Mon, 10 Feb 2025

Package ncdump updated to version 0.0.5 with previous version 0.0.3 dated 2017-05-02

Title: Extract Metadata from 'NetCDF' Files as Data Frames
Description: Tools for handling 'NetCDF' metadata in data frames. The metadata is provided as relations in tabular form, to avoid having to scan printed header output or to navigate nested lists of raw metadata.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package mpitbR updated to version 1.0.1 with previous version 1.0.0 dated 2024-03-27

Title: Calculate Alkire-Foster Multidimensional Poverty Measures
Description: Estimate Multidimensional Poverty Indices disaggregated by population subgroups based on the Alkire and Foster method (2011) <doi:10.1016/j.jpubeco.2010.11.006>. This includes the calculation of standard errors and confidence intervals. Other partial indices such as incidence, intensity and indicator-specific measures as well as intertemporal changes analysis can also be estimated. The standard errors and confidence intervals are calculated considering the complex survey design.
Author: Ignacio Girela [aut, cre, cph] , CONICET [fnd]
Maintainer: Ignacio Girela <ignacio.girela@unc.edu.ar>

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Package gsDesign updated to version 3.6.6 with previous version 3.6.5 dated 2024-11-14

Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes their properties. Particular focus on time-to-event, binary, and continuous outcomes. Largely based on methods described in Jennison, Christopher and Turnbull, Bruce W., 2000, "Group Sequential Methods with Applications to Clinical Trials" ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre], Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>

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Package unmarked updated to version 1.5.0 with previous version 1.4.3 dated 2024-09-01

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut], Ken Kellner [cre, aut], Ian Fiske [aut], David Miller [aut], Andy Royle [aut], Jeff Hostetler [aut], Rebecca Hutchinson [aut], Adam Smith [aut], Lea Pautrel [aut], Marc Kery [ctb], Mike Meredith [ctb], Auriel Fournier [ctb], A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>

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New package quanteda.textmodels with initial version 0.9.10
Package: quanteda.textmodels
Title: Scaling Models and Classifiers for Textual Data
Version: 0.9.10
Description: Scaling models and classifiers for sparse matrix objects representing textual data in the form of a document-feature matrix. Includes original implementations of 'Laver', 'Benoit', and Garry's (2003) <doi:10.1017/S0003055403000698>, 'Wordscores' model, the Perry and 'Benoit' (2017) <doi:10.48550/arXiv.1710.08963> class affinity scaling model, and the 'Slapin' and 'Proksch' (2008) <doi:10.1111/j.1540-5907.2008.00338.x> 'wordfish' model, as well as methods for correspondence analysis, latent semantic analysis, and fast Naive Bayes and linear 'SVMs' specially designed for sparse textual data.
Depends: R (>= 3.1.0), methods
Imports: glmnet, Matrix (>= 1.2), quanteda (>= 4.0.0), RSpectra, Rcpp (>= 0.12.12), stringi
Suggests: ca, covr, fastNaiveBayes, knitr, lsa, microbenchmark, naivebayes, quanteda.textplots, spelling, testthat, rmarkdown
LinkingTo: Rcpp, RcppArmadillo (>= 0.7.600.1.0), quanteda
URL: https://github.com/quanteda/quanteda.textmodels
License: GPL-3
Encoding: UTF-8
LazyData: true
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-10 18:45:31 UTC; kbenoit
Author: Kenneth Benoit [cre, aut, cph] , Kohei Watanabe [aut] , Haiyan Wang [aut] , Patrick O. Perry [aut] , Benjamin Lauderdale [aut] , Johannes Gruber [aut] , William Lowe [aut] , Vikas Sindhwani [cph] , European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@quanteda.org>
Repository: CRAN
Date/Publication: 2025-02-10 23:50:11 UTC

More information about quanteda.textmodels at CRAN
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Package move2 updated to version 0.4.4 with previous version 0.4.2 dated 2024-12-18

Title: Processing and Analysing Animal Trajectories
Description: Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Author: Bart Kranstauber [aut, cre] , Kamran Safi [aut] , Anne K. Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>

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Package locuszoomr updated to version 0.3.7 with previous version 0.3.6 dated 2025-01-25

Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>

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More information about locuszoomr at CRAN
Permanent link

Package lifeR updated to version 1.0.3 with previous version 1.0.2 dated 2024-05-14

Title: Identify Sites for Your Bird List
Description: A suite of tools to use the 'eBird' database (<https://ebird.org/home/>) and APIs to compare users' species lists to recent observations and create a report of the top sites to visit to see new species.
Author: Jeffrey Oliver [aut, cre]
Maintainer: Jeffrey Oliver <jcoliver@arizona.edu>

Diff between lifeR versions 1.0.2 dated 2024-05-14 and 1.0.3 dated 2025-02-10

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More information about lifeR at CRAN
Permanent link

Package fstcore updated to version 0.10.0 with previous version 0.9.18 dated 2023-12-02

Title: R Bindings to the 'Fstlib' Library
Description: The 'fstlib' library provides multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the 'LZ4' and 'ZSTD' compressors.
Author: Mark Klik [aut, cre, cph] , Yuta Mori [ctb, cph] , Przemyslaw Skibinski [ctb, cph] , Tino Reichardt [ctb, cph] , Yann Collet [ctb, cph] , Facebook, Inc. [cph]
Maintainer: Mark Klik <markklik@gmail.com>

Diff between fstcore versions 0.9.18 dated 2023-12-02 and 0.10.0 dated 2025-02-10

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More information about fstcore at CRAN
Permanent link

Package soilDB updated to version 2.8.8 with previous version 2.8.7 dated 2025-01-16

Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

Diff between soilDB versions 2.8.7 dated 2025-01-16 and 2.8.8 dated 2025-02-10

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More information about soilDB at CRAN
Permanent link

Package sfhotspot updated to version 0.9.0 with previous version 0.8.0 dated 2023-09-19

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 0.8.0 dated 2023-09-19 and 0.9.0 dated 2025-02-10

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More information about sfhotspot at CRAN
Permanent link

New package siera with initial version 0.1.0
Package: siera
Title: Generate Analysis Results Programmes Using ARS Metadata
Version: 0.1.0
Maintainer: Malan Bosman <malanbos@gmail.com>
Description: Analysis Results Standard (ARS), a foundational standard by CDISC (Clinical Data Interchange Standards Consortium), provides a logical data model for metadata describing all components to calculate Analysis Results. <https://www.cdisc.org/standards/foundational/analysis-results-standard> Using 'siera' package, ARS metadata is ingested (JSON or Excel format), producing programmes to generate Analysis Results Datasets (ARDs).
License: MIT + file LICENSE
Encoding: UTF-8
Imports: magrittr, dplyr, tibble, tidyr, jsonlite, stringr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-02-08 18:59:41 UTC; mbosm
Author: Malan Bosman [aut, cre], Clymb Clinical [cph, fnd]
Repository: CRAN
Date/Publication: 2025-02-10 19:10:02 UTC

More information about siera at CRAN
Permanent link

Package rib updated to version 0.25.3 with previous version 0.23.1 dated 2024-10-17

Title: An Implementation of 'Interactive Brokers' API
Description: Allows interaction with 'Interactive Brokers' 'Trader Workstation' <https://interactivebrokers.github.io/tws-api/>. Handles the connection over the network and the exchange of messages. Data is encoded and decoded between user and wire formats. Data structures and functionality closely mirror the official implementations.
Author: Luca Billi [aut, cre]
Maintainer: Luca Billi <noreply.section+dev@gmail.com>

Diff between rib versions 0.23.1 dated 2024-10-17 and 0.25.3 dated 2025-02-10

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More information about rib at CRAN
Permanent link

Package primarycensored updated to version 1.1.0 with previous version 1.0.0 dated 2024-10-28

Title: Primary Event Censored Distributions
Description: Provides functions for working with primary event censored distributions and 'Stan' implementations for use in Bayesian modeling. Primary event censored distributions are useful for modeling delayed reporting scenarios in epidemiology and other fields (Charniga et al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for arbitrary delay distributions, a range of common primary distributions, and allows for truncation and secondary event censoring to be accounted for (Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of common distributions also have analytical solutions implemented, allowing for faster computation. In addition, it provides multiple methods for fitting primary event censored distributions to data via optional dependencies.
Author: Sam Abbott [aut, cre, cph] , Sam Brand [aut] , Adam Howes [ctb] , James Mba Azam [ctb] , Carl Pearson [aut] , Sebastian Funk [aut] , Kelly Charniga [aut]
Maintainer: Sam Abbott <contact@samabbott.co.uk>

Diff between primarycensored versions 1.0.0 dated 2024-10-28 and 1.1.0 dated 2025-02-10

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 83 files changed, 1358 insertions(+), 741 deletions(-)

More information about primarycensored at CRAN
Permanent link

New package CMatching with initial version 2.4
Package: CMatching
Title: Matching Algorithms for Causal Inference with Clustered Data
Version: 2.4
Date: 2025-02-08
Maintainer: Massimo Cannas <massimo.cannas@unica.it>
Description: Provides functions to perform matching algorithms for causal inference with clustered data, as described in B. Arpino and M. Cannas (2016) <doi:10.1002/sim.6880>. Pure within-cluster and preferential within-cluster matching are implemented. Both algorithms provide causal estimates with cluster-adjusted estimates of standard errors.
Depends: R (>= 2.6.0), Matching
Imports: stats,lmtest,multiwayvcov,lme4
License: GPL-2
NeedsCompilation: no
Encoding: UTF-8
Packaged: 2025-02-08 16:59:28 UTC; massimo
Author: Massimo Cannas [aut, cre], Bruno Arpino [ctb], Elena Colicino [ctb]
Repository: CRAN
Date/Publication: 2025-02-10 19:10:05 UTC

More information about CMatching at CRAN
Permanent link

New package FastRet with initial version 1.1.4
Package: FastRet
Title: Retention Time Prediction in Liquid Chromatography
Version: 1.1.4
Description: A framework for predicting retention times in liquid chromatography. Users can train custom models for specific chromatography columns, predict retention times using existing models, or adjust existing models to account for altered experimental conditions. The provided functionalities can be accessed either via the R console or via a graphical user interface. Related work: Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
License: GPL-3
Language: en-US
URL: https://github.com/spang-lab/FastRet/, https://spang-lab.github.io/FastRet/
BugReports: https://github.com/spang-lab/FastRet/issues
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: bslib, caret, cluster, data.table, digest, DT, future, ggplot2, glmnet, htmltools, promises, rcdk, readxl, shiny (>= 1.8.1), shinybusy, shinyhelper, shinyjs, xgboost, xlsx
Suggests: cli, devtools, knitr, languageserver, lintr, pkgdown, pkgbuild, pkgload, rlang, rmarkdown, servr, tibble, testthat (>= 3.0.0), toscutil, usethis, withr
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-07 19:09:03 UTC; tobi
Author: Christian Amesoeder [aut, cph] , Marian Schoen [aut, cph], Tobias Schmidt [aut, cre, cph] , Fadi Fadil [ctb, cph] , Katja Dettmer [ths, cph] , Peter Oefner [ths, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-10 18:30:02 UTC

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Package CDCPLACES updated to version 1.1.9 with previous version 1.1.8 dated 2024-09-18

Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>) by geography, state, measure, and release year. This package also contains a function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>

Diff between CDCPLACES versions 1.1.8 dated 2024-09-18 and 1.1.9 dated 2025-02-10

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Package misuvi updated to version 0.1.1 with previous version 0.1.0 dated 2024-05-15

Title: Access the Michigan Substance Use Vulnerability Index (MI-SUVI)
Description: Easily import the MI-SUVI data sets. The user can import data sets with full metrics, percentiles, Z-scores, or rankings. Data is available at both the County and Zip Code Tabulation Area (ZCTA) levels. This package also includes a function to import shape files for easy mapping and a function to access the full technical documentation. All data is sourced from the Michigan Department of Health and Human Services.
Author: Brenden Smith [aut, cre, cph]
Maintainer: Brenden Smith <brendensmithmi@gmail.com>

Diff between misuvi versions 0.1.0 dated 2024-05-15 and 0.1.1 dated 2025-02-10

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Package eatRep updated to version 0.15.1 with previous version 0.15.0 dated 2025-01-08

Title: Educational Assessment Tools for Replication Methods
Description: Replication methods to compute some basic statistic operations (means, standard deviations, frequency tables, percentiles, mean comparisons using weighted effect coding, generalized linear models, and linear multilevel models) in complex survey designs comprising multiple imputed or nested imputed variables and/or a clustered sampling structure which both deserve special procedures at least in estimating standard errors. See the package documentation for a more detailed description along with references.
Author: Sebastian Weirich [aut, cre], Martin Hecht [aut], Karoline Sachse [aut], Benjamin Becker [aut], Edna Grewers [ctb]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>

Diff between eatRep versions 0.15.0 dated 2025-01-08 and 0.15.1 dated 2025-02-10

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Package spEDM updated to version 1.4 with previous version 1.3 dated 2025-02-01

Title: Spatial Empirical Dynamic Modeling
Description: Inferring causal associations in cross-sectional earth system data through empirical dynamic modeling (EDM), with extensions to convergent cross mapping from Sugihara et al. (2012) <doi:10.1126/science.1227079>, partial cross mapping as outlined in Leng et al. (2020) <doi:10.1038/s41467-020-16238-0>, and cross mapping cardinality as described in Tao et al. (2023)<doi:10.1016/j.fmre.2023.01.007>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>

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Package vvauditor updated to version 0.7.0 with previous version 0.6.0 dated 2024-02-26

Title: Creates Assertion Tests
Description: Offers a comprehensive set of assertion tests to help users validate the integrity of their data. These tests can be used to check for specific conditions or properties within a dataset and help ensure that data is accurate and reliable. The package is designed to make it easy to add quality control checks to data analysis workflows and to aid in identifying and correcting any errors or inconsistencies in data.
Author: Tomer Iwan [aut, cre, cph], Hajo Bons [aut, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>

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Package rvinecopulib updated to version 0.7.1.1.1 with previous version 0.7.1.1.0 dated 2025-01-21

Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine copula modeling. The 'rvinecopulib' package implements the core features of the popular 'VineCopula' package, in particular inference algorithms for both vine copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker and more modern API, improved performances, especially in high dimensions, nonparametric and multi-parameter families, and the ability to model discrete variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only C++ library (currently version 0.7.1). Thus users do not need to install 'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre], Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>

Diff between rvinecopulib versions 0.7.1.1.0 dated 2025-01-21 and 0.7.1.1.1 dated 2025-02-10

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Package NMAoutlier updated to version 0.2.0 with previous version 0.1.18 dated 2021-10-11

Title: Detecting Outliers in Network Meta-Analysis
Description: A set of functions providing several outlier (i.e., studies with extreme findings) and influential detection measures and methodologies in network meta-analysis : - simple outlier and influential detection measures - outlier and influential detection measures by considering study deletion (shift the mean) - plots for outlier and influential detection measures - Q-Q plot for network meta-analysis - Forward Search algorithm in network meta-analysis. - forward plots to monitor statistics in each step of the forward search algorithm - forward plots for summary estimates and their confidence intervals in each step of forward search algorithm.
Author: Maria Petropoulou [aut, cre] , Guido Schwarzer [aut] , Agapios Panos [aut], Dimitris Mavridis [aut]
Maintainer: Maria Petropoulou <maria.petropoulou@uniklinik-freiburg.de>

Diff between NMAoutlier versions 0.1.18 dated 2021-10-11 and 0.2.0 dated 2025-02-10

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Package nanoparquet updated to version 0.4.1 with previous version 0.4.0 dated 2025-01-29

Title: Read and Write 'Parquet' Files
Description: Self-sufficient reader and writer for flat 'Parquet' files. Can read most 'Parquet' data types. Can write many 'R' data types, including factors and temporal types. See docs for limitations.
Author: Gabor Csardi [aut, cre], Hannes Muehleisen [aut, cph] , Google Inc. [cph], Apache Software Foundation [cph], Posit Software, PBC [cph], RAD Game Tools [cph], Valve Software [cph], Tenacious Software LLC [cph], Facebook, Inc. [cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between nanoparquet versions 0.4.0 dated 2025-01-29 and 0.4.1 dated 2025-02-10

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Package GeDS updated to version 0.2.6 with previous version 0.2.5 dated 2025-01-21

Title: Geometrically Designed Spline Regression
Description: Spline Regression, Generalized Additive Models, and Component-wise Gradient Boosting, utilizing Geometrically Designed (GeD) Splines. GeDS regression is a non-parametric method inspired by geometric principles, for fitting spline regression models with variable knots in one or two independent variables. It efficiently estimates the number of knots and their positions, as well as the spline order, assuming the response variable follows a distribution from the exponential family. GeDS models integrate the broader category of Generalized (Non-)Linear Models, offering a flexible approach to modeling complex relationships. A description of the method can be found in Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2023) <doi:10.1016/j.amc.2022.127493>. Further extending its capabilities, GeDS's implementation includes Generalized Additive Models (GAM) and Functional Gradient Boosting (FGB), enabling versatile multivariate predictor modeling, as discuss [...truncated...]
Author: Dimitrina S. Dimitrova [aut], Vladimir K. Kaishev [aut], Andrea Lattuada [aut], Emilio L. Saenz Guillen [aut, cre], Richard J. Verrall [aut]
Maintainer: Emilio L. Saenz Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>

Diff between GeDS versions 0.2.5 dated 2025-01-21 and 0.2.6 dated 2025-02-10

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New package TSLA with initial version 0.1.1
Package: TSLA
Title: Tree-Guided Rare Feature Selection and Logic Aggregation
Version: 0.1.1
Imports: stats, Matrix, Rcpp, pROC, PRROC, ape, phytools, data.tree
LinkingTo: Rcpp, RcppArmadillo
Maintainer: Jianmin Chen <jianminc000@gmail.com>
Description: Implementation of the tree-guided feature selection and logic aggregation approach introduced in Chen et al. (2024) <doi:10.1080/01621459.2024.2326621>. The method enables the selection and aggregation of large-scale rare binary features with a known hierarchical structure using a convex, linearly-constrained regularized regression framework. The package facilitates the application of this method to both linear regression and binary classification problems by solving the optimization problem via the smoothing proximal gradient descent algorithm (Chen et al. (2012) <doi:10.1214/11-AOAS514>).
Depends: R (>= 4.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2025-02-07 19:37:35 UTC; cjm
Author: Jianmin Chen [aut, cre], Kun Chen [aut]
Repository: CRAN
Date/Publication: 2025-02-10 11:30:03 UTC

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New package powerHE with initial version 1.0.0
Package: powerHE
Title: Power and Sample Size Calculations with Hierarchical Endpoints
Version: 1.0.0
Description: Calculate sample size or power for hierarchical endpoints. The package can handle any type of outcomes (binary, continuous, count, ordinal, time-to-event) and any number of such endpoints. It allows users to calculate sample size with a given power or to calculate power with a given sample size for hypothesis testing based on win ratios, win odds, net benefit, or DOOR (desirability of outcome ranking) as treatment effect between two groups for hierarchical endpoints. The methods of this package are described further in the paper by Barnhart, H. X. et al. (2024, <doi:10.1080/19466315.2024.2365629>).
License: GPL (>= 2)
Encoding: UTF-8
Imports: skellam
NeedsCompilation: no
Packaged: 2025-02-07 05:15:03 UTC; sarahwu
Author: Sarah Wu [aut, cre], Dylan Thibault [aut]
Maintainer: Sarah Wu <O2E@duke.edu>
Repository: CRAN
Date/Publication: 2025-02-10 11:20:02 UTC

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Package ecmwfr updated to version 2.0.3 with previous version 2.0.2 dated 2024-09-27

Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Data Stores. Allows for easy downloads of weather forecasts and climate reanalysis data in R. Data stores covered include the Climate Data Store (CDS; <https://cds.climate.copernicus.eu>), Atmosphere Data Store (ADS; <https://ads.atmosphere.copernicus.eu>) and Early Warning Data Store (CEMS; <https://ewds.climate.copernicus.eu>).
Author: Koen Hufkens [aut, cre, cph] , Reto Stauffer [ctb] , Elio Campitelli [ctb] , BlueGreen Labs [fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>

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Permanent link

Package cTOST updated to version 1.0.1 with previous version 1.0.0 dated 2024-01-31

Title: Finite Sample Correction of the Two One-Sided Tests in the Univariate Framework
Description: A system containing easy-to-use tools to compute the bioequivalence assessment in the univariate framework using the methods proposed in Boulaguiem et al. (2023) <doi:10.1101/2023.03.11.532179>.
Author: Younes Boulaguiem [aut, cre, cph], Stephane Guerrier [aut, cph], Dominique-Laurent Couturier [aut, cph]
Maintainer: Younes Boulaguiem <younes.boulaguiem@gmail.com>

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New package BayesERtools with initial version 0.2.0
Package: BayesERtools
Title: Bayesian Exposure-Response Analysis Tools
Version: 0.2.0
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Description: Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
URL: https://genentech.github.io/BayesERtools/, https://genentech.github.io/BayesERbook/
Imports: dplyr, tidyr, purrr, ggplot2, gt, cli, rlang, rstanarm, loo, tidybayes, bayestestR, posterior, withr
Suggests: testthat (>= 3.0.0), covr, knitr, rmarkdown, rstan, rstanemax (>= 0.1.7), htmltools, digest, ggforce, xgxr, scales, readr, patchwork, projpred, rsample, yardstick
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-07 20:17:35 UTC; yoshidk6
Author: Kenta Yoshida [aut, cre] , Francois Mercier [aut] , Genentech, Inc. [cph]
Repository: CRAN
Date/Publication: 2025-02-10 11:30:13 UTC

More information about BayesERtools at CRAN
Permanent link

Package Rrepest updated to version 1.5.2 with previous version 1.3.0 dated 2023-11-24

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,...). It also allows for analyses with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre], Francesco Avvisati [aut], Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>

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Package paws updated to version 0.8.0 with previous version 0.7.0 dated 2024-09-17

Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Author: David Kretch [aut], Adam Banker [aut], Dyfan Jones [cre], Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package onpoint updated to version 1.1 with previous version 1.0.6 dated 2024-09-17

Title: Helper Functions for Point Pattern Analysis
Description: Growing collection of helper functions for point pattern analysis. Most functions are designed to work with the 'spatstat' (<http://spatstat.org>) package. The focus of most functions are either null models or summary functions for spatial point patterns. For a detailed description of all null models and summary functions, see Wiegand and Moloney (2014, ISBN:9781420082548).
Author: Maximilian H.K. Hesselbarth [aut, cre]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>

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Permanent link

New package retmort with initial version 1.0.0
Package: retmort
Title: Estimate User-Based Tagging Mortality and Tag Loss in Mark-Recapture Studies
Version: 1.0.0
Description: We provide several avenues to predict and account for user-based mortality and tag loss during mark-recapture studies. When planning a study on a target species, the retentionmort_generation() function can be used to produce multiple synthetic mark-recapture datasets to anticipate the error associated with a planned field study to guide method development to reduce error. Similarly, if field data was already collected, the retentionmort() function can be used to predict the error from already generated data to adjust for user-based mortality and tag loss. The test_dataset_retentionmort() function will provide an example dataset of how data should be inputted into the function to run properly. Lastly, the retentionmort_figure() function can be used on any dataset generated from either model function to produce an 'rmarkdown' printout of preliminary analysis associated with the model, including summary statistics and figures. Methods and results pertaining to the formation of this packag [...truncated...]
License: MIT + file LICENSE
Imports: dplyr, ggplot2, gridExtra, patchwork, readr, rmarkdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-07 15:01:45 UTC; Brendan
Author: Brendan Campbell [aut, cre] , Jasper McCutcheon [aut] , Rileigh Hudock [aut] , Noah Motz [aut] , Madison Windsor [aut] , Aaron Carlisle [aut] , Edward Hale [aut]
Maintainer: Brendan Campbell <bpc@udel.edu>
Repository: CRAN
Date/Publication: 2025-02-10 09:40:02 UTC

More information about retmort at CRAN
Permanent link

Package rdecision updated to version 1.3.0 with previous version 1.2.1 dated 2024-06-09

Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] , Kim Fairbairn [aut] , Paola Cognigni [aut]
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>

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Package landscapemetrics updated to version 2.2.1 with previous version 2.2 dated 2025-01-10

Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current literature on landscape metrics. This package supports 'terra' SpatRaster objects as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
Author: Maximilian H.K. Hesselbarth [aut, cre] , Marco Sciaini [aut] , Jakub Nowosad [aut] , Sebastian Hanss [aut] , Laura J. Graham [ctb] , Jeffrey Hollister [ctb] , Kimberly A. With [ctb] , Florian Prive [ctb] function), Project Nayuki [ctb] , Matt Strima [...truncated...]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>

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Package watcher updated to version 0.1.1 with previous version 0.1.0 dated 2025-02-06

Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library. Watch files, or directories recursively, for changes in the background. Log activity, or run an R function every time a change event occurs.
Author: Charlie Gao [aut, cre] , Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package spinBayes updated to version 0.2.2 with previous version 0.2.1 dated 2024-03-12

Title: Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection
Description: Many complex diseases are known to be affected by the interactions between genetic variants and environmental exposures beyond the main genetic and environmental effects. Existing Bayesian methods for gene-environment (G×E) interaction studies are challenged by the high-dimensional nature of the study and the complexity of environmental influences. We have developed a novel and powerful semi-parametric Bayesian variable selection method that can accommodate linear and nonlinear G×E interactions simultaneously (Ren et al. (2020) <doi:10.1002/sim.8434>). Furthermore, the proposed method can conduct structural identification by distinguishing nonlinear interactions from main effects only case within Bayesian framework. Spike-and-slab priors are incorporated on both individual and group level to shrink coefficients corresponding to irrelevant main and interaction effects to zero exactly. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently [...truncated...]
Author: Jie Ren [aut, cre], Fei Zhou [aut], Xiaoxi Li [aut], Cen Wu [aut], Yu Jiang [aut]
Maintainer: Jie Ren <renjie0910@gmail.com>

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Package paws.end.user.computing updated to version 0.8.0 with previous version 0.7.0 dated 2024-09-11

Title: 'Amazon Web Services' End User Computing Services
Description: Interface to 'Amazon Web Services' end user computing services, including collaborative document editing, mobile intranet, and more <https://aws.amazon.com/>.
Author: David Kretch [aut], Adam Banker [aut], Dyfan Jones [cre], Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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More information about paws.end.user.computing at CRAN
Permanent link

Package hexDensity updated to version 1.4.8 with previous version 1.4.5 dated 2024-10-10

Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data. Hexagonal grid has many beneficial properties like equidistant neighbours and less edge bias, making it better for spatial analyses than the more commonly used rectangular grid. Carr, D. B. et al. (1987) <doi:10.2307/2289444>. Diggle, P. J. (2010) <doi:10.1201/9781420072884>. Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>. Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] , Yunshun Chen [aut] , Dan Carr [ctb], binning routine ported by Nicholas Lewin-Koh [ctb], Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>

Diff between hexDensity versions 1.4.5 dated 2024-10-10 and 1.4.8 dated 2025-02-10

 DESCRIPTION             |    6 +-
 MD5                     |   16 +++----
 NAMESPACE               |    4 -
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 R/hexDensity.R          |   77 +++++++++++++++++++++++------------
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More information about hexDensity at CRAN
Permanent link

Package terra updated to version 1.8-21 with previous version 1.8-15 dated 2025-01-24

Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] , Marcia Barbosa [ctb], Roger Bivand [ctb] , Andrew Brown [ctb], Michael Chirico [ctb], Emanuele Cordano [ctb] , Krzysztof Dyba [ctb] , Edzer Pebesma [ctb] , Barry Rowlingson [ctb], Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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More information about terra at CRAN
Permanent link

Package nullabor updated to version 0.3.15 with previous version 0.3.12 dated 2024-07-21

Title: Tools for Graphical Inference
Description: Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.
Author: Hadley Wickham [aut, ctb] , Niladri Roy Chowdhury [aut, ctb], Di Cook [aut, cre] , Heike Hofmann [aut, ctb] , Mans Thulin [aut, ctb]
Maintainer: Di Cook <dicook@monash.edu>

Diff between nullabor versions 0.3.12 dated 2024-07-21 and 0.3.15 dated 2025-02-10

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 man/null_lm.Rd                       |   14 ++++--
 man/null_permute.Rd                  |    2 
 man/null_ts.Rd                       |    2 
 man/resid_perm.Rd                    |only
 man/tips.Rd                          |   18 ++++----
 vignettes/nullabor-distributions.Rmd |only
 vignettes/nullabor-examples.Rmd      |    2 
 vignettes/nullabor-regression.Rmd    |only
 32 files changed, 233 insertions(+), 141 deletions(-)

More information about nullabor at CRAN
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