace versions 1.0.1 dated 2025-01-22 and 1.0.2 dated 2025-02-14

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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>

Diff between BayesChange versions 1.1.0 dated 2025-02-13 and 1.1.1 dated 2025-02-14

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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>

Diff between simStateSpace versions 1.2.8 dated 2025-01-23 and 1.2.9 dated 2025-02-14

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More information about simStateSpace at CRAN
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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>

Diff between censored versions 0.3.2 dated 2024-06-11 and 0.3.3 dated 2025-02-14

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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>

Diff between transltr versions 0.0.1 dated 2025-01-24 and 0.1.0 dated 2025-02-14

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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>

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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>

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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>

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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>

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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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