CRANberries

Fri, 03 May 2024

New package survivalVignettes with initial version 0.1.6
Package: survivalVignettes
Version: 0.1.6
Date: 2024-05-02
Title: Survival Analysis Vignettes and Optional Datasets
Depends: R (>= 3.5.0), survival
Imports: graphics
Suggests: knitr, rmarkdown, bookdown, survey, geepack, mstate, R.rsp
URL: https://github.com/bethatkinson/survivalVignettes
BugReports: https://github.com/bethatkinson/survivalVignettes/issues
Description: Vignettes for the 'survival' package. Split from the 'survival' package since the vignettes were getting large. Also, since 'survival' is a recommended package it cannot make use of other packages outside of base+recommended (e.g. 'rmarkdown').
License: LGPL (>= 2)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-05-02 14:53:50 UTC; atkinson
Author: Terry M Therneau [aut], Elizabeth Atkinson [cre, ctb], Cynthia Crowson [ctb]
Maintainer: Elizabeth Atkinson <atkinson@mayo.edu>
Repository: CRAN
Date/Publication: 2024-05-03 23:20:02 UTC

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New package EMJMCMC with initial version 1.5.0
Package: EMJMCMC
Title: Evolutionary Mode Jumping Markov Chain Monte Carlo Expert Toolbox
Version: 1.5.0
Date: 2024-05-02
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Description: Implementation of the Mode Jumping Markov Chain Monte Carlo algorithm from Hubin, A., Storvik, G. (2018) <doi:10.1016/j.csda.2018.05.020>, Genetically Modified Mode Jumping Markov Chain Monte Carlo from Hubin, A., Storvik, G., & Frommlet, F. (2020) <doi:10.1214/18-BA1141>, Hubin, A., Storvik, G., & Frommlet, F. (2021) <doi:10.1613/jair.1.13047>, and Hubin, A., Heinze, G., & De Bin, R. (2023) <doi:10.3390/fractalfract7090641>, and Reversible Genetically Modified Mode Jumping Markov Chain Monte Carlo from Hubin, A., Frommlet, F., & Storvik, G. (2021) <doi:10.48550/arXiv.2110.05316>, which allow for estimating posterior model probabilities and Bayesian model averaging across a wide set of Bayesian models including linear, generalized linear, generalized linear mixed, generalized nonlinear, generalized nonlinear mixed, and logic regression models.
License: GPL
Depends: R (>= 3.4.1), bigmemory
Imports: glmnet, biglm, hash, BAS, stringi, parallel, methods, speedglm, stats, withr
Suggests: testthat (>= 3.0.0), bindata, clusterGeneration, reshape2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-05-02 07:33:43 UTC; waldir
Author: Aliaksandr Hubin [aut], Waldir Leoncio [cre, aut], Geir Storvik [ctb], Florian Frommlet [ctb]
Repository: CRAN
Date/Publication: 2024-05-03 23:10:02 UTC

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New package DBTCShiny with initial version 0.1.2
Package: DBTCShiny
Title: Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis 'shiny' Application
Version: 0.1.2
Maintainer: Robert G Young <rgyoung6@gmail.com>
Description: Metabarcoding analysis using the 'DBTC' package is implemented here using 'shiny' in an interactive graphical user interface to conduct Metabarcode analyses and visualize and filter results.
License: GPL-2 | GPL-3
Encoding: UTF-8
URL: <https://github.com/rgyoung6/DBTCShiny>
Depends:
Imports: DBTC, DT, ggplot2, leaflet, leaflet.extras, magrittr, shiny, shinyFiles, shinyjs, shinycssloaders, shinydashboard, shinyWidgets,
Language: en-GB
NeedsCompilation: no
Packaged: 2024-05-03 15:11:47 UTC; robgy
Author: Robert G Young [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-05-03 23:30:02 UTC

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New package SoilConservation with initial version 1.0.0
Package: SoilConservation
Title: Soil and Water Conservation
Version: 1.0.0
Date: 2024-04-28
Imports: stats
Acknowledgements: This work was carried out with support from CNPq, National Council for Scientific and Technological Development (number of the process 152652/2022-1)
Depends: R (>= 3.5.1)
Description: Includes four functions: RFactor_calc(), RFactor_est(), KFactor() and SoilLoss(). The rainfall erosivity factors can be calculated or estimated, and soil erodibility will be estimated by the equation extracted from the monograph. Soil loss will be estimated by the product of five factors (rainfall erosivity, soil erodibility, length and steepness slope, cover-management factor and support practice factor. In the future, additional functions can be included. This efforts to advance research in soil and water conservation, with fast and accurate results.
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Author: Dione Pereira Cardoso [aut, cre] , Paulo Cesar Ossani [aut] , Junior Cesar Avanzi [aut]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Repository: CRAN
Packaged: 2024-05-03 13:15:26 UTC; Ossan
Date/Publication: 2024-05-03 13:50:02 UTC

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New package OpenLand with initial version 1.0.3
Package: OpenLand
Title: Quantitative Analysis and Visualization of LUCC
Version: 1.0.3
Description: Tools for the analysis of land use and cover (LUC) time series. It includes support for loading spatiotemporal raster data and synthesized spatial plotting. Several LUC change (LUCC) metrics in regular or irregular time intervals can be extracted and visualized through one- and multistep sankey and chord diagrams. A complete intensity analysis according to Aldwaik and Pontius (2012) <doi:10.1016/j.landurbplan.2012.02.010> is implemented, including tools for the generation of standardized multilevel output graphics.
License: GPL-3
URL: https://reginalexavier.github.io/OpenLand/, https://github.com/reginalexavier/OpenLand
BugReports: https://github.com/reginalexavier/OpenLand/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Imports: dplyr (>= 0.8.3), tidyr (>= 1.0.0), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), grid, circlize (>= 0.4.8), networkD3 (>= 0.4), raster (>= 3.0.7), methods
Suggests: tmap, knitr, rmarkdown, covr, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-05-03 13:06:15 UTC; tredgi
Author: Reginal Exavier [aut, cre] , Peter Zeilhofer [aut]
Maintainer: Reginal Exavier <reginalexavier@rocketmail.com>
Repository: CRAN
Date/Publication: 2024-05-03 13:40:02 UTC

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New package lievens with initial version 0.0.1
Package: lievens
Title: Real-Time PCR Data Sets by Lievens et al. (2012)
Version: 0.0.1
Description: Real-time quantitative polymerase chain reaction (qPCR) data sets by Lievens et al. (2012) <doi:10.1093/nar/gkr775>. Provides one single tabular tidy data set in long format, encompassing three dilution series, targeted against the soybean Lectin endogene. Each dilution series was assayed in one of the following PCR-efficiency-modifying conditions: no PCR inhibition, inhibition by isopropanol and inhibition by tannic acid. The inhibitors were co-diluted along with the dilution series. The co-dilution series consists of a five-point, five-fold serial dilution. For each concentration there are 18 replicates. Each amplification curve is 60 cycles long. Original raw data file is available at the Supplementary Data section at Nucleic Acids Research Online <doi:10.1093/nar/gkr775>.
License: CC BY 4.0
Encoding: UTF-8
Imports: tibble
Depends: R (>= 2.10)
LazyData: true
URL: https://rmagno.eu/lievens/, https://github.com/ramiromagno/lievens
BugReports: https://github.com/ramiromagno/lievens/issues
NeedsCompilation: no
Packaged: 2024-05-02 23:18:32 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-05-03 13:10:02 UTC

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New package LATERmodel with initial version 0.2.0
Package: LATERmodel
Title: Linear Approach to Threshold with Ergodic Rate for Reaction Times
Version: 0.2.0
Description: Implements the Linear Approach to Threshold with Ergodic Rate (LATER) model, which predicts distributions of reaction times and summarises them with as little as two free parameters. Allows for easy visualisation and comparison of datasets, along with fitting of datasets using the LATER model.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, ggplot2, rlang, stats, tibble, parallel, moments
Depends: R (>= 4.1)
LazyData: true
Suggests: lintr, styler, testthat (>= 3.0.0), vdiffr, printr, withr
URL: https://github.com/unimelbmdap/LATERmodel, https://unimelbmdap.github.io/LATERmodel/
BugReports: https://github.com/unimelbmdap/LATERmodel/issues
NeedsCompilation: no
Packaged: 2024-05-03 06:16:05 UTC; mquiroga
Author: Maria del Mar Quiroga [aut, cre] , Damien Mannion [aut] , Edoardo Tescari [aut] , Andrew Anderson [aut] , The University of Melbourne [cph, fnd]
Maintainer: Maria del Mar Quiroga <mar.quiroga@unimelb.edu.au>
Repository: CRAN
Date/Publication: 2024-05-03 13:20:02 UTC

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New package ExpImage with initial version 0.10.0
Package: ExpImage
Title: Analysis of Images in Experiments
Version: 0.10.0
Description: Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas) <https://www.expstat.com/pacotes-do-r/expimage>.
Depends: raster
Imports: rstudioapi,progress,randomForest,ggplot2,crayon, doParallel,parallel, foreach,schemr
URL: https://www.youtube.com/channel/UCDGyvLCJnv9RtTY1YMBMVNQ, https://github.com/cran/ExpImage
License: GPL-3
Encoding: UTF-8
Language: pt-BR
Suggests: BiocManager, EBImage, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-05-03 12:13:10 UTC; AlcineiAzevedo
Author: Alcinei Mistico Azevedo [aut, cre]
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>
Repository: CRAN
Date/Publication: 2024-05-03 13:40:06 UTC

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New package bRacatus with initial version 2.0.0
Package: bRacatus
Title: A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data
Version: 2.0.0
Language: en-GB
Description: Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Depends: R (>= 3.5.0)
Imports: data.table, geojsonio, graphics, grDevices, jsonlite, methods, plotfunctions, raster, rgbif, rnaturalearth, sf, sp, stats
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/EduardoArle/bRacatus
BugReports: https://github.com/EduardoArle/bRacatus/issues
LazyData: true
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-05-03 07:52:01 UTC; carloseduardoaribeiro
Author: Eduardo Arle [aut, cre], Alexander Zizka [aut], Patrick Weigelt [ctb], Sam Levin [ctb], Carsten Meyer [ths]
Maintainer: Eduardo Arle <eduardoarle@tauex.tau.ac.il>
Repository: CRAN
Date/Publication: 2024-05-03 13:30:02 UTC

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New package streetscape with initial version 1.0.0
Package: streetscape
Title: Collect And Investigate Street Views For Urban Science
Version: 1.0.0
Description: A collection of functions to search and download street view imagery ('Mapilary' <https://www.mapillary.com/developer/api-documentation>) and to extract, quantify, and visualize visual features. Moreover, there are functions provided to generate Qualtrics survey in TXT format using the collection of street views for various research purposes.
License: GPL-3
Depends: R (>= 4.1)
Language: en_GB
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Imports: rlang, methods, dplyr, sf, sp, httr, reticulate, osmdata, quickPWCR, mapview, SuperpixelImageSegmentation, OpenImageR, pbmcapply, parallelly
NeedsCompilation: no
Packaged: 2024-05-02 19:13:16 UTC; yangxiaohao
Author: Xiaohao Yang [aut, cre, cph], Derek Van Berkel [aut], Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Repository: CRAN
Date/Publication: 2024-05-03 13:00:03 UTC

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New package reflectR with initial version 2.0.2
Package: reflectR
Title: Automatic Scoring of the Cognitive Reflection Test
Version: 2.0.2
Imports: stringr
Description: A tool for researchers and psychologists to automatically code open-ended responses to the Cognitive Reflection Test (CRT), a widely used class of tests in cognitive science and psychology for assessing an individual's propensity to override an incorrect gut response and engage in further reflection to find a correct answer. This package facilitates the standardization of Cognitive Reflection Test responses analysis across large datasets in cognitive psychology, decision-making, and related fields. By automating the coding process, it not only reduces manual effort but also aims to reduce the variability introduced by subjective interpretation of open-ended responses, contributing to a more consistent and reliable analysis. 'reflectR' supports automatic coding and machine scoring for the original English-language version of CRT (Frederick, 2005) <doi:10.1257/089533005775196732>, as well as for CRT4 and CRT7, 4- and 7-item versions, respectively (Toplak et al., 2014) <doi:10.10 [...truncated...]
URL: https://github.com/g-corbelli/reflectR
BugReports: https://github.com/g-corbelli/reflectR/issues
License: GPL-3
Encoding: UTF-8
Suggests: spelling
Language: en-US
NeedsCompilation: no
Author: Giuseppe Corbelli [aut, cre]
Maintainer: Giuseppe Corbelli <giuseppe.corbelli@uninettunouniversity.net>
Packaged: 2024-05-02 20:57:26 UTC; GC
Repository: CRAN
Date/Publication: 2024-05-03 13:00:06 UTC

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New package loggit2 with initial version 2.2.2
Package: loggit2
Title: Easy-to-Use, Dependencyless Logger
Description: An easy-to-use 'ndjson' (newline-delimited 'JSON') logger. It provides a set of wrappings for base R's message(), warning(), and stop() functions that maintain identical functionality, but also log the handler message to an 'ndjson' log file. No change in existing code is necessary to use this package, and should only require additions to fully leverage the power of the logging system.
Version: 2.2.2
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 3.0.0)
URL: https://github.com/MEO265/loggit2
BugReports: https://github.com/MEO265/loggit2/issues
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-05-02 17:02:54 UTC; Matthias
Author: Matthias Ollech [cre, aut], Ryan Price [fnd, aut]
Maintainer: Matthias Ollech <ollech@gmx.com>
Repository: CRAN
Date/Publication: 2024-05-03 12:30:06 UTC

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New package linelistBayes with initial version 1.0
Package: linelistBayes
Title: Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches
Version: 1.0
Date: 2024-04-30
Maintainer: Chad Milando <cmilando@bu.edu>
Description: Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.
License: GPL-3
Imports: Rcpp (>= 1.0.11), magrittr, lubridate, coda, dplyr
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 2.10)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-05-02 20:34:54 UTC; cwm
Author: Chad Milando [aut, cre], Tenglong Li [ctb], Laura White [ctb]
Repository: CRAN
Date/Publication: 2024-05-03 13:00:10 UTC

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New package ablasso with initial version 1.0
Package: ablasso
Title: Arellano-Bond LASSO Estimator for Dynamic Linear Panel Models
Version: 1.0
Maintainer: Junyu Chen <junyu.chen@outlook.de>
Description: Implements the Arellano-Bond estimation method combined with LASSO for dynamic linear panel models. See Chernozhukov et al. (2024) "Arellano-Bond LASSO Estimator for Dynamic Linear Panel Models". arXiv preprint <doi:10.48550/arXiv.2402.00584>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: hdm, matrixStats, mvtnorm, stats
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2024-05-02 20:33:33 UTC; junyuchen
Author: Victor Chernozhukov [aut], Ivan Fernandez-Val [aut], Chen Huang [aut], Weining Wang [aut], Junyu Chen [cre]
Repository: CRAN
Date/Publication: 2024-05-03 13:00:13 UTC

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Thu, 02 May 2024

New package rmdl with initial version 0.1.0
Package: rmdl
Title: Language to Manage Many Models
Version: 0.1.0
Description: A system for describing and manipulating the many models that are generated in causal inference and data analysis projects, as based on the causal theory and criteria of Austin Bradford Hill (1965) <doi:10.1177/003591576505800503>. This system includes the addition of formal attributes that modify base `R` objects, including terms and formulas, with a focus on variable roles in the "do-calculus" of modeling, as described in Pearl (2010) <doi:10.2202/1557-4679.1203>. For example, the definition of exposure, outcome, and interaction are implicit in the roles variables take in a formula. These premises allow for a more fluent modeling approach focusing on variable relationships, and assessing effect modification, as described by VanderWeele and Robins (2007) <doi:10.1097/EDE.0b013e318127181b>. The essential goal is to help contextualize formulas and models in causality-oriented workflows.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0), vctrs (>= 0.5.0), tibble (>= 3.0.0),
Imports: stats, utils, generics, methods, dplyr, broom, tidyr, rlang, pillar, purrr, janitor
Suggests: testthat (>= 3.0.0), covr, cli, rmarkdown, knitr, ggplot2, gt, survival, cmprsk, tidycmprsk
VignetteBuilder: knitr
URL: https://github.com/shah-in-boots/rmdl
BugReports: https://github.com/shah-in-boots/rmdl/issues
NeedsCompilation: no
Packaged: 2024-05-02 16:48:30 UTC; asshah4
Author: Anish S. Shah [aut, cre, cph]
Maintainer: Anish S. Shah <ashah282@uic.edu>
Repository: CRAN
Date/Publication: 2024-05-02 22:20:02 UTC

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New package filibustr with initial version 0.2.1
Package: filibustr
Title: Data Utilities for Congressional Research
Version: 0.2.1
Description: Provides easy-to-understand and consistent interfaces for accessing data on the U.S. Congress. The functions in 'filibustr' streamline the process for importing data on Congress into R, removing the need to download and work from CSV files and the like. Data sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate website (<https://www.senate.gov/>), and more.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: crul, dplyr, haven, httr2, lifecycle, R.utils, readr, rlang, rvest, stringr, tidyr, tidyselect
URL: https://github.com/feinleib/filibustr
BugReports: https://github.com/feinleib/filibustr/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-25 05:11:36 UTC; mhfeinleib
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-02 16:22:37 UTC

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New package symbolicQspray with initial version 1.0.0
Package: symbolicQspray
Title: Multivariate Polynomials with Symbolic Parameters in their Coefficients
Version: 1.0.0
Description: Introduces the 'symbolicQspray' objects. Such an object represents a multivariate polynomial whose coefficients are fractions of multivariate polynomials with rational coefficients. The package allows arithmetic on such polynomials. It is based on the 'qspray' and 'ratioOfQsprays' packages. Some functions for 'qspray' polynomials have their counterpart for 'symbolicQspray' polynomials. A 'symbolicQspray' polynomial should not be seen as a polynomial on the field of fractions of rational polynomials, but should rather be seen as a polynomial with rational coefficients depending on some parameters, symbolically represented, with a dependence given by fractions of rational polynomials.
License: GPL-3
URL: https://github.com/stla/symbolicQspray
BugReports: https://github.com/stla/symbolicQspray/issues
Depends: qspray (>= 3.0.0), ratioOfQsprays
Imports: gmp, methods, Rcpp, utils
Suggests: testthat (>= 3.0.0)
LinkingTo: BH, qspray, ratioOfQsprays, Rcpp, RcppArmadillo, RcppCGAL
Encoding: UTF-8
SystemRequirements: C++17, gmp, mpfr
NeedsCompilation: yes
Packaged: 2024-05-01 05:15:19 UTC; SDL96354
Author: Stephane Laurent [aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2024-05-02 16:00:02 UTC

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New package RAZIAD with initial version 0.0.1
Package: RAZIAD
Title: Regression Analysis of Zero-Inflated and Zero-Altered(Hurdle) Data
Version: 0.0.1
Maintainer: Niloufar Dousti Mousavi <niloufar.dousti@gmail.com>
Description: It performs regression analysis for zero-inflated and zero-altered data, enabling modeling of sparse response variable distributions and assessing their association with covariates. It computes Maximum Likelihood Estimates (MLE) and conducts model selection using AIC and BIC criteria. Additionally, it calculates Fisher Information, confidence intervals, standard errors, and z-scores for all model parameters.
Encoding: UTF-8
Imports: Matrix, extraDistr, stats
Depends: R (>= 4.3.1.0)
LazyData: true
Suggests: testthat (>= 3.0.0)
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2024-05-01 19:29:45 UTC; nilouimac
Author: Niloufar Dousti Mousavi [aut, cre, cph], Hani Aldirawi [aut, cph], Donald Hedeker [aut, cph], Jie Yang [aut, cph]
Repository: CRAN
Date/Publication: 2024-05-02 15:12:43 UTC

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New package ollamar with initial version 1.1.1
Package: ollamar
Title: 'Ollama' Language Models
Version: 1.1.1
Description: An interface to easily run local language models with 'Ollama' <https://ollama.com> server and API endpoints (see <https://github.com/ollama/ollama/blob/main/docs/api.md> for details). It lets you run open-source large language models locally on your machine.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: glue, httr2, jsonlite, tibble
BugReports: https://github.com/hauselin/ollama-r/issues
URL: https://hauselin.github.io/ollama-r/, https://github.com/hauselin/ollama-r
NeedsCompilation: no
Packaged: 2024-05-02 01:09:48 UTC; hause
Author: Hause Lin [aut, cre, cph]
Maintainer: Hause Lin <hauselin@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-02 15:12:40 UTC

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New package lancor with initial version 0.1.2
Package: lancor
Title: Statistical Inference via Lancaster Correlation
Version: 0.1.2
Description: Implementation of the methods described in Holzmann, Klar (2024) <doi:10.48550/arXiv.2303.17872>. Lancaster correlation is a correlation coefficient which equals the absolute value of the Pearson correlation for the bivariate normal distribution, and is equal to or slightly less than the maximum correlation coefficient for a variety of bivariate distributions. Rank and moment-based estimators and corresponding confidence intervals are implemented, as well as independence tests based on these statistics.
Imports: acepack, arrangements, boot, graphics, sn, stats
License: GPL-2
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-05-02 06:52:25 UTC; Klar
Author: Bernhard Klar [aut, cre] , Hajo Holzmann [aut]
Maintainer: Bernhard Klar <bernhard.klar@kit.edu>
Repository: CRAN
Date/Publication: 2024-05-02 15:22:42 UTC

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New package FAOSTAT with initial version 2.3.1
Package: FAOSTAT
Title: Download Data from the FAOSTAT Database
Version: 2.3.1
Date: 2024-05-02
Author: Michael C. J., Markus Gesmann, Filippo Gheri, Paul Rougieux <paul.rougieux@gmail.com>, Sebastian Campbell
Maintainer: Paul Rougieux <paul.rougieux@gmail.com>
Description: Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations. A list of functions to download statistics from FAOSTAT (database of the FAO <https://www.fao.org/faostat/>) and WDI (database of the World Bank <https://data.worldbank.org/>), and to perform some harmonization operations.
URL: https://gitlab.com/paulrougieux/faostatpackage
BugReports: https://gitlab.com/paulrougieux/faostatpackage/-/issues
Imports: RJSONIO (>= 0.96-0), plyr (>= 1.7.1), data.table (>= 1.8.2), MASS (>= 7.3-22), classInt (>= 0.1-19), labeling (>= 0.1), httr (>= 1.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: yes
ZipData: no
VignetteBuilder: knitr
Suggests: knitr, testthat
NeedsCompilation: no
Packaged: 2024-05-02 14:16:54 UTC; paul
Repository: CRAN
Date/Publication: 2024-05-02 15:22:45 UTC

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New package DiscreteTests with initial version 0.1.1
Package: DiscreteTests
Title: Vectorised Computation of P-Values and Their Supports for Several Discrete Statistical Tests
Version: 0.1.1
Date: 2024-05-02
Description: Provides vectorised functions for computing p-values of various common discrete statistical tests as described e.g. in Agresti (2002) <doi:10.1002/0471249688>. Exact and approximate computation methods are provided. For exact p-values, several procedures of determining two-sided p-values are included, which are outlined in more detail in Hirji (2006) <doi:10.1201/9781420036190>.
License: GPL-3
Encoding: UTF-8
Language: en-GB
Imports: R6, checkmate
URL: https://github.com/DISOhda/DiscreteTests
BugReports: https://github.com/DISOhda/DiscreteTests/issues
NeedsCompilation: no
Packaged: 2024-05-02 07:11:35 UTC; Florian Junge
Author: Florian Junge [cre, aut], Christina Kihn [aut], Sebastian Doehler [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Repository: CRAN
Date/Publication: 2024-05-02 15:22:49 UTC

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New package crm12Comb with initial version 0.1.3
Package: crm12Comb
Title: Phase I/II CRM Based Drug Combination Design
Version: 0.1.3
Maintainer: Junying Wang <junying.wang@stonybrook.edu>
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: dplyr, ggplot2, ggforce
Suggests: knitr, rmarkdown
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-05-02 14:40:13 UTC; junyingwang
Author: Junying Wang [cre, aut], Song Wu [aut], Jie Yang [aut]
Repository: CRAN
Date/Publication: 2024-05-02 15:52:43 UTC

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New package panstarrs with initial version 0.2.2
Package: panstarrs
Title: Interface to the Pan-STARRS API
Version: 0.2.2
Description: An interface to the API for 'Pan-STARRS1', a data archive of the PS1 wide-field astronomical survey. The package allows access to the PS1 catalog and to the PS1 images. (see <https://outerspace.stsci.edu/display/PANSTARRS/> for more information). You can use it to plan astronomical observations, make guidance pictures, find magnitudes in five broadband filters (g, r, i, z, y) and more.
License: MIT + file LICENSE
URL: https://uskovgs.github.io/PanSTARRS/
BugReports: https://github.com/uskovgs/PanSTARRS/issues
Depends: R (>= 3.5)
Imports: bit64, checkmate, curl, data.table, httr, jsonlite
Suggests: dplyr, knitr, magick, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-05-02 13:43:54 UTC; uskov
Author: Grigory Uskov [cre, aut]
Maintainer: Grigory Uskov <uskov.russia@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-02 14:02:37 UTC

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New package cvasi with initial version 0.10.4
Package: cvasi
Title: Calibration, Validation, and Simulation of TKTD Models
Version: 0.10.4
Description: Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of 'tidyr' workflows employing the pipe symbol. Time-consuming tasks can be parallelized.
URL: https://github.com/cvasi-tktd/cvasi
BugReports: https://github.com/cvasi-tktd/cvasi/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cli, glue, rlang, stringr, dplyr, tibble, purrr, furrr, tidyr, magrittr, utils, stats, methods, grid, ggplot2, deSolve, lubridate, attempt, units
Suggests: future, testthat, morse, knitr, rmarkdown, lemna, roxyglobals, rjags
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-05-01 07:15:43 UTC; ENCAZ
Author: Nils Kehrein [aut, cre], Dirk Nickisch [aut], Johannes Witt [ctb], Andre Gergs [ctb]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-02 14:42:51 UTC

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New package rsocialwatcher with initial version 0.1.0
Package: rsocialwatcher
Title: 'Facebook Marketing API' Social Watcher
Version: 0.1.0
Description: Facilitates querying data from the ‘Facebook Marketing API', particularly for social science research <https://developers.facebook.com/docs/marketing-apis/>. Data from the 'Facebook Marketing API' has been used for a variety of social science applications, such as for poverty estimation (Marty and Duhaut (2024) <doi:10.1038/s41598-023-49564-6>), disease surveillance (Araujo et al. (2017) <doi:10.48550/arXiv.1705.04045>), and measuring migration (Alexander, Polimis, and Zagheni (2020) <doi:10.1007/s11113-020-09599-3>). The package facilitates querying the number of Facebook daily/monthly active users for multiple location types (e.g., from around a specific coordinate to an administrative region) and for a number of attribute types (e.g., interests, behaviors, education level, etc). The package supports making complex queries within one API call and making multiple API calls across different locations and/or parameters.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://worldbank.github.io/rsocialwatcher/
BugReports: https://github.com/worldbank/rsocialwatcher/issues
Suggests: knitr, rmarkdown
Imports: dplyr, lubridate, jsonlite, httr, curl, stringr, splitstackshape, sf, purrr
NeedsCompilation: no
Packaged: 2024-05-01 01:26:08 UTC; robmarty
Author: Robert Marty [aut, cre]
Maintainer: Robert Marty <rmarty@worldbank.org>
Repository: CRAN
Date/Publication: 2024-05-02 13:10:02 UTC

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New package RcppBlaze with initial version 1.0.0
Package: RcppBlaze
Title: 'Rcpp' Integration for the 'Blaze' High-Performance 'C++' Math Library
Version: 1.0.0
Date: 2024-04-27
Maintainer: Ching-Chuan Chen <zw12356@gmail.com>
URL: https://github.com/Chingchuan-chen/RcppBlaze, https://bitbucket.org/blaze-lib/blaze
BugReports: https://github.com/Chingchuan-chen/RcppBlaze/issues
Description: Blaze is an open-source, high-performance 'C++' math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain-specific language with HPC-grade performance, making it one of the most intuitive and fastest 'C++' math libraries available. The 'RcppBlaze' package includes the header files from the 'Blaze' library with disabling some functionalities related to link to the thread and system libraries which make 'RcppBlaze' be a header-only library. Therefore, users do not need to install 'Blaze'.
Depends: R (>= 4.2.0)
Imports: Rcpp (>= 1.0.0), Matrix (>= 1.5-0)
LinkingTo: Rcpp
Suggests: MatrixExtra, microbenchmark, tinytest, pkgKitten
LazyLoad: yes
Encoding: UTF-8
License: BSD_3_clause + file LICENSE
NeedsCompilation: yes
Packaged: 2024-04-30 12:06:16 UTC; root
Author: Ching-Chuan Chen [aut, cre, ctr] , Klaus Iglberger [aut] , Georg Georg [aut] , Tobias Scharpff [aut]
Repository: CRAN
Date/Publication: 2024-05-02 13:12:42 UTC

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New package healthequal with initial version 1.0.0
Package: healthequal
Title: Compute Summary Measures of Health Inequality
Version: 1.0.0
Description: Compute 21 summary measures of health inequality and its corresponding confidence intervals for ordered and non-ordered dimensions using disaggregated data. Measures for ordered dimensions (e.g., Slope Index of Inequality, Absolute Concentration Index) also accept individual and survey data.
License: AGPL (>= 3)
URL: https://github.com/WHOequity/healthequal, https://whoequity.github.io/healthequal/
BugReports: https://github.com/WHOequity/healthequal/issues
Depends: R (>= 3.5.0)
Imports: dplyr, emmeans, marginaleffects, rlang, srvyr, survey
Suggests: bookdown, knitr, rmarkdown, sandwich, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-05-01 08:52:16 UTC; kirkbyk
Author: Daniel A. Antiporta [aut] , Patricia Menendez [aut] , Katherine Kirkby [aut, cre] , Ahmad Hosseinpoor [aut] , World Health Organization [cph]
Maintainer: Katherine Kirkby <kirkbyk@who.int>
Repository: CRAN
Date/Publication: 2024-05-02 13:22:38 UTC

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New package BMconcor with initial version 2.0.0
Package: BMconcor
Title: CONCOR for Structural- And Regular-Equivalence Blockmodeling
Version: 2.0.0
Description: The four functions svdcp() ('cp' for column partitioned), svdbip() or svdbip2() ('bip' for bipartitioned), and svdbips() ('s' for a simultaneous optimization of a set of 'r' solutions), correspond to a singular value decomposition (SVD) by blocks notion, by supposing each block depending on relative subspaces, rather than on two whole spaces as usual SVD does. The other functions, based on this notion, are relative to two column partitioned data matrices x and y defining two sets of subsets x_i and y_j of variables and amount to estimate a link between x_i and y_j for the pair (x_i, y_j) relatively to the links associated to all the other pairs. These methods were first presented in: Lafosse R. & Hanafi M.,(1997) <https://eudml.org/doc/106424> and Hanafi M. & Lafosse, R. (2001) <https://eudml.org/doc/106494>.
License: GPL (>= 3)
URL: https://fatelarico.github.io/BMconcor/
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-05-01 09:32:49 UTC; fabio
Author: Roger Lafosse [aut], Fabio Ashtar Telarico [cre, aut]
Maintainer: Fabio Ashtar Telarico <Fabio-Ashtar.Telarico@fdv.uni-lj.si>
Repository: CRAN
Date/Publication: 2024-05-02 13:22:42 UTC

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New package RobinCar with initial version 0.2.0
Package: RobinCar
Title: Robust Estimation and Inference in Covariate-Adaptive Randomization
Version: 0.2.0
Description: Performs robust estimation and inference when using covariate adjustment and/or covariate-adaptive randomization in randomized controlled trials. Ting Ye, Jun Shao, Yanyao Yi, Qinyuan Zhao (2023) <doi:10.1080/01621459.2022.2049278>. Ting Ye, Marlena Bannick, Yanyao Yi, Jun Shao (2023) <doi:10.1080/24754269.2023.2205802>. Ting Ye, Jun Shao, Yanyao Yi (2023) <doi:10.1093/biomet/asad045>. Marlena Bannick, Jun Shao, Jingyi Liu, Yu Du, Yanyao Yi, Ting Ye (2024) <doi:10.48550/arXiv.2306.10213>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, magrittr, tidyr, emulator, numDeriv, tidyverse, stats, rlang, survival, fastDummies, data.table, broom, SuperLearner, AIPW, MASS
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, ranger, forcats, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-30 21:33:26 UTC; marlena
Author: Marlena Bannick [cre, aut] , Ting Ye [aut], Yanyao Yi [aut], Faith Bian [aut]
Maintainer: Marlena Bannick <mnorwood@uw.edu>
Repository: CRAN
Date/Publication: 2024-05-02 12:52:55 UTC

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Wed, 01 May 2024

New package AZIAD with initial version 0.0.3
Package: AZIAD
Title: Analyzing Zero-Inflated and Zero-Altered Data
Version: 0.0.3
Maintainer: Niloufar Dousti Mousavi <niloufar.dousti@gmail.com>
Description: Description: Computes maximum likelihood estimates of general, zero-inflated, and zero-altered models for discrete and continuous distributions. It also performs Kolmogorov-Smirnov (KS) tests and likelihood ratio tests for general, zero-inflated, and zero-altered data. Additionally, it obtains the inverse of the Fisher information matrix and confidence intervals for the parameters of general, zero-inflated, and zero-altered models. The package simulates random deviates from zero-inflated or hurdle models to obtain maximum likelihood estimates. Based on the work of Aldirawi et al. (2022) <doi:10.1007/s42519-021-00230-y> and Dousti Mousavi et al. (2023) <doi:10.1080/00949655.2023.2207020>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: extraDistr (>= 1.9.1), methods (>= 4.0.3), foreach (>= 1.5.2), doParallel (>= 1.0.16), parallel (>= 4.1.2), QRM(>= 0.3-31), stats (>= 4.1.2), corpcor (>= 1.6.10), base(>= 4.1.2), EnvStats(>= 2.6.0)
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2024-05-01 16:17:16 UTC; nilouimac
Author: Niloufar Dousti Mousavi [aut, cre, cph], Hani Aldirawi [aut, cph], Jie Yang [aut, cph]
Suggests: testthat (>= 3.0.0)
Repository: CRAN
Date/Publication: 2024-05-01 23:24:59 UTC

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New package TSEAL with initial version 0.1.2
Package: TSEAL
Title: Time Series Analysis Library
Version: 0.1.2
Description: The library allows to perform a multivariate time series classification based on the use of Discrete Wavelet Transform for feature extraction, a step wise discriminant to select the most relevant features and finally, the use of a linear or quadratic discriminant for classification. Note that all these steps can be done separately which allows to implement new steps. Velasco, I., Sipols, A., de Blas, C. S., Pastor, L., & Bayona, S. (2023) <doi:10.1186/S12938-023-01079-X>. Percival, D. B., & Walden, A. T. (2000,ISBN:0521640687). Maharaj, E. A., & Alonso, A. M. (2014) <doi:10.1016/j.csda.2013.09.006>.
License: Artistic-2.0
URL: https://github.com/vg-lab/TSEAL
BugReports: https://github.com/vg-lab/TSEAL/issues
Depends: R (>= 4.3.0)
Imports: bigmemory, caret, checkmate, magrittr, MASS, methods, parallel, parallelly, pryr, statcomp, stats, synchronicity, utils, waveslim, wdm
Suggests: spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-30 12:58:17 UTC; ivan_
Author: Ivan Velasco [aut, cre, cph]
Maintainer: Ivan Velasco <ivan.velasco@urjc.es>
Repository: CRAN
Date/Publication: 2024-05-01 18:42:17 UTC

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New package SCtools with initial version 0.3.3
Package: SCtools
Title: Extensions for Synthetic Controls Analysis
Version: 0.3.3
Date: 2024-04-26
Description: Extends the functionality of the package 'Synth' as detailed in Abadie, Diamond, and Hainmueller (2011) <doi:10.18637/jss.v042.i13>. Includes generating and plotting placebos, post/pre-MSPE (Mean Squared Prediction Error) significance tests and plots, and calculating average treatment effects for multiple treated units.
BugReports: https://github.com/bcastanho/SCtools/issues
Maintainer: Bruno Castanho Silva <b.paula.castanho.e.silva@fu-berlin.de>
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), future (>= 1.6.2)
Imports: ggplot2, Synth, stringr, stats, cvTools, furrr, dplyr, purrr, tidyr, magrittr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-30 12:17:49 UTC; brno
Author: Bruno Castanho Silva [aut, cre] , Michael DeWitt [aut]
Repository: CRAN
Date/Publication: 2024-05-01 18:32:15 UTC

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New package rifreg with initial version 0.1.0
Package: rifreg
Title: Estimate Recentered Influence Function Regression
Version: 0.1.0
Maintainer: Samuel Meier <samuel.meier+cran@immerda.ch>
Description: Provides functions to compute recentered influence functions (RIF) of a distributional variable at the mean, quantiles, variance, gini or any custom functional of interest. The package allows to regress the RIF on any number of covariates. Generic print, plot and summary functions are also provided. Reference: Firpo, Sergio, Nicole M. Fortin, and Thomas Lemieux. (2009) <doi:10.3982/ECTA6822>. "Unconditional Quantile Regressions.".
License: GPL (>= 3)
Depends: ggplot2, R (>= 2.10)
Imports: Formula, Hmisc, methods, parallel, pbapply, sandwich, stats
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-04-30 12:57:59 UTC; tercy
Author: David Gallusser [aut], Samuel Meier [aut, cre]
Repository: CRAN
Date/Publication: 2024-05-01 18:42:07 UTC

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New package mtarm with initial version 0.1.0
Package: mtarm
Title: Bayesian Estimation of Multivariate Threshold Autoregressive Models
Version: 0.1.0
Author: Luis Hernando Vanegas [aut, cre], Sergio Alejandro Calderon [aut], Luz Marina Rondon [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Description: Estimation, inference and forecasting using the Bayesian approach for multivariate threshold autoregressive (TAR) models in which the distribution used to describe the noise process belongs to the class of Gaussian variance mixtures.
Imports: methods, stats, utils, graphics, Formula, grDevices, GIGrvg, coda
BugReports: https://github.com/lhvanegasp/mtar/issues
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
License: GPL-2 | GPL-3
Packaged: 2024-04-30 13:32:49 UTC; 57312
Repository: CRAN
Date/Publication: 2024-05-01 18:42:10 UTC

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New package forensicolors with initial version 1.0.0
Package: forensicolors
Title: Forensic Colors
Version: 1.0.0
Description: Computes likelihood ratios based on pigmentation traits. Also, it allows computing conditional probabilities for unidentified individuals based on missing person characteristics. A set of tailored plots are incorporated to analyze likelihood ratio distributions.
License: GPL (>= 3)
Encoding: UTF-8
Imports: forrel, pedtools, plotly, dplyr, ggplot2
URL: https://github.com/MarsicoFL/forensicolors
BugReports: https://github.com/MarsicoFL/forensicolors/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-04-30 12:25:14 UTC; franco
Author: Franco Marsico [aut, cre], Thore Egeland [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-01 18:32:12 UTC

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New package FeatureExtraction with initial version 3.5.2
Package: FeatureExtraction
Title: Generating Features for a Cohort
Version: 3.5.2
Date: 2024-04-24
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Depends: R (>= 3.5.0), DatabaseConnector (>= 3.0.0), Andromeda
Imports: methods, dplyr, rJava, jsonlite, SqlRender (>= 1.6.0), ParallelLogger (>= 2.0.2), cli, pillar, readr, rlang, RSQLite, DBI, checkmate
Suggests: testthat, knitr, rmarkdown, Eunomia (>= 2.0.0), withr, curl, httr
License: Apache License 2.0
VignetteBuilder: knitr
URL: https://github.com/OHDSI/FeatureExtraction
BugReports: https://github.com/OHDSI/FeatureExtraction/issues
NeedsCompilation: no
Encoding: UTF-8
Language: en-US
Packaged: 2024-04-30 18:12:51 UTC; ginberg
Author: Martijn Schuemie [aut], Marc Suchard [aut], Patrick Ryan [aut], Jenna Reps [aut], Anthony Sena [aut], Ger Inberg [aut, cre], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2024-05-01 18:54:41 UTC

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New package vein with initial version 1.1.3
Package: vein
Title: Vehicular Emissions Inventories
Version: 1.1.3
Date: 2024-04-30
Description: Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.
License: MIT + file LICENSE
URL: https://github.com/atmoschem/vein
BugReports: https://github.com/atmoschem/vein/issues
LazyData: no
Depends: R (>= 3.5.0)
Imports: sf (>= 1.0.1), data.table, units, graphics, stats, dotCall64, cptcity, grDevices
Suggests: knitr, rmarkdown, testthat
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-05-01 04:18:01 UTC; sergio
VignetteBuilder: knitr
Author: Sergio Ibarra-Espinosa [aut, cre] , Daniel Schuch [ctb] , Joao Bazzo [ctb] , Mario Gavidia-Calderon [ctb] , Karl Ropkins [ctb]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-01 13:50:02 UTC

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Tue, 30 Apr 2024

New package stackgbm with initial version 0.1.0
Package: stackgbm
Title: Stacked Gradient Boosting Machines
Version: 0.1.0
Description: A minimalist implementation of model stacking by Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1> for boosted tree models. A classic, two-layer stacking model is implemented, where the first layer generates features using gradient boosting trees, and the second layer employs a logistic regression model that uses these features as inputs. Utilities for training the base models and parameters tuning are provided, allowing users to experiment with different ensemble configurations easily. It aims to provide a simple and efficient way to combine multiple gradient boosting models to improve predictive model performance and robustness.
License: MIT + file LICENSE
URL: https://nanx.me/stackgbm/, https://github.com/nanxstats/stackgbm
BugReports: https://github.com/nanxstats/stackgbm/issues
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Imports: pROC, progress, rlang
Suggests: knitr, lightgbm, msaenet, rmarkdown, xgboost
NeedsCompilation: no
Packaged: 2024-04-29 04:16:05 UTC; nanx
Author: Nan Xiao [aut, cre, cph]
Maintainer: Nan Xiao <me@nanx.me>
Repository: CRAN
Date/Publication: 2024-04-30 11:20:02 UTC

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New package ShapDoE with initial version 1.0.0
Package: ShapDoE
Title: Approximation of the Shapley Values Based on Experimental Designs
Version: 1.0.0
Maintainer: Liuqing Yang <yliuqing0714@163.com>
Description: Estimating the Shapley values using the algorithm in the paper Liuqing Yang, Yongdao Zhou, Haoda Fu, Min-Qian Liu and Wei Zheng (2024) <doi:10.1080/01621459.2023.2257364> "Fast Approximation of the Shapley Values Based on Order-of-Addition Experimental Designs". You provide the data and define the value function, it retures the estimated Shapley values based on sampling methods or experimental designs.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: gtools
NeedsCompilation: no
Packaged: 2024-04-29 12:28:44 UTC; lydia
Author: Liuqing Yang [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-30 11:42:47 UTC

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New package PPbigdata with initial version 1.0.0
Package: PPbigdata
Title: Projection Pursuit for Big Data Based on Data Nuggets
Version: 1.0.0
Date: 2024-4-1
Author: Yajie Duan [aut, cre], Javier Cabrera [aut]
Maintainer: Yajie Duan <yajieritaduan@gmail.com>
Description: Perform 1-dim/2-dim projection pursuit, grand tour and guided tour for big data based on data nuggets. Reference papers: [1] Beavers et al., (2024) <doi:10.1080/10618600.2024.2341896>. [2] Duan, Y., Cabrera, J., & Emir, B. (2023). "A New Projection Pursuit Index for Big Data." <doi:10.48550/arXiv.2312.06465>.
Depends: R (>= 4.0), stats, datanugget(>= 1.2.4), MASS
Imports: dplyr, magrittr, weights, rstiefel, gtools, tourr, mclust, graphics, grDevices
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-29 20:06:43 UTC; yd254
Repository: CRAN
Date/Publication: 2024-04-30 11:42:50 UTC

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New package petersenlab with initial version 1.0.0
Package: petersenlab
Title: A Collection of R Functions by the Petersen Lab
Version: 1.0.0
Maintainer: Isaac T. Petersen <isaac-t-petersen@uiowa.edu>
Depends: R (>= 4.1.0)
Imports: stats, graphics, utils, nlme, Hmisc, digest, dplyr, ggplot2, lavaan, mitools, mix, mvtnorm, psych, stringr, xtable, grDevices, plyr, reshape2, RColorBrewer, viridisLite, tidyselect, scales
Suggests: testthat (>= 3.0.0), waldo, withr
Description: A collection of R functions that are widely used by the Petersen Lab. Included are functions for various purposes, including evaluating the accuracy of judgments and predictions, performing scoring of assessments, generating correlation matrices, conversion of data between various types, data management, psychometric evaluation, extensions related to latent variable modeling, various plotting capabilities, and other miscellaneous useful functions. By making the package available, we hope to make our methods reproducible and replicable by others and to help others perform their data processing and analysis methods more easily and efficiently. The codebase is in <doi:10.5281/zenodo.7602890>. The package is described in Petersen (2024) <doi:10.1201/9781003357421>, <doi:10.5281/zenodo.6466590>.
URL: https://github.com/DevPsyLab/petersenlab, https://devpsylab.github.io/petersenlab/
BugReports: https://github.com/DevPsyLab/petersenlab/issues
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-28 22:13:14 UTC; Isaac
Author: Isaac T. Petersen [aut, cre] , Developmental Psychopathology Lab at the University of Iowa [ctb]
Repository: CRAN
Date/Publication: 2024-04-30 11:10:02 UTC

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New package KMLtoSHAPE with initial version 0.1.0
Package: KMLtoSHAPE
Title: Preserving Attribute Values: Converting KML to Shapefile
Version: 0.1.0
Depends: R(>= 2.10)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Description: The developed function is designed to facilitate the seamless conversion of KML (Keyhole Markup Language) files to Shapefiles while preserving attribute values. It provides a straightforward interface for users to effortlessly import KML data, extract relevant attributes, and export them into the widely compatible Shapefile format. The package ensures accurate representation of spatial data while maintaining the integrity of associated attribute information. For details see, Flores, G. (2021). <DOI:10.1007/978-3-030-63665-4_15>. Whether for spatial analysis, visualization, or data interoperability, it simplifies the conversion process and empowers users to seamlessly work with geospatial datasets.
License: GPL (>= 2.0)
Encoding: UTF-8
Imports: raster,stringr,sf
NeedsCompilation: no
Packaged: 2024-04-29 07:24:40 UTC; Asus
Author: Nirmal Kumar [aut, cph], Nobin Chandra Paul [aut, cre]
Maintainer: Nobin Chandra Paul <nobin.paul@icar.gov.in>
Repository: CRAN
Date/Publication: 2024-04-30 11:20:05 UTC

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New package goat with initial version 1.0
Package: goat
Title: Gene Set Analysis Using the Gene Set Ordinal Association Test
Version: 1.0
Description: Perform gene set enrichment analyses using the Gene set Ordinal Association Test (GOAT) algorithm and visualize your results. Koopmans, F. (2024) <doi:10.1101/2023.12.10.570979>.
URL: https://github.com/ftwkoopmans/goat/
License: Apache License (>= 2)
Depends: R (>= 4.1.0), dplyr (>= 1.0.3)
Imports: tibble (>= 3.0.0), tidyselect (>= 1.2.0), tidyr (>= 1.1.2), data.table (>= 1.14.0), Matrix (>= 1.4-0), readxl (>= 1.4.1), writexl (>= 1.4.1), Rcpp (>= 1.0.9), vctrs (>= 0.3.8), MonoPoly (>= 0.3-10), ggplot2 (>= 3.3.0), pheatmap (>= 1.0.8), treemap (>= 2.4), igraph (>= 1.2.5), ggraph (>= 2.0.0)
Suggests: AnnotationDbi, GO.db, org.Hs.eg.db, fgsea, testthat (>= 3.0.0)
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Language: en-US
NeedsCompilation: yes
Packaged: 2024-04-28 22:29:53 UTC; Frank
Author: Frank Koopmans [aut, cre]
Maintainer: Frank Koopmans <ftwkoopmans@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-30 11:10:07 UTC

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New package BioCro with initial version 3.1.3
Package: BioCro
Version: 3.1.3
Date: 2024-04-22
Title: Modular Crop Growth Simulations
Description: A cross-platform representation of models as sets of equations that facilitates modularity in model building and allows users to harness modern techniques for numerical integration and data visualization. Documentation is provided by several vignettes included in this package; also see Lochocki et al. (2022) <doi:10.1093/insilicoplants/diac003>.
Depends: R (>= 3.6.0)
Imports: stats
Suggests: testthat (>= 3.2.0), knitr, rmarkdown, bookdown, lattice, deSolve
VignetteBuilder: knitr
SystemRequirements: C++11, GNU make
License: MIT + file LICENSE
LazyData: true
ByteCompile: TRUE
URL: https://github.com/biocro/biocro, https://biocro.github.io
NeedsCompilation: yes
Packaged: 2024-04-29 16:32:57 UTC; Justin
Author: Justin M. McGrath [cre, aut] , Edward B. Lochocki [aut] , Scott Rohde [aut] , Deepak Jaiswal [aut] , Megan L. Matthews [aut] , Fernando E. Miguez [aut] , Stephen P. Long [aut] , Dan Wang [ctb], David LeBauer [ctb] , BioCro authors [cph], Boost Organi [...truncated...]
Maintainer: Justin M. McGrath <jmcgrath@illinois.edu>
Repository: CRAN
Date/Publication: 2024-04-30 11:42:54 UTC

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New package scdtb with initial version 0.1.0
Package: scdtb
Title: Single Case Design Tools
Version: 0.1.0
Description: In some situations where researchers would like to demonstrate causal effects, it is hard to obtain a sample size that would allow for a well-powered randomized controlled trial. Single case designs are experimental designs that can be used to demonstrate causal effects with only one participant or with only a few participants. The 'scdtb' package provides a suite of tools for analyzing data from studies that use single case designs. The nap() function can be used to compute the nonoverlap of all pairs as outlined by the What Works Clearinghouse (2022) <https://ies.ed.gov/ncee/wwc/Handbooks>. The package also offers the mixed_model_analysis() and cross_lagged() functions which implement mixed effects models and cross lagged analyses as described in Maric & van der Werff (2020) <doi:10.4324/9780429273872-9>. The randomization_test() function implements randomization tests based on methods presented in Onghena (2020) <doi:10.4324/9780429273872-8>. The scdtb() 'shiny [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/mightymetrika/scdtb
BugReports: https://github.com/mightymetrika/scdtb/issues
Depends: R (>= 2.10)
LazyData: true
Suggests: testthat (>= 3.0.0)
Imports: broom.mixed, DT, ggplot2, mmcards, nlme, shiny, shinythemes
NeedsCompilation: no
Packaged: 2024-04-28 16:11:06 UTC; Administrator
Author: Mackson Ncube [aut, cre], mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-30 08:50:02 UTC

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New package sacRebleu with initial version 0.1.3
Package: sacRebleu
Title: Metrics for Assessing the Quality of Generated Text
Version: 0.1.3
Date: 2024-04-05
Description: Implementation of the BLEU-Score in 'C++' to evaluate the quality of generated text. The BLEU-Score, introduced by Papineni et al. (2002) <doi:10.3115/1073083.1073135>, is a metric for evaluating the quality of generated text. It is based on the n-gram overlap between the generated text and reference texts. Additionally, the package provides some smoothing methods as described in Chen and Cherry (2014) <doi:10.3115/v1/W14-3346>.
License: GPL (>= 2)
SystemRequirements: Rust tool chain w/ cargo, libclang/llvm-config
Depends: R (>= 4.2.0)
Imports: checkmate, Rcpp (>= 1.0.12), tok
LinkingTo: Rcpp
URL: https://github.com/LazerLambda/sacRebleu
BugReports: https://github.com/LazerLambda/sacRebleu/issues
Suggests: knitr, rmarkdown, hfhub, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2024-04-28 15:33:40 UTC; philko
Author: Philipp Koch [aut, cre]
Maintainer: Philipp Koch <PhillKoch@protonmail.com>
Repository: CRAN
Date/Publication: 2024-04-30 08:40:03 UTC

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New package ratioOfQsprays with initial version 1.0.0
Package: ratioOfQsprays
Title: Fractions of Multivariate Polynomials with Rational Coefficients
Version: 1.0.0
Description: Based on the 'qspray' package, this package introduces the new type 'ratioOfQsprays'. An object of type 'qspray' represents a multivariate polynomial with rational coefficients while an object of type 'ratioOfQsprays', defined by two 'qspray' objects, represents a fraction of two multivariate polynomials with rational coefficients. Arithmetic operations for these objects are available, and they always return irreducible fractions. Other features include: differentiation, evaluation, conversion to a function, and fine control of the way to print a 'ratioOfQsprays' object. The 'C++' library 'CGAL' is used to make the fractions irreducible.
License: GPL-3
URL: https://github.com/stla/ratioOfQsprays
BugReports: https://github.com/stla/ratioOfQsprays/issues
Depends: qspray (>= 3.0.0)
Imports: gmp, methods, Rcpp, Ryacas, utils
Suggests: testthat (>= 3.0.0)
LinkingTo: BH, qspray, Rcpp, RcppArmadillo, RcppCGAL
Encoding: UTF-8
SystemRequirements: C++17, gmp, mpfr
NeedsCompilation: yes
Packaged: 2024-04-28 18:53:36 UTC; SDL96354
Author: Stephane Laurent [aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2024-04-30 09:00:02 UTC

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New package peacots with initial version 1.3.2
Package: peacots
Title: Periodogram Peaks in Correlated Time Series
Version: 1.3.2
Date: 2024-04-28
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series. Citation: Louca, Stilianos and Doebeli, Michael (2015) <doi:10.1890/14-0126.1>.
License: GPL-3
Depends: stats,graphics
NeedsCompilation: no
Packaged: 2024-04-28 15:25:13 UTC; stilianoslouca
Author: Stilianos Louca [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-30 08:40:06 UTC

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New package karlen with initial version 0.0.2
Package: karlen
Title: Real-Time PCR Data Sets by Karlen et al. (2007)
Version: 0.0.2
Description: Real-time quantitative polymerase chain reaction (qPCR) data sets by Karlen et al. (2007) <doi:10.1186/1471-2105-8-131>. Provides one single tabular tidy data set in long format, encompassing 32 dilution series, for seven PCR targets and four biological samples. The targeted amplicons are within the murine genes: Cav1, Ccn2, Eln, Fn1, Rpl27, Hspg2, and Serpine1, respectively. Dilution series: scheme 1 (Cav1, Eln, Hspg2, Serpine1): 1-fold, 10-fold, 50-fold, and 100-fold; scheme 2 (Ccn2, Rpl27, Fn1): 1-fold, 10-fold, 50-fold, 100-fold and 1000-fold. For each concentration there are five replicates, except for the 1000-fold concentration, where only two replicates were performed. Each amplification curve is 40 cycles long. Original raw data file is Additional file 2 from "Statistical significance of quantitative PCR" by Y. Karlen, A. McNair, S. Perseguers, C. Mazza, and N. Mermod (2007) <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-8-131/MediaObjects/12859_20 [...truncated...]
License: CC BY 4.0
Encoding: UTF-8
Imports: tibble
Depends: R (>= 2.10)
LazyData: true
URL: https://rmagno.eu/karlen/, https://github.com/ramiromagno/karlen
BugReports: https://github.com/ramiromagno/karlen/issues
NeedsCompilation: no
Packaged: 2024-04-28 14:28:17 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-30 08:30:07 UTC

More information about karlen at CRAN
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New package freewall with initial version 1.0.0
Package: freewall
Title: A Wrapper of the JavaScript Library 'Freewall'
Version: 1.0.0
Description: Creates dynamic grid layouts of images that can be included in 'Shiny' applications and R markdown documents.
License: GPL-3
URL: https://github.com/stla/freewall
BugReports: https://github.com/stla/freewall/issues
Imports: htmlwidgets, htmltools, jquerylib
Suggests: shiny
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-28 15:33:08 UTC; SDL96354
Author: Stephane Laurent [aut, cre], Minh Nguyen [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2024-04-30 09:00:05 UTC

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New package dendroNetwork with initial version 0.5.4
Package: dendroNetwork
Title: Create Networks of Dendrochronological Series using Pairwise Similarity
Version: 0.5.4
Maintainer: Ronald Visser <r.m.visser@saxion.nl>
Depends: R (>= 4.1.0)
Imports: dplR (>= 1.7.2), igraph, stringr, reshape2, RCy3, dplyr, RColorBrewer, tidyr, foreach, lifecycle, doParallel, stats, grDevices
Description: Creating dendrochronological networks based on the similarity between tree-ring series or chronologies. The package includes various functions to compare tree-ring curves building upon the 'dplR' package. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance of wood as described in Visser (2021) <DOI:10.5334/jcaa.79> or wood-use within a structure/context/site as described in Visser and Vorst (2022) <DOI:10.1163/27723194-bja10014>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DiagrammeR
VignetteBuilder: knitr
URL: https://github.com/ropensci/dendroNetwork, https://ropensci.github.io/dendroNetwork/
BugReports: https://github.com/ropensci/dendroNetwork/issues
NeedsCompilation: no
Packaged: 2024-04-28 14:42:37 UTC; rvi04
Author: Ronald Visser [aut, cre] , Angelino Salentino [ctb] , Andy Bunn [ctb] , Kaija Gahm [rev] , Zachary Gajewski [rev]
Repository: CRAN
Date/Publication: 2024-04-30 08:40:10 UTC

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New package comorbidPGS with initial version 0.3.4
Package: comorbidPGS
Title: Assessing Predisposition Between Phenotypes using Polygenic Scores
Version: 0.3.4
Description: Using polygenic scores (PGS, or PRS/GRS for binary outcomes), this package allows to investigate shared predisposition between different conditions, and do fast association analysis, export plots and views of the PGS distribution using 'ggplot2' object.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: ggplot2, stats, utils, MASS, nnet, parallel
LazyData: true
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-28 20:47:22 UTC; vpascat
Author: Vincent Pascat [aut, cre]
Maintainer: Vincent Pascat <vincent.pascat@univ-lille.fr>
Repository: CRAN
Date/Publication: 2024-04-30 09:00:08 UTC

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Sun, 28 Apr 2024

New package cwbtools with initial version 0.4.2
Package: cwbtools
Title: Tools to Create, Modify and Manage 'CWB' Corpora
Version: 0.4.2
Date: 2024-04-28
Description: The 'Corpus Workbench' ('CWB', <https://cwb.sourceforge.io/>) offers a classic and mature approach for working with large, linguistically and structurally annotated corpora. The 'CWB' is memory efficient and its design makes running queries fast, see Evert (2011) <https://eprints.lancs.ac.uk/id/eprint/62721>. The 'cwbtools' package offers pure 'R' tools to create indexed corpus files as well as high-level wrappers for the original 'C' implementation of 'CWB' as exposed by the 'RcppCWB' package (<https://CRAN.R-project.org/package=RcppCWB>). Additional functionality to add and modify annotations of corpora from within 'R' makes working with 'CWB' indexed corpora much more flexible and convenient. The 'cwbtools' package in combination with the 'R' packages 'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR' (<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure to support the combination of quantitative and qu [...truncated...]
Imports: data.table, R6, xml2, stringi, curl, RcppCWB (>= 0.6.3), pbapply, methods, tools, cli, jsonlite, httr, rstudioapi, zen4R (>= 0.9), lifecycle, fs
Suggests: tm (>= 0.7.3), knitr, markdown, tokenizers (>= 0.2.1), tidytext, SnowballC, janeaustenr, testthat, rmarkdown, aws.s3, quanteda, dplyr
VignetteBuilder: knitr
License: GPL-3
Language: en-US
Encoding: UTF-8
URL: https://github.com/PolMine/cwbtools
BugReports: https://github.com/PolMine/cwbtools/issues
NeedsCompilation: no
Packaged: 2024-04-28 21:23:42 UTC; andreasblatte
Author: Andreas Blaette [aut, cre], Christoph Leonhardt [aut]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Repository: CRAN
Date/Publication: 2024-04-28 22:20:06 UTC

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New package sisti with initial version 0.0.1
Package: sisti
Title: Real-Time PCR Data Sets by Sisti et al. (2010)
Version: 0.0.1
Description: This data package contains four datasets of quantitative PCR (qPCR) amplification curves that were used as supplementary data in the research article by Sisti et al. (2010), <doi:10.1186/1471-2105-11-186>. The primary dataset comprises a ten-fold dilution series spanning copy numbers from 3.14 × 10^7 to 3.14 × 10^2, with twelve replicates per concentration. These samples are based on a pGEM-T Promega plasmid containing a 104 bp fragment of the mitochondrial gene NADH dehydrogenase 1 (MT-ND1), amplified using the ND1/ND2 primer pair. The remaining three datasets contain qPCR results in the presence of specific PCR inhibitors: tannic acid, immunoglobulin G (IgG), and quercetin, respectively, to assess their effects on the amplification process. These datasets are useful for researchers interested in PCR kinetics. The original raw data file is available as Additional File 1: <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-11-186/MediaObjects/12859_2009_3643_MOE [...truncated...]
License: CC BY 4.0
Encoding: UTF-8
Imports: tibble
Depends: R (>= 2.10)
LazyData: true
URL: https://rmagno.eu/sisti/, https://github.com/ramiromagno/sisti
BugReports: https://github.com/ramiromagno/sisti/issues
NeedsCompilation: no
Packaged: 2024-04-28 02:24:37 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-28 11:00:02 UTC

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New package cryptorng with initial version 0.1.2
Package: cryptorng
Title: Access System Cryptographic Pseudorandom Number Generators
Version: 0.1.2
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Description: Generate random bytes from the Cryptographically Secure Pseudorandom Number Generator (CSPRNG) provided by the underlying operating system. These system CSPRNGs are seeded internally by the OS with entropy it gathers and use random number generation algorithms which are considered cryptographically secure. The following system functions are used: arc4random_buf() on macOS and BSD; BCryptgenRandom() on Windows; Sys_getrandom() on Linux.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
URL: https://github.com/coolbutuseless/cryptorng
BugReports: https://github.com/coolbutuseless/cryptorng/issues
NeedsCompilation: yes
Packaged: 2024-04-27 20:58:24 UTC; mike
Author: Mike Cheng [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-28 10:50:03 UTC

More information about cryptorng at CRAN
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New package accessr with initial version 1.0.1
Package: accessr
Title: Command Line Tools to Produce Accessible Documents using 'R Markdown'
Version: 1.0.1
Date: 2024-04-28
Description: Provides functions to produce accessible 'HTML' slides, 'HTML', 'Word' and 'PDF' documents from input 'R markdown' files. Accessible 'PDF' files are produced only on a 'Windows' Operating System. One aspect of accessibility is providing a headings structure that is recognised by a screen reader, providing a navigational tool for a blind or partially-sighted person. A key aim is to produce documents of different formats easily from each of a collection of 'R markdown' source files. Input 'R markdown' files are rendered using the render() function from the 'rmarkdown' package <https://cran.r-project.org/package=rmarkdown>. A 'zip' file containing multiple output files can be produced from one function call. A user-supplied template 'Word' document can be used to determine the formatting of an output 'Word' document. Accessible 'PDF' files are produced from 'Word' documents using 'OfficeToPDF' <https://github.com/cognidox/OfficeToPDF>. A convenience function, install_otp() is [...truncated...]
Depends: R (>= 3.3.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: rmarkdown
Suggests: dplyr, knitr, flextable, htmltools, huxtable, jpeg, officer, officedown, pagedown, png, tools, utils, xfun, zip, testthat (>= 3.0.0)
SystemRequirements: OfficeToPDF - https://github.com/cognidox/OfficeToPDF, pandoc (>= 1.14) - https://pandoc.org
URL: https://paulnorthrop.github.io/accessr/, https://github.com/paulnorthrop/accessr
BugReports: https://github.com/paulnorthrop/accessr/issues
NeedsCompilation: no
Packaged: 2024-04-28 08:22:47 UTC; Paul
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2024-04-28 11:00:06 UTC

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New package nFunNN with initial version 1.0
Package: nFunNN
Title: Nonlinear Functional Principal Component Analysis using Neural Networks
Version: 1.0
Description: Implementation for 'nFunNN' method, which is a novel nonlinear functional principal component analysis method using neural networks. The crucial function of this package is nFunNNmodel().
License: GPL (>= 3)
Encoding: UTF-8
Imports: fda, splines, stats, torch
NeedsCompilation: no
Packaged: 2024-04-26 01:50:25 UTC; 11013
Author: Rou Zhong [aut, cre], Jingxiao Zhang [aut]
Maintainer: Rou Zhong <zhong_rou@163.com>
Repository: CRAN
Date/Publication: 2024-04-28 09:40:02 UTC

More information about nFunNN at CRAN
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New package FnR with initial version 1.0.0
Package: FnR
Title: Inbreeding and Numerator Relationship Coefficients
Version: 1.0.0
Description: Compute inbreeding coefficients using the method of Meuwissen and Luo (1992) <doi:10.1186/1297-9686-24-4-305>, and numerator relationship coefficients between individuals using the method of Van Vleck (2007) <https://pubmed.ncbi.nlm.nih.gov/18050089/>.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/nilforooshan/FnR
BugReports: https://github.com/nilforooshan/FnR/issues
NeedsCompilation: no
Packaged: 2024-04-26 08:23:18 UTC; monil0
Author: Mohammad Ali Nilforooshan [aut, cre]
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-28 09:40:05 UTC

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New package braids with initial version 1.0.0
Package: braids
Title: The Braid Groups
Version: 1.0.0
Description: Deals with the braid groups. Includes creation of some specific braids, group operations, free reduction, and Bronfman polynomials. Braid theory has applications in fluid mechanics and quantum physics. The code is adapted from the 'Haskell' library 'combinat', and is based on Birman and Brendle (2005) <doi:10.48550/arXiv.math/0409205>.
License: GPL-3
URL: https://github.com/stla/braids
BugReports: https://github.com/stla/braids/issues
Imports: maybe
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-26 16:57:22 UTC; SDL96354
Author: Stephane Laurent [aut, cre], Balazs Komuves [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2024-04-28 10:00:03 UTC

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Sat, 27 Apr 2024

New package vvdoctor with initial version 0.0.1
Package: vvdoctor
Title: Statistical Test App with R 'shiny'
Version: 0.0.1
Description: Provides a user-friendly R 'shiny' app for performing various statistical tests on datasets. It allows users to upload data in numerous formats and perform statistical analyses. The app dynamically adapts its options based on the selected columns and supports both single and multiple column comparisons. The app's user interface is designed to streamline the process of selecting datasets, columns, and test options, making it easy for users to explore and interpret their data. The underlying functions for statistical tests are well-organized and can be used independently within other R scripts.
URL: https://github.com/vusaverse/vvdoctor, https://vusaverse.github.io/vvdoctor/
License: MIT + file LICENSE
Encoding: UTF-8
Imports: datamods, DescTools, DT, exact2x2, irr, magrittr, rintrojs, rstatix, shiny, shinyjs, shinyWidgets
NeedsCompilation: no
Packaged: 2024-04-25 18:54:27 UTC; tin900
Author: Tomer Iwan [aut, cre], Corneel Den Hartogh [ctb] , Jesus Blanco [ctb], VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Repository: CRAN
Date/Publication: 2024-04-27 18:10:02 UTC

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New package medparser with initial version 0.1.0
Package: medparser
Title: MedPC Text Parser
Version: 0.1.0
Author: Olivia Ortelli, Tony Colarusso
Maintainer: Olivia Ortelli <oortelli@wakehealth.edu>
Description: Parses information from text files with specific utility aimed at pulling information from Med Associate's (MPC) files. These functions allow for further analysis of MPC files.
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-25 20:51:14 UTC; oorte
Repository: CRAN
Date/Publication: 2024-04-27 18:20:03 UTC

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New package healthdb with initial version 0.1.0
Package: healthdb
Title: Working with Healthcare Database
Version: 0.1.0
Description: A system for identifying diseases or events from healthcare databases and preparing data for epidemiological studies. It includes capabilities not supported by 'SQL', such as matching strings by 'stringr' style regular expressions, and can compute comorbidity scores (Quan et al. (2005) <doi:10.1097/01.mlr.0000182534.19832.83>) directly on a database server. The implementation is based on 'dbplyr' with full 'tidyverse' compatibility.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: data.table, dbplyr, dplyr (>= 1.1.0), glue, lubridate, magrittr, purrr, rlang, stringr, tidyr
URL: https://github.com/KevinHzq/healthdb, https://kevinhzq.github.io/healthdb/
BugReports: https://github.com/KevinHzq/healthdb/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), withr, RSQLite
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-25 18:50:49 UTC; kevin.hu
Author: Kevin Hu [aut, cre, cph]
Maintainer: Kevin Hu <kevin.hu@bccdc.ca>
Repository: CRAN
Date/Publication: 2024-04-27 18:10:08 UTC

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New package DBTC with initial version 0.1.0
Package: DBTC
Title: Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis
Version: 0.1.0
Maintainer: Robert G Young <rgyoung6@gmail.com>
Description: First using 'dada2' R tools to analyse metabarcode data, the 'DBTC' package then uses the BLAST algorithm to search unknown sequences against local databases, and then takes reduced matched results and provides best taxonomic assignments.
License: GPL-2 | GPL-3
Encoding: UTF-8
URL: <https://github.com/rgyoung6/DBTC>
Depends:
Imports: dada2, ggplot2, parallel, pbapply, plyr, ShortRead, stats, taxonomizr, utils
Language: en-GB
NeedsCompilation: no
Packaged: 2024-04-25 22:38:18 UTC; robgy
Author: Robert G Young [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-27 18:20:07 UTC

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New package chattr with initial version 0.1.0
Package: chattr
Title: Interact with Large Language Models in 'RStudio'
Version: 0.1.0
Description: Enables user interactivity with large-language models ('LLM') inside the 'RStudio' integrated development environment (IDE). The user can interact with the model using the 'shiny' app included in this package, or directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub' 'Copilot', and 'LlamaGPT'.
URL: https://github.com/mlverse/chattr, https://mlverse.github.io/chattr/
BugReports: https://github.com/mlverse/chattr/issues
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rstudioapi, lifecycle, processx, jsonlite, config, httr2 (>= 1.0.1), purrr, rlang, bslib, shiny, clipr, callr, yaml, glue, cli, fs
Depends: R (>= 2.10)
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0), shinytest2, withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-25 19:01:27 UTC; edgar
Author: Edgar Ruiz [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Repository: CRAN
Date/Publication: 2024-04-27 18:10:12 UTC

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New package BFI with initial version 1.1.4
Package: BFI
Title: Bayesian Federated Inference
Version: 1.1.4
Date/Publication: 2024-04-27 18:20:11 UTC
Author: Hassan Pazira [aut, cre] , Emanuele Massa [aut] , Marianne A. Jonker [aut]
Maintainer: Hassan Pazira <hassan.pazira@radboudumc.nl>
Description: The Bayesian Federated Inference ('BFI') method combines inference results obtained from local data sets in the separate centers. In this version of the package, the 'BFI' methodology is programmed for linear and logistic regression models; see Jonker, Pazira and Coolen (2024) <doi:10.1002/sim.10072>.
License: MIT + file LICENSE
URL: https://hassanpazira.github.io/BFI/
Encoding: UTF-8
Suggests: knitr, rmarkdown, roxygen2, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
LazyData: true
Imports: devtools, stats
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-25 20:14:17 UTC; hassanpazira
Repository: CRAN

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New package bulkQC with initial version 1.1
Package: bulkQC
Title: Quality Control and Outlier Identification in Bulk for Multicenter Trials
Version: 1.1
Date: 2024-04-25
Author: Joseph Rigdon <jrigdon@wakehealth.edu>
Maintainer: Joseph Rigdon <jrigdon@wakehealth.edu>
Description: Multicenter randomized trials involve the collection and analysis of data from numerous study participants across multiple sites. Outliers may be present. To identify outliers, this package examines data at the individual level (univariate and multivariate) and site-level (with and without covariate adjustment). Methods are outlined in further detail in Rigdon et al (to appear).
License: GPL-3
Depends: isotree, stddiff
NeedsCompilation: no
Packaged: 2024-04-25 12:32:20 UTC; jrigdon
Repository: CRAN
Date/Publication: 2024-04-27 17:50:02 UTC

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Thu, 25 Apr 2024

New package MDMA with initial version 1.1.0
Package: MDMA
Title: Mathijs Deen's Miscellaneous Auxiliaries
Date: 2024-04-25
Version: 1.1.0
Maintainer: Mathijs Deen <dev@mathijsdeen.com>
Description: Provides a variety of functions useful for data analysis, selection, manipulation, and graphics.
Depends: R (>= 4.2)
Imports: stats, MASS, graphics, methods, grDevices, car
License: GPL-3
URL: https://github.com/mathijsdeen/MDMA
BugReports: https://github.com/mathijsdeen/MDMA/issues
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-25 10:20:59 UTC; mathijs-r
Author: Mathijs Deen [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-25 16:40:02 UTC

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New package epigrowthfit with initial version 0.15.2
Package: epigrowthfit
Version: 0.15.2
Date: 2024-04-24
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 (>= 4.3.0)
LinkingTo: RcppEigen (>= 0.3.4.0.0), TMB
Imports: Matrix (>= 1.6-2), TMB, grDevices, graphics, methods, nlme, stats, tools, utils
Suggests: emdbook
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-24 20:27:28 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: 2024-04-25 16:20:02 UTC

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New package boggy with initial version 0.0.1
Package: boggy
Title: Real-Time PCR Data Sets by Boggy et al. (2010)
Version: 0.0.1
Description: Real-time quantitative polymerase chain reaction (qPCR) data sets by Boggy et al. (2008) <doi:10.1371/journal.pone.0012355>. This package provides a dilution series for one PCR target: a random sequence that minimizes secondary structure and off-target primer binding. The data set is a six-point, ten-fold dilution series. For each concentration there are two replicates. Each amplification curve is 40 cycles long. Original raw data file: <https://journals.plos.org/plosone/article/file?type=supplementary&id=10.1371/journal.pone.0012355.s004>.
License: CC BY 4.0
Encoding: UTF-8
Imports: tibble
Depends: R (>= 2.10)
LazyData: true
URL: https://rmagno.eu/boggy/, https://github.com/ramiromagno/boggy
BugReports: https://github.com/ramiromagno/boggy/issues
NeedsCompilation: no
Packaged: 2024-04-24 15:41:49 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-25 16:10:02 UTC

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New package SpatGC with initial version 0.1.0
Package: SpatGC
Title: Bayesian Modeling of Spatial Count Data
Version: 0.1.0
Maintainer: Mahsa Nadifar <mahsa.nst@gmail.com>
Description: Provides a collection of functions for preparing data and fitting Bayesian count spatial regression models, with a specific focus on the Gamma-Count (GC) model. The GC model is well-suited for modeling dispersed count data, including under-dispersed or over-dispersed counts, or counts with equivalent dispersion, using Integrated Nested Laplace Approximations (INLA). The package includes functions for generating data from the GC model, as well as spatially correlated versions of the model. See Nadifar, Baghishani, Fallah (2023) <doi:10.1007/s13253-023-00550-5>.
License: GPL (>= 2)
URL: https://github.com/mahsanst/SpatGC
Encoding: UTF-8
Depends: R (>= 4.0)
Additional_repositories: https://inla.r-inla-download.org/R/testing
Imports: mvtnorm, stats, spdep, sf
Suggests: INLA (>= 23.06.15)
NeedsCompilation: no
Packaged: 2024-04-24 19:15:06 UTC; u23027917
Author: Mahsa Nadifar [aut, cre] , Hossein Baghishani [aut]
Repository: CRAN
Date/Publication: 2024-04-25 15:40:05 UTC

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New package quickPWCR with initial version 1.0
Package: quickPWCR
Title: Quickly construct and rating large binary pairwiesd comparisons
Version: 1.0
Date: 2024-04-23
Description: A collection of functions for constructing large pairwised comparisons and rating them using Elo rating system with supporting parallel processing. The method of random sample pairs is based on Reservoir Sampling proposed by JVitter (1985) <doi:10.1145/3147.3165>.
License: GPL-3
Encoding: UTF-8
Language: en_GB
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown
Imports: Rcpp, parallel, pbmcapply, dplyr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-04-24 21:05:09 UTC; yangxiaohao
Author: Xiaohao Yang [aut, cre, cph]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Repository: CRAN
Date/Publication: 2024-04-25 15:50:12 UTC

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New package doublIn with initial version 0.1.0
Package: doublIn
Title: Estimate Incubation or Latency Time using Doubly Interval Censored Observations
Version: 0.1.0
Maintainer: Vera Arntzen <v.h.arntzen@math.leidenuniv.nl>
Description: Visualize contact tracing data using a 'shiny' app and estimate the incubation or latency time of an infectious disease respecting the following characteristics in the analysis; (i) doubly interval censoring with (partly) overlapping or distinct windows; (ii) an infection risk corresponding to exponential growth; (iii) right truncation allowing for individual truncation times; (iv) different choices concerning the family of the distribution. For our earlier work, we refer to Arntzen et al. (2023) <doi:10.1002/sim.9726>. A paper describing our approach in detail will follow.
License: GPL (>= 3)
Encoding: UTF-8
Imports: coda, flexsurv, ggplot2, rjags, magrittr, tidyverse, DT, epicontacts, lubridate, mStats, plotly, shiny, shinyWidgets, shinydashboard, shinythemes, visNetwork, xtable, dplyr, methods
Suggests: testthat (>= 3.0.0), shinytest
NeedsCompilation: no
Packaged: 2024-04-24 15:29:29 UTC; veraarntzen
Author: Vera Arntzen [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-04-25 16:00:02 UTC

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New package disastr.api with initial version 1.0.6
Package: disastr.api
Title: Wrapper for the UN OCHA ReliefWeb Disaster Events API
Version: 1.0.6
Date: 2024-04-23
Author: Christoph Dworschak [aut, cre]
Maintainer: Christoph Dworschak <dworschak@posteo.de>
Description: Access and manage the application programming interface (API) of the United Nations Office for the Coordination of Humanitarian Affairs' (OCHA) ReliefWeb disaster events at <https://reliefweb.int/disasters>. The package requires a minimal number of dependencies. It offers functionality to retrieve a user-defined sample of disaster events from ReliefWeb, providing an easy alternative to scraping the ReliefWeb website. It enables a seamless integration of regular data updates into the research work flow.
License: GPL-3
Encoding: UTF-8
Language: en-US
Imports: httr, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2024-04-23 15:13:18 UTC; root
Repository: CRAN
Date/Publication: 2024-04-25 15:20:02 UTC

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New package asm with initial version 0.1.0
Package: asm
Title: Optimal Convex M-Estimation for Linear Regression via Antitonic Score Matching
Version: 0.1.0
License: GPL (>= 3)
Description: Performs linear regression with respect to a data-driven convex loss function that is chosen to minimize the asymptotic covariance of the resulting M-estimator. The convex loss function is estimated in 5 steps: (1) form an initial OLS (ordinary least squares) or LAD (least absolute deviation) estimate of the regression coefficients; (2) use the resulting residuals to obtain a kernel estimator of the error density; (3) estimate the score function of the errors by differentiating the logarithm of the kernel density estimate; (4) compute the L2 projection of the estimated score function onto the set of decreasing functions; (5) take a negative antiderivative of the projected score function estimate. Newton's method (with Hessian modification) is then used to minimize the convex empirical risk function. Further details of the method are given in Feng et al. (2024) <doi:10.48550/arXiv.2403.16688>.
Encoding: UTF-8
Depends: R (>= 3.1)
Imports: fdrtool, pracma, Iso, MASS, quantreg
NeedsCompilation: no
Packaged: 2024-04-24 20:10:53 UTC; minx
Author: Yu-Chun Kao [aut], Min Xu [aut, cre], Oliver Feng [aut]
Maintainer: Min Xu <min.cut@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-25 15:40:02 UTC

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New package adepro with initial version 4.1.0
Package: adepro
Title: A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles
Version: 4.1.0
Author: Nicole Rethemeier, Christoph Tasto, Steffen Jeske
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Description: Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Depends: R (>= 3.5.0), shinyBS, seriation (>= 1.2.9)
License: GPL-3
URL: https://github.com/Bayer-Group/BIC-AdEPro
Encoding: UTF-8
Imports: graphics, MASS, V8, forcats, here, utils, shinyjs, shiny, audio, shape, Cairo, dplyr, readr, rlang, tidyr, haven, stats, shinyWidgets
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-25 07:05:16 UTC; SGFPJ
Repository: CRAN
Date/Publication: 2024-04-25 14:50:02 UTC

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Wed, 24 Apr 2024

New package tsgarch with initial version 1.0.0
Package: tsgarch
Title: Univariate GARCH Models
Version: 1.0.0
Maintainer: Alexios Galanos <alexios@4dscape.com>
Depends: R (>= 3.5.0), methods, tsmethods
LinkingTo: Rcpp (>= 0.10.6), RcppArmadillo, TMB(>= 1.7.20), RcppEigen
Imports: TMB (>= 1.7.20), Rcpp, nloptr, Rdpack, numDeriv, xts, zoo, future.apply, future, progressr, flextable, stats, utils, data.table, tsdistributions, lubridate, sandwich
Description: Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
License: GPL-2
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/tsmodels/tsgarch/issues
ByteCompile: true
URL: https://github.com/tsmodels/tsgarch
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-23 14:22:30 UTC; alexios
Author: Alexios Galanos [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-24 14:30:02 UTC

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New package sqltargets with initial version 0.0.1
Package: sqltargets
Title: Targets Extension for 'SQL' Queries
Version: 0.0.1
Maintainer: David Ranzolin <daranzolin@gmail.com>
Description: Provides an extension for 'SQL' queries as separate file within targets pipelines. The shorthand creates two targets, the query file and the query result.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, DBI, fs, glue, purrr, readr, rlang, RSQLite, stringr, tarchetypes, targets, withr
URL: https://github.com/daranzolin/sqltargets
BugReports: https://github.com/daranzolin/sqltargets/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-23 20:18:05 UTC; dranzolin
Author: David Ranzolin [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-24 14:50:02 UTC

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New package snvecR with initial version 3.9.3
Package: snvecR
Title: Calculate Earth’s Obliquity and Precession in the Past
Version: 3.9.3
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: astrochron, ggplot2, tidyr, testthat, roxygen2, knitr, withr, curl, rmarkdown
Imports: deSolve, cli (>= 3.4.0), stats, dplyr, tibble, purrr, readr, tidyselect, rlang (>= 0.4.11), glue, tools, backports (>= 1.1.6)
Depends: R (>= 3.6.0)
VignetteBuilder: knitr
URL: https://japhir.github.io/snvecR/, https://github.com/japhir/snvecR
BugReports: https://github.com/japhir/snvecR/issues
NeedsCompilation: yes
Packaged: 2024-04-23 09:45:10 UTC; japhir
Author: Ilja Kocken [aut, cre, trl, cph] , Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Repository: CRAN
Date/Publication: 2024-04-24 14:10:02 UTC

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New package SIAtools with initial version 0.1.0
Package: SIAtools
Title: 'ShinyItemAnalysis' Modules Development Toolkit
Version: 0.1.0
Description: A comprehensive suite of functions designed for constructing and managing 'ShinyItemAnalysis' modules, supplemented with detailed guides, ready-to-use templates, linters, and tests. This package allows developers to seamlessly create and integrate one or more modules into their existing packages or to start a new module project from scratch.
License: GPL (>= 3)
URL: https://applstat.github.io/SIAtools/
Depends: R (>= 3.6.0)
Imports: cli, desc, fs, magrittr, purrr, rlang, shiny, usethis, yaml
Suggests: glue, knitr, lintr, pkgload, rmarkdown, roxygen2, rstudioapi, spelling, testthat (>= 3.0.0), tibble, tidyr, withr, xml2
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-23 15:49:36 UTC; netik
Author: Jan Netik [cre, aut] , Patricia Martinkova [aut]
Maintainer: Jan Netik <netik@cs.cas.cz>
Repository: CRAN
Date/Publication: 2024-04-24 14:40:02 UTC

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New package plotcli with initial version 0.1.0
Package: plotcli
Title: Command Line Interface Plotting
Version: 0.1.0
Date: 2024-04-01
Description: The 'plotcli' package provides terminal-based plotting in R. It supports colored scatter plots, line plots, bar plots, and box plots. The package allows users to customize plot appearance, add titles, labels, ticks, and legends, and output the plot as a text-based visualization.
License: LGPL-3
URL: https://github.com/cheuerde/plotcli
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R6, ggplot2
Imports: utils, crayon, knitr, rmarkdown, stringr, rlang
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-04-23 08:34:53 UTC; cheuer
Author: Claas Heuer [aut, cre]
Maintainer: Claas Heuer <claasheuer@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-24 14:10:07 UTC

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New package mlr3summary with initial version 0.1.0
Package: mlr3summary
Title: Model and Learner Summaries for 'mlr3'
Version: 0.1.0
Description: Concise and interpretable summaries for machine learning models and learners of the 'mlr3' ecosystem. The package takes inspiration from the summary function for (generalized) linear models but extends it to non-parametric machine learning models, based on generalization performance, model complexity, feature importances and effects, and fairness metrics.
License: LGPL-3
Depends: R (>= 3.5.0)
Imports: backports, checkmate (>= 2.0.0), data.table, mlr3 (>= 0.12.0), mlr3misc, cli, future.apply (>= 1.5.0),
Suggests: testthat (>= 3.1.0), iml, mlr3pipelines, mlr3fairness, mlr3learners, fastshap, ranger, rpart
Language: en-US
NeedsCompilation: no
Encoding: UTF-8
LazyData: true
Packaged: 2024-04-23 13:05:15 UTC; susanne
Author: Susanne Dandl [aut, cre] , Marc Becker [aut] , Bernd Bischl [aut] , Giuseppe Casalicchio [aut] , Ludwig Bothmann [aut]
Maintainer: Susanne Dandl <dandls.datascience@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-24 14:20:02 UTC

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New package CalcThemAll.PRM with initial version 1.1.1
Package: CalcThemAll.PRM
Title: Calculate Pesticide Risk Metric (PRM) Values from Multiple Pesticides...Calc Them All
Version: 1.1.1
Description: Contains functions which can be used to calculate Pesticide Risk Metric values in aquatic environments from concentrations of multiple pesticides with known species sensitive distributions (SSDs). Pesticides provided by this package have all be validated however if the user has their own pesticides with SSD values they can append them to the pesticide_info table to include them in estimates.
Encoding: UTF-8
License: GPL (>= 3)
Imports: dplyr, lubridate, magrittr, MASS, stats, VGAM, plotly, zoo, DT
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-23 13:44:40 UTC; Alexander
Author: Alexander Bezzina [aut, cre, cph], Jennifer Strauss [aut], Catherine Neelamraju [aut], Hayley Kaminski [aut]
Maintainer: Alexander Bezzina <alex.h.bezzina@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-24 14:30:05 UTC

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New package slap with initial version 2024.4.1
Package: slap
Title: Simplified Error Handling
Version: 2024.4.1
Description: Alternative to using withCallingHandlers() in the simple case of catch and rethrow. The `%!%` operator evaluates the expression on its left hand side, and if an error occurs, the right hand side is used to construct a new error that embeds the original error.
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Imports: cli, rlang
URL: https://github.com/tadascience/slap, https://slap.tada.science
BugReports: https://github.com/tadascience/slap/issues
NeedsCompilation: no
Packaged: 2024-04-23 07:36:18 UTC; romainfrancois
Author: Romain Francois [aut, cre], tada.science [cph, fnd]
Maintainer: Romain Francois <romain@tada.science>
Repository: CRAN
Date/Publication: 2024-04-24 14:00:02 UTC

More information about slap at CRAN
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New package prediction with initial version 0.3.17
Package: prediction
Title: Tidy, Type-Safe 'prediction()' Methods
Description: A one-function package containing 'prediction()', a type-safe alternative to 'predict()' that always returns a data frame. The 'summary()' method provides a data frame with average predictions, possibly over counterfactual versions of the data (a la the 'margins' command in 'Stata'). Marginal effect estimation is provided by the related package, 'margins' <https://cran.r-project.org/package=margins>. The package currently supports common model types (e.g., "lm", "glm") from the 'stats' package, as well as numerous other model classes from other add-on packages. See the README or main package documentation page for a complete listing.
License: MIT + file LICENSE
Version: 0.3.17
Date: 2024-04-23
URL: https://github.com/leeper/prediction
BugReports: https://github.com/leeper/prediction/issues
Depends: R (>= 3.5.0)
Imports: utils, stats, data.table
Suggests: datasets, methods, testthat
Enhances: AER, aod, betareg, biglm, brglm, caret, crch, e1071, earth, ff, gam (>= 1.15), gee, glmnet, glmx, kernlab, lme4, MASS, mclogit, mda, mlogit, MNP, nlme, nnet, ordinal, plm, pscl, quantreg, rpart, sampleSelection, speedglm, survey (>= 3.31-5), survival, truncreg, VGAM
ByteCompile: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-24 01:35:49 UTC; centa
Author: Thomas J. Leeper [aut, cre] , Carl Ganz [ctb], Vincent Arel-Bundock [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-24 07:40:10 UTC

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Tue, 23 Apr 2024

New package textrar with initial version 0.8.0
Package: textrar
Title: Interface to 'TexTra' from R
Version: 0.8.0
Description: A wrapper for the 'TexTra' API <https://mt-auto-minhon-mlt.ucri.jgn-x.jp/>, a web service for translating texts between different languages. 'TexTra' API account is required to use the service.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/matutosi/textrar
Imports: jsonlite, httr
Suggests: knitr, rmarkdown, spelling
Language: en-US
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-04-23 05:25:07 UTC; matutosi
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-23 11:50:03 UTC

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New package pargasite with initial version 2.1.0
Package: pargasite
Title: Pollution-Associated Risk Geospatial Analysis Site
Version: 2.1.0
Description: Offers tools to estimate and visualize levels of major pollutants (CO, NO2, SO2, Ozone, PM2.5 and PM10) across the conterminous United States for user-defined time ranges. Provides functions to retrieve pollutant data from the U.S. Environmental Protection Agency’s 'Air Quality System' (AQS) API service <https://aqs.epa.gov/aqsweb/documents/data_api.html> for interactive visualization through a 'shiny' application, allowing users to explore pollutant levels for a given location over time relative to the National Ambient Air Quality Standards (NAAQS).
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Imports: cli, gstat, leaflet, leafsync, methods, raqs, rlang, sf (>= 1.0-15), shiny, shinycssloaders, stars (>= 0.6-5), stats, utils
Depends: R (>= 4.1.0)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-22 21:27:39 UTC; jaehyun
Author: Jaehyun Joo [aut, cre], Rebecca Greenblatt [aut], Avantika Diwadkar [aut], Nisha Narayanan [aut], Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo@outlook.com>
Repository: CRAN
Date/Publication: 2024-04-23 11:20:02 UTC

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New package Eunomia with initial version 2.0.0
Package: Eunomia
Title: Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets
Version: 2.0.0
Date: 2024-04-22
Maintainer: Frank DeFalco <fdefalco@ohdsi.org>
Description: Facilitates access to sample datasets from the 'EunomiaDatasets' repository (<https://github.com/ohdsi/EunomiaDatasets>).
License: Apache License 2.0
URL: https://github.com/OHDSI/Eunomia
BugReports: https://github.com/OHDSI/Eunomia/issues
Imports: readr, rlang, RSQLite, DBI, arrow, CommonDataModel
Suggests: testthat, withr, duckdb, DatabaseConnector
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-22 21:30:32 UTC; fjd
Author: Frank DeFalco [aut, cre], Martijn Schuemie [aut], Anthony Sena [aut], Natthawut Adulyanukosol [aut], Star Liu [aut], Adam Black [aut], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2024-04-23 11:30:05 UTC

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New package BayesSurvive with initial version 0.0.1
Package: BayesSurvive
Title: Bayesian Survival Models for High-Dimensional Data
Version: 0.0.1
Date: 2024-04-22
Description: An implementation of Bayesian survival models with graph-structured selection priors for sparse identification of omics features predictive of survival (Madjar et al., 2021 <doi:10.1186/s12859-021-04483-z>) and its extension to use a fixed graph via a Markov Random Field (MRF) prior for capturing known structure of omics features, e.g. disease-specific pathways from the Kyoto Encyclopedia of Genes and Genomes database.
URL: https://github.com/ocbe-uio/BayesSurvive
BugReports: https://github.com/ocbe-uio/BayesSurvive/issues
License: GPL-3
Depends: R (>= 4.0)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo (>= 0.9.000)
Imports: Rcpp, ggplot2, GGally, mvtnorm, survival, riskRegression, utils, stats
Suggests: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-22 20:20:09 UTC; zhiz
Author: Zhi Zhao [aut, cre], Katrin Madjar [aut], Tobias Oestmo Hermansen [aut], Manuela Zucknick [ctb], Joerg Rahnenfuehrer [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Repository: CRAN
Date/Publication: 2024-04-23 11:20:06 UTC

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New package bayesMeanScale with initial version 0.1.0
Package: bayesMeanScale
Title: Bayesian Post-Estimation on the Mean Scale
Version: 0.1.0
URL: https://github.com/dalenbe2/bayesMeanScale
BugReports: https://github.com/dalenbe2/bayesMeanScale/issues
Description: Computes Bayesian posterior distributions of predictions, marginal effects, and differences of marginal effects for various generalized linear models. Importantly, the posteriors are on the mean (response) scale, allowing for more natural interpretation than summaries on the link scale. Also, predictions and marginal effects of the count probabilities for Poisson and negative binomial models can be computed.
License: GPL (>= 3)
Encoding: UTF-8
Imports: bayestestR, data.table, magrittr
Depends: R (>= 3.5.0)
Suggests: flextable, knitr, rmarkdown, rstanarm, tibble, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-23 00:00:35 UTC; daviddalenberg
Author: David M. Dalenberg [aut, cre]
Maintainer: David M. Dalenberg <dalenbe2@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-23 11:30:02 UTC

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New package relMix with initial version 1.4
Package: relMix
Title: Relationship Inference for DNA Mixtures
Version: 1.4
Date: 2024-04-12
Description: Analysis of DNA mixtures involving relatives by computation of likelihood ratios that account for dropout and drop-in, mutations, silent alleles and population substructure. This is useful in kinship cases, like non-invasive prenatal paternity testing, where deductions about individuals' relationships rely on DNA mixtures, and in criminal cases where the contributors to a mixed DNA stain may be related. Relationships are represented by pedigrees and can include kinship between more than two individuals. The main function is relMix() and its graphical user interface relMixGUI(). The implementation and method is described in Dorum et al. (2017) <doi:doi.org/10.1007/s00414-016-1526-x>, Hernandis et al. (2019) <doi:doi.org/10.1016/j.fsigss.2019.09.085> and Kaur et al. (2016) <doi:doi.org/10.1007/s00414-015-1276-1>.
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: Familias (>= 2.6.1), gWidgets2, gWidgets2tcltk, flextable, officer, pedFamilias, pedtools
Suggests: knitr, pander, rmarkdown, tkrplot
License: GPL (>= 2)
URL: https://gdorum.github.io/relMix/
NeedsCompilation: no
Packaged: 2024-04-22 08:57:01 UTC; dogu
Author: Guro Dorum [aut, cre], Elias Hernandis [aut], Navreet Kaur [ctb], Thore Egeland [ctb]
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-23 10:50:02 UTC

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New package bbk with initial version 0.1.0
Package: bbk
Title: Client for the Bundesbank API
Version: 0.1.0
Description: Download data and metadata from the 'Bundesbank SDMX Web Service API' found at <https://www.bundesbank.de/en/statistics/time-series-databases/help-for-sdmx-web-service/web-service-interface-data>.
License: MIT + file LICENSE
URL: https://m-muecke.github.io/bbk/, https://github.com/m-muecke/bbk
BugReports: https://github.com/m-muecke/bbk/issues
Depends: R (>= 4.1.0)
Imports: httr2, utils, xml2
Suggests: ggplot2, scales, testthat (>= 3.0.0), tibble
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-22 20:05:45 UTC; mmuecke
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-23 09:30:02 UTC

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New package RobRegression with initial version 0.1.0
Package: RobRegression
Title: Robust Multivariate Regression
Version: 0.1.0
Description: Robust methods for estimating the parameters of multivariate Gaussian linear models.
License: GPL (>= 2)
Encoding: UTF-8
Imports: Rcpp, foreach, doParallel, mvtnorm,parallel,RSpectra , capushe, KneeArrower, fastmatrix, DescTools
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-04-22 17:56:54 UTC; pug56
Author: Antoine Godichon-Baggioni [aut, cre, cph], Stephane Robin [aut], Laure Sansonnet [aut]
Maintainer: Antoine Godichon-Baggioni <antoine.godichon_baggioni@upmc.fr>
Repository: CRAN
Date/Publication: 2024-04-23 09:00:02 UTC

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New package PCBS with initial version 0.1.0
Package: PCBS
Title: Principle Component BiSulfite
Version: 0.1.0
Description: A system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principle Component BiSulfite, 'PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
URL: https://github.com/katlande/PCBS
BugReports: https://github.com/katlande/PCBS/issues
Imports: ggplot2, tibble, ggrepel, dplyr, data.table
NeedsCompilation: no
Packaged: 2024-04-22 17:45:12 UTC; kathrynlande
Author: Kathryn Lande [aut, cre, cph]
Maintainer: Kathryn Lande <kathryn.lande@mail.mcgill.ca>
Repository: CRAN
Date/Publication: 2024-04-23 09:00:05 UTC

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New package GregoryQuadrature with initial version 1.0.0
Package: GregoryQuadrature
Title: Gregory Weights for Function Integration
Version: 1.0.0
Description: Computes Gregory weights for a given number nodes and function order. Anthony Ralston and Philip Rabinowitz (2001) <ISBN:9780486414546>.
License: GPL-3
Encoding: UTF-8
Imports: pracma
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/dhetting/GregoryQuadrature
BugReports: https://github.com/dhetting/GregoryQuadrature/issues
NeedsCompilation: no
Packaged: 2024-04-22 15:59:46 UTC; dhetting
Author: Dylan Hettinger [aut, cre, cph] , Bengt Fornberg [aut]
Maintainer: Dylan Hettinger <dhettinger@mines.edu>
Repository: CRAN
Date/Publication: 2024-04-23 08:40:02 UTC

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Mon, 22 Apr 2024

New package Clustering with initial version 1.7.10
Package: Clustering
Title: Techniques for Evaluating Clustering
Description: The design of this package allows us to run different clustering packages and compare the results between them, to determine which algorithm behaves best from the data provided. See Martos, L.A.P., García-Vico, Á.M., González, P. et al.(2023) <doi:10.1007/s13748-022-00294-2> "Clustering: an R library to facilitate the analysis and comparison of cluster algorithms.", Martos, L.A.P., García-Vico, Á.M., González, P. et al. "A Multiclustering Evolutionary Hyperrectangle-Based Algorithm" <doi:10.1007/s44196-023-00341-3> and L.A.P., García-Vico, Á.M., González, P. et al. "An Evolutionary Fuzzy System for Multiclustering in Data Streaming" <doi:10.1016/j.procs.2023.12.058>.
Version: 1.7.10
Date: 2024-04-20
Author: Luis Alfonso Perez Martos [aut, cre]
Maintainer: Luis Alfonso Perez Martos <lapm0001@gmail.com>
URL: https://github.com/laperez/clustering
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Repository: CRAN
Imports: amap, apcluster, cluster, ClusterR, data.table, dplyr, foreach, future, ggplot2, gmp, methods, pracma, pvclust, shiny, sqldf, stats, tools, utils, xtable, toOrdinal
Suggests: DT, shinyalert, shinyFiles, shinyjs, shinythemes, shinyWidgets, tidyverse, shinycssloaders
NeedsCompilation: no
Packaged: 2024-04-22 18:47:54 UTC; luis
Depends: R (>= 3.5.0)
Date/Publication: 2024-04-22 19:10:11 UTC

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New package basecamb with initial version 1.1.5
Package: basecamb
Title: Utilities for Streamlined Data Import, Imputation and Modelling
Version: 1.1.5
Description: Provides functions streamlining the data analysis workflow: Outsourcing data import, renaming and type casting to a *.csv. Manipulating imputed datasets and fitting models on them. Summarizing models.
Depends: R (>= 4.0.0)
Imports: assertthat, dplyr, mice, Hmisc, survival, stats, purrr, MASS, sae
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), rms
URL: https://CRAN.R-project.org/package=basecamb, https://github.com/codeblue-team/basecamb
BugReports: https://github.com/codeblue-team/basecamb/issues
NeedsCompilation: no
Packaged: 2024-04-21 17:58:45 UTC; Peter
Author: J. Peter Marquardt [aut, cre] , Till D. Best [aut]
Maintainer: J. Peter Marquardt <peter@kmarquardt.de>
Repository: CRAN
Date/Publication: 2024-04-22 19:10:07 UTC

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New package tidylda with initial version 0.0.5
Package: tidylda
Title: Latent Dirichlet Allocation Using 'tidyverse' Conventions
Version: 0.0.5
Description: Implements an algorithm for Latent Dirichlet Allocation (LDA), Blei et at. (2003) <https://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf>, using style conventions from the 'tidyverse', Wickham et al. (2019)<doi:10.21105/joss.01686>, and 'tidymodels', Kuhn et al.<https://tidymodels.github.io/model-implementation-principles/>. Fitting is done via collapsed Gibbs sampling. Also implements several novel features for LDA such as guided models and transfer learning based on ongoing and, as yet, unpublished research.
License: MIT + file LICENSE
URL: https://github.com/TommyJones/tidylda/
BugReports: https://github.com/TommyJones/tidylda/issues
Depends: R (>= 3.5.0)
Imports: dplyr, generics, gtools, Matrix, methods, mvrsquared (>= 0.1.0), Rcpp (>= 1.0.2), rlang, stats, stringr, tibble, tidyr, tidytext
Suggests: ggplot2, knitr, parallel, quanteda, testthat, tm, slam, spelling, covr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppThread
Encoding: UTF-8
Language: en-US
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-20 21:24:04 UTC; tommy
Author: Tommy Jones [aut, cre] , Brendan Knapp [ctb] , Barum Park [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-22 18:20:02 UTC

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New package slca with initial version 1.0.0
Package: slca
Title: Structural Modeling for Multiple Latent Class Variables
Version: 1.0.0
Maintainer: Youngsun Kim <yskstat@gmail.com>
Description: Provides comprehensive tools for the implementation of Structural Latent Class Models (SLCM), including Latent Transition Analysis (LTA; Linda M. Collins and Stephanie T. Lanza, 2009) <doi:10.1002/9780470567333>, Latent Class Profile Analysis (LCPA; Hwan Chung et al., 2010) <doi:10.1111/j.1467-985x.2010.00674.x>, and Joint Latent Class Analysis (JLCA; Saebom Jeon et al., 2017) <doi:10.1080/10705511.2017.1340844>, and any other extended models involving multiple latent class variables.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: DiagrammeR, magrittr, MASS, Rcpp, stats
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2024-04-20 20:00:31 UTC; kim0sun
Author: Youngsun Kim [aut, cre] , Hwan Chung [aut]
Repository: CRAN
Date/Publication: 2024-04-22 18:42:39 UTC

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New package Rtwobitlib with initial version 0.3.5
Package: Rtwobitlib
Title: '2bit' 'C' Library
Description: A trimmed down copy of the "kent-core source tree" turned into a 'C' library for manipulation of '.2bit' files. See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7> for a quick overview of the '2bit' format. The "kent-core source tree" can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>. Only the '.c' and '.h' files from the source tree that are related to manipulation of '.2bit' files were kept. Note that the package is primarily useful to developers of other R packages who wish to use the '2bit' 'C' library in their own 'C'/'C++' code.
URL: https://github.com/hpages/Rtwobitlib
BugReports: https://github.com/hpages/Rtwobitlib/issues
Version: 0.3.5
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tools
Suggests: testthat, knitr, rmarkdown
SystemRequirements: GNU make
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-20 06:42:19 UTC; hpages
Author: Herve Pages [aut, cre], UC Regents [cph]
Maintainer: Herve Pages <hpages.on.github@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-22 18:32:43 UTC

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New package PanelTM with initial version 1.0
Package: PanelTM
Title: Two- And Three-Way Dynamic Panel Threshold Regression Model for Change Point Detection
Version: 1.0
Maintainer: F. Marta L. Di Lascio <marta.dilascio@unibz.it>
Description: Estimation of two- and three-way dynamic panel threshold regression models (Di Lascio and Perazzini (2024) <https://repec.unibz.it/bemps104.pdf>; Di Lascio and Perazzini (2022, ISBN:978-88-9193-231-0); Seo and Shin (2016) <doi:10.1016/j.jeconom.2016.03.005>) through the generalized method of moments based on the first difference transformation and the use of instrumental variables. The models can be used to find a change point detection in the time series. In addition, random number generation is also implemented.
License: GPL (>= 2)
Depends: R (>= 4.3.0), methods, stats, pracma
Imports:
NeedsCompilation: no
Packaged: 2024-04-20 13:37:37 UTC; FDiLascio
Author: Selene Perazzini [aut], F. Marta L. Di Lascio [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-22 18:42:42 UTC

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New package guescini with initial version 0.1.0
Package: guescini
Title: Real-Time PCR Data Sets by Guescini et al. (2008)
Version: 0.1.0
Description: Real-time quantitative polymerase chain reaction (qPCR) data by Guescini et al. (2008) <doi:10.1186/1471-2105-9-326> in tidy format. This package provides two data sets where the amplification efficiency has been modulated: either by changing the amplification mix concentration, or by increasing the concentration of IgG, a PCR inhibitor. Original raw data files: <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-326/MediaObjects/12859_2008_2311_MOESM1_ESM.xls> and <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-326/MediaObjects/12859_2008_2311_MOESM5_ESM.xls>.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
URL: https://github.com/ramiromagno/guescini, https://rmagno.eu/guescini/
BugReports: https://github.com/ramiromagno/guescini/issues
Depends: R (>= 2.10)
Imports: tibble
NeedsCompilation: no
Packaged: 2024-04-21 00:22:31 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-22 18:50:02 UTC

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New package drclust with initial version 0.1
Package: drclust
Title: Simultaneous Clustering and (or) Dimensionality Reduction
Version: 0.1
Date: 2024-04-19
Description: Methods for simultaneous clustering and dimensionality reduction such as: Double k-means, Reduced k-means, Factorial k-means, Clustering with Disjoint PCA but also methods for exclusively dimensionality reduction: Disjoint PCA, Disjoint FA. The statistical methods implemented refer to the following articles: de Soete G., Carroll J. (1994) "K-means clustering in a low-dimensional Euclidean space" <doi:10.1007/978-3-642-51175-2_24> ; Vichi M. (2001) "Double k-means Clustering for Simultaneous Classification of Objects and Variables" <doi:10.1007/978-3-642-59471-7_6> ; Vichi M., Kiers H.A.L. (2001) "Factorial k-means analysis for two-way data" <doi:10.1016/S0167-9473(00)00064-5> ; Vichi M., Saporta G. (2009) "Clustering and disjoint principal component analysis" <doi:10.1016/j.csda.2008.05.028> ; Vichi M. (2017) "Disjoint factor analysis with cross-loadings" <doi:10.1007/s11634-016-0263-9>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: Rcpp, RcppArmadillo, fpc, cluster, factoextra, pheatmap
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-04-19 15:48:27 UTC; Ionel
Author: Ionel Prunila [aut, cre], Maurizio Vichi [aut]
Maintainer: Ionel Prunila <ionel.prunila@uniroma1.it>
Repository: CRAN
Date/Publication: 2024-04-22 18:22:47 UTC

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New package donutsk with initial version 0.1.1
Package: donutsk
Title: Construct Advanced Donut Charts
Version: 0.1.1
Description: Build donut/pie charts with 'ggplot2' layer by layer, exploiting the advantages of polar symmetry. Leverage layouts to distribute labels effectively. Connect labels to donut segments using pins. Streamline annotation and highlighting.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/dkibalnikov/donutsk, https://dkibalnikov.github.io/donutsk/
BugReports: https://github.com/dkibalnikov/donutsk/issues
Depends: ggplot2 (>= 3.5.0), R (>= 4.2.0)
Imports: dplyr (>= 1.1.2), glue (>= 1.6.2), rlang (>= 1.1.1)
Suggests: knitr, rmarkdown, scales (>= 1.3.0), stringr (>= 1.5.0), testthat (>= 3.0.0), tidyr (>= 1.3.0)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-21 10:42:22 UTC; Dmitrii_Kibalnikov
Author: Dmitry Kibalnikov [aut, cre, cph]
Maintainer: Dmitry Kibalnikov <d.kibalnikov@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-22 18:50:06 UTC

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New package aifeducation with initial version 0.3.3
Package: aifeducation
Title: Artificial Intelligence for Education
Version: 0.3.3
Description: In social and educational settings, the use of Artificial Intelligence (AI) is a challenging task. Relevant data is often only available in handwritten forms, or the use of data is restricted by privacy policies. This often leads to small data sets. Furthermore, in the educational and social sciences, data is often unbalanced in terms of frequencies. To support educators as well as educational and social researchers in using the potentials of AI for their work, this package provides a unified interface for neural nets in 'keras', 'tensorflow', and 'pytorch' to deal with natural language problems. In addition, the package ships with a shiny app, providing a graphical user interface. This allows the usage of AI for people without skills in writing python/R scripts. The tools integrate existing mathematical and statistical methods for dealing with small data sets via pseudo-labeling (e.g. Lee (2013) <https://www.researchgate.net/publication/280581078_Pseudo-Label_The_Simple_and_Efficie [...truncated...]
License: GPL-3
URL: https://fberding.github.io/aifeducation/
BugReports: https://github.com/cran/aifeducation/issues
Depends: R (>= 3.5.0)
Imports: abind, foreach, doParallel, iotarelr(>= 0.1.5), irr, irrCAC, methods, Rcpp (>= 1.0.10), reshape2, reticulate (>= 1.34.0), smotefamily, stringr, rlang, utils
Suggests: text2vec, tidytext, topicmodels, udpipe, quanteda, knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, shiny, shinyFiles, shinyWidgets, shinydashboard, shinyjs, fs, readtext, readxl
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-20 19:54:50 UTC; WissMit
Author: Berding Florian [aut, cre] , Pargmann Julia [ctb], Riebenbauer Elisabeth [ctb], Rebmann Karin [ctb], Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Repository: CRAN
Date/Publication: 2024-04-22 18:22:50 UTC

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New package TreeRingShape with initial version 3.0.3
Package: TreeRingShape
Title: Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing and Interpolating Model
Version: 3.0.3
Maintainer: Megumi ISHIDA <ishidam@sanchikanri.com>
Description: Record all tree-ring Shapefile of tree disk with GIS soft ('Qgis'<https://www.qgis.org/en/site/>) and interpolating model from high resolution tree disk image.
License: GPL (>= 2)
Depends: R (>= 3.6.2)
Imports: methods, sf
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
URL: https://github.com/ishidamgm/TreeRingShape, https://ishidamgm.github.io/TreeRingShape/, https://www.sanchikanri.com/treering/TreeRingShape.html
BugReports: https://github.com/ishidamgm/TreeRingShape/issues
NeedsCompilation: no
Packaged: 2024-04-19 21:09:17 UTC; i
Author: Megumi ISHIDA [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-22 15:12:37 UTC

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New package ViSe with initial version 0.1.2
Package: ViSe
Title: Visualizing Sensitivity
Version: 0.1.2
Depends: R (>= 3.1.0)
Imports: stats, ggplot2, methods, dplyr, tidyr, scales, cowplot, shiny
Maintainer: Erin M. Buchanan <buchananlab@gmail.com>
Description: Designed to help the user to determine the sensitivity of an proposed causal effect to unconsidered common causes. Users can create visualizations of sensitivity, effect sizes, and determine which pattern of effects would support a causal claim for between group differences. Number needed to treat formula from Kraemer H.C. & Kupfer D.J. (2006) <doi:10.1016/j.biopsych.2005.09.014>.
License: LGPL-3
Encoding: UTF-8
URL: http://www.aggieerin.com/ViSe/
Suggests: knitr, rmarkdown, plotly
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-19 13:06:05 UTC; erinbuchanan
Author: Erin M. Buchanan [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-22 14:32:33 UTC

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New package TrendLSW with initial version 1.0.1
Package: TrendLSW
Title: Wavelet Methods for Analysing Locally Stationary Time Series
Version: 1.0.1
Depends: R (>= 4.1.0)
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Description: Fitting models for, and simulation of, trend locally stationary wavelet (TLSW) time series models, which take account of time-varying trend and dependence structure in a univariate time series. The TLSW model, and its estimation, is described in McGonigle, Killick and Nunes (2022a) <doi:10.1111/jtsa.12643>, (2022b) <doi:10.1214/22-EJS2044>. New users will likely want to start with the TLSW function.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: wavethresh, locits
URL: https://github.com/EuanMcGonigle/TrendLSW
BugReports: https://github.com/EuanMcGonigle/TrendLSW/issues
Suggests: testthat (>= 3.0.0), vdiffr
NeedsCompilation: no
Packaged: 2024-04-19 15:27:32 UTC; euanmcgonigle
Author: Euan T. McGonigle [aut, cre], Rebecca Killick [aut], Matthew Nunes [aut]
Repository: CRAN
Date/Publication: 2024-04-22 14:42:38 UTC

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New package sim.BA with initial version 0.1.0
Package: sim.BA
Title: Simulation-Based Bias Analysis for Observational Studies
Version: 0.1.0
Description: Allows user to conduct a simulation based quantitative bias analysis using covariate structures generated with individual-level data to characterize the bias arising from unmeasured confounding. Users can specify their desired data generating mechanisms to simulate data and quantitatively summarize findings in an end-to-end application using this package.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Encoding: UTF-8
Imports: chk (>= 0.9.1), cobalt (>= 4.5.3), ggplot2 (>= 3.4.4), scales (>= 1.3.0), pbapply (>= 1.7-2), rlang (>= 1.1.3), stats, survival, utils
Suggests: MatchIt (>= 4.5.5), WeightIt (>= 0.14.2), parallel, openxlsx (>= 4.2.5.2), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-18 14:18:22 UTC; NoahGreifer
Author: Rishi Desai [aut, cre] , Noah Greifer [aut]
Maintainer: Rishi Desai <rdesai@bwh.harvard.edu>
Repository: CRAN
Date/Publication: 2024-04-22 14:42:35 UTC

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New package ConfidenceEllipse with initial version 1.0.0
Package: ConfidenceEllipse
Title: Computation of 2D and 3D Elliptical Joint Confidence Regions
Version: 1.0.0
Maintainer: Christian L. Goueguel <christian.goueguel@gmail.com>
Description: Computing elliptical joint confidence regions at a specified confidence level. It provides the flexibility to estimate either classical or robust confidence regions, which can be visualized in 2D or 3D plots. The classical approach assumes normality and uses the mean and covariance matrix to define the confidence regions. Alternatively, the robustified version employs estimators like minimum covariance determinant (MCD) and M-estimator, making them less sensitive to outliers and departures from normality. Furthermore, the functions allow users to group the dataset based on categorical variables and estimate separate confidence regions for each group. This capability is particularly useful for exploring potential differences or similarities across subgroups within a dataset. Varmuza and Filzmoser (2009, ISBN:978-1-4200-5947-2). Johnson and Wichern (2007, ISBN:0-13-187715-1). Raymaekers and Rousseeuw (2019) <DOI:10.1080/00401706.2019.1677270>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: cellWise, dplyr, forcats, ggplot2, magrittr, pcaPP, purrr, rgl, rlang, stats, tibble, tidyr, tidyselect
URL: https://christiangoueguel.github.io/ConfidenceEllipse/, https://github.com/ChristianGoueguel/ConfidenceEllipse
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
Language: en-US
BugReports: https://github.com/ChristianGoueguel/ConfidenceEllipse/issues
NeedsCompilation: no
Packaged: 2024-04-19 16:55:15 UTC; christiangoueguel
Author: Christian L. Goueguel [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-22 14:52:38 UTC

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Fri, 19 Apr 2024

New package spOccupancy with initial version 0.7.6
Package: spOccupancy
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
Version: 0.7.6
Author: Jeffrey Doser [aut, cre], Andrew Finley [aut], Marc Kery [ctb]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2 [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://www.jeffdoser.com/files/spoccupancy-web, https://github.com/doserjef/spOccupancy
BugReports: https://github.com/doserjef/spOccupancy/issues
Depends: R (>= 3.5.0)
Imports: stats, coda, abind, RANN, lme4, foreach, doParallel, spAbundance, methods
Suggests: testthat
NeedsCompilation: yes
Packaged: 2024-04-18 17:37:25 UTC; jeff
Repository: CRAN
Date/Publication: 2024-04-19 12:22:41 UTC

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New package RbyExample with initial version 0.0.100
Package: RbyExample
Title: Data for the Book "R by Example"
Version: 0.0.100
Description: Data for the examples and exercises in the book "R by Example". Jim Albert and Maria Rizzo (2012, ISBN 978-1-4614-1365-3).
License: GPL (>= 2)
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
URL: https://github.com/mariarizzo/RbyExample
NeedsCompilation: no
Packaged: 2024-04-18 19:37:43 UTC; maria
Author: Maria Rizzo [aut, cre], Jim Albert [aut]
Repository: CRAN
Date/Publication: 2024-04-19 10:53:02 UTC

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New package puremoe with initial version 1.0.0
Package: puremoe
Title: Pubmed Unified REtrieval for Multi-Output Exploration
Version: 1.0.0
Maintainer: Jason Timm <JaTimm@salud.unm.edu>
Description: Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts <https://pubmed.ncbi.nlm.nih.gov/>, bibliometrics from 'iCite' <https://icite.od.nih.gov/>, pubtations from 'PubTator3' <https://www.ncbi.nlm.nih.gov/research/pubtator3/>, and full-text records from 'PMC' <https://www.ncbi.nlm.nih.gov/pmc/>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: rentrez, textshape, xml2, data.table, httr, pbapply, jsonlite, rappdirs
Suggests: knitr, rmarkdown
URL: https://github.com/jaytimm/puremoe, https://jaytimm.github.io/puremoe/
BugReports: https://github.com/jaytimm/puremoe/issues
NeedsCompilation: no
Packaged: 2024-04-18 23:07:27 UTC; jtimm
Author: Jason Timm [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-19 10:22:46 UTC

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New package CreditRisk with initial version 0.1.7
Package: CreditRisk
Title: Evaluation of Credit Risk with Structural and Reduced Form Models
Version: 0.1.7
Date: 2024-04-18
Maintainer: Alessandro Cimarelli <alessandro.cimarelli@icloud.com>
Description: Evaluation of default probability of sovereign and corporate entities based on structural or intensity based models and calibration on market Credit Default Swap quotes. References: Damiano Brigo, Massimo Morini, Andrea Pallavicini (2013) <doi:10.1002/9781118818589>. Print ISBN: 9780470748466, Online ISBN: 9781118818589. © 2013 John Wiley & Sons Ltd.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: stats
Suggests: testthat
NeedsCompilation: no
Packaged: 2024-04-19 08:00:09 UTC; alessandro.cimarelli
Repository: CRAN
Date/Publication: 2024-04-19 10:53:09 UTC
Author: Alessandro Cimarelli [aut, cre], Nicolo Manca [aut]

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New package citmre with initial version 0.1.0
Package: citmre
Title: Colombian Index Tool Market Rate Exchange
Version: 0.1.0
Description: Downloads the Representative Market Rate Exchange (RMRE) from the <www.datos.gov.co> source. Allows setting the data series in time frequencies, splitting the time series through start and end functions, transforming the data set in log returns or levels, and making a Dynamic graph.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, httr, jsonlite, lubridate, plotly, rvest, stats, xml2, xts
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/DavRodEcon/citmre, https://davrodecon.github.io/citmre/
BugReports: https://github.com/DavRodEcon/citmre/issues
NeedsCompilation: no
Packaged: 2024-04-18 20:11:01 UTC; davidrodriguez
Author: Sergio Sierra-Lujan [aut, cph] , David Rodriguez [aut, cre]
Maintainer: David Rodriguez <davestss@hotmail.com>
Repository: CRAN
Date/Publication: 2024-04-19 10:22:51 UTC

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Thu, 18 Apr 2024

New package latentFactoR with initial version 0.0.6
Package: latentFactoR
Title: Data Simulation Based on Latent Factors
Version: 0.0.6
Date: 2024-04-17
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Description: Generates data based on latent factor models. Data can be continuous, polytomous, dichotomous, or mixed. Skews, cross-loadings, wording effects, population errors, and local dependencies can be added. All parameters can be manipulated. Data categorization is based on Garrido, Abad, and Ponsoda (2011) <doi:10.1177/0013164410389489>.
Depends: R (>= 3.6.0)
License: GPL (>= 3.0)
Imports: BBmisc, EGAnet, fspe, googledrive, ineq, lavaan, Matrix, methods, mlr, mvtnorm, psych, rstudioapi, xgboost
Suggests: ggplot2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-18 20:35:05 UTC; alextops
Author: Alexander Christensen [aut, cre] , Luis Eduardo Garrido [aut] , Maria Dolores Nieto Canaveras [aut], Hudson Golino [aut] , Marcos Jimenez [aut], Francisco Abad [ctb], Eduardo Garcia-Garzon [ctb], Vithor Franco [aut]
Repository: CRAN
Date/Publication: 2024-04-18 21:23:04 UTC

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New package WordListsAnalytics with initial version 0.2.0
Package: WordListsAnalytics
Title: Multiple Data Analysis Tools for Property Listing Tasks
Version: 0.2.0
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Description: Application to estimate statistical values using properties provided by a group of individuals to describe concepts using 'shiny'. It estimates the underlying distribution to generate new descriptive words Canessa et al. (2023) <doi:10.3758/s13428-022-01811-w>, applies a new clustering model, and uses simulations to estimate the probability that two persons describe the same words based on their descriptions Canessa et al. (2022) <doi:10.3758/s13428-022-02030-z>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: ggplot2, readr, dplyr, reshape2, grDevices, stats, graphics
Depends: shiny, R (>= 4.2.0)
NeedsCompilation: no
Packaged: 2024-04-18 15:46:33 UTC; Cris
Author: Sebastian Moreno [aut, cre], Cristobal Heredia [aut], Enrique Canessa [ths], Sergio Chaigneau [ths]
Repository: CRAN
Date/Publication: 2024-04-18 19:42:45 UTC

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New package login with initial version 0.9.3
Package: login
Title: 'shiny' Login Module
Version: 0.9.3
Date: 2024-04-17
Maintainer: Jason Bryer <jason@bryer.org>
Description: Framework for adding authentication to 'shiny' applications. Provides flexibility as compared to other options for where user credentials are saved, allows users to create their own accounts, and password reset functionality. Bryer (2024) <doi:10.5281/zenodo.10987876>.
License: GPL (>= 3)
URL: https://github.com/jbryer/login, https://jbryer.github.io/login/
BugReports: https://github.com/jbryer/login/issues
Imports: cookies, DBI, digest, emayili, htmltools, shiny, shinybusy, shinyjs, stringr, utils
Suggests: knitr, rmarkdown
Enhances: RSQLite
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-18 16:08:38 UTC; jbryer
Author: Jason Bryer [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-18 19:32:48 UTC

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New package InterNL with initial version 0.1.0
Package: InterNL
Title: Time Series Intervention Model Using Non-Linear Function
Version: 0.1.0
Author: Dr. Amrit Kumar Paul [aut], Dr. Md Yeasin [aut, cre], Dr. Ranjit Kumar Paul [aut], Mr. Subhankar Biswas [aut], Dr. HS Roy [aut], Dr. Prakash Kumar [aut]
Maintainer: Dr. Md Yeasin <yeasin.iasri@gmail.com>
Description: Intervention analysis is used to investigate structural changes in data resulting from external events. Traditional time series intervention models, viz. Autoregressive Integrated Moving Average model with exogeneous variables (ARIMA-X) and Artificial Neural Networks with exogeneous variables (ANN-X), rely on linear intervention functions such as step or ramp functions, or their combinations. In this package, the Gompertz, Logistic, Monomolecular, Richard and Hoerl function have been used as non-linear intervention function. The equation of the above models are represented as: Gompertz: A * exp(-B * exp(-k * t)); Logistic: K / (1 + ((K - N0) / N0) * exp(-r * t)); Monomolecular: A * exp(-k * t); Richard: A + (K - A) / (1 + exp(-B * (C - t)))^(1/beta) and Hoerl: a*(b^t)*(t^c).This package introduced algorithm for time series intervention analysis employing ARIMA and ANN models with a non-linear intervention function. This package has been developed using algorithm of Yeasin et al. <do [...truncated...]
License: GPL-3
Encoding: UTF-8
Imports: stats, forecast, MLmetrics
NeedsCompilation: no
Packaged: 2024-04-18 09:01:40 UTC; YEASIN
Repository: CRAN
Date/Publication: 2024-04-18 19:13:03 UTC

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New package geonode4R with initial version 0.1
Package: geonode4R
Title: Interface to 'GeoNode' REST API
Version: 0.1
Date: 2024-04-18
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Description: Provides an interface to the 'GeoNode' API, allowing to upload and publish metadata and data in 'GeoNode'. For more information about the 'GeoNode' API, see <https://geonode.org/>.
Depends: R (>= 3.1.0)
Imports: R6, openssl, httr, keyring, readr
Suggests: testthat, roxygen2, covr, shiny, knitr, markdown
License: MIT + file LICENSE
URL: https://github.com/eblondel/geonode4R, https://eblondel.github.io/geonode4R/, https://geonode.org/
BugReports: https://github.com/eblondel/geonode4R/issues
Encoding: UTF-8
LazyLoad: yes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-18 14:41:20 UTC; emman
Author: Emmanuel Blondel [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-18 19:22:58 UTC

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New package DyMEP with initial version 0.1.0
Package: DyMEP
Title: Dynamic Multi Environment Phenology-Model
Version: 0.1.0
Author: Flavian Tschurr
Maintainer: Flavian Tschurr <flavian.tschurr@usys.ethz.ch>
Description: Mechanistically models/predicts the phenology (macro-phases) of 10 crop plants (trained on a big dataset over 80 years derived from the German weather service (DWD) <https://opendata.dwd.de/>). Can be applied for remote sensing purposes, dynamically check the best subset of available covariates for the given dataset and crop.
License: LGPL (>= 3)
Encoding: UTF-8
Imports: stats, utils
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-18 06:10:17 UTC; ftschurr
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-04-18 19:03:14 UTC

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New package CirceR with initial version 1.3.3
Package: CirceR
Title: Construct Cohort Inclusion and Restriction Criteria Expressions
Version: 1.3.3
Date: 2024-03-20
Maintainer: Chris Knoll <cknoll@ohdsi.org>
Description: Wraps the 'CIRCE' (<https://github.com/ohdsi/circe-be>) 'Java' library allowing cohort definition expressions to be edited and converted to 'Markdown' or 'SQL'.
License: Apache License 2.0
URL: https://ohdsi.github.io/CirceR/, https://github.com/OHDSI/CirceR/
BugReports: https://github.com/OHDSI/CirceR/issues/
SystemRequirements: Java (>= 8)
Depends: R (>= 3.5.0)
Imports: rJava, RJSONIO
Suggests: testthat, knitr, rmarkdown
NeedsCompilation: no
Language: en-US
Encoding: UTF-8
Packaged: 2024-04-18 16:42:02 UTC; cknoll1
Author: Chris Knoll [aut, cre], Martijn Schuemie [aut]
Repository: CRAN
Date/Publication: 2024-04-18 19:42:49 UTC

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New package ARUtools with initial version 0.6.2
Package: ARUtools
Title: Management and Processing of Autonomous Recording Unit (ARU) Data
Version: 0.6.2
Description: Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings. Extract Metadata from your recordings, select a subset of recordings for interpretation, and prepare files for processing on the 'WildTrax' <https://wildtrax.ca/> platform. Read and process metadata from recordings collected using the SongMeter and BAR-LT types of ARUs.
License: MIT + file LICENSE
URL: https://arutools.github.io/ARUtools/, https://github.com/ARUtools/ARUtools
BugReports: https://github.com/ARUtools/ARUtools/issues
Depends: R (>= 4.0)
Imports: dplyr, fs (>= 1.6.1), glue, here, hms (>= 1.1.2), lifecycle, lubridate, lutz, parzer, purrr, readr, rlang (>= 0.4), seewave (>= 2.2.3), sf, spsurvey (>= 5.0.1), stringr, suncalc, tidyr, units, withr
Suggests: covr, ggplot2, job, jsonlite, knitr, parallel, patchwork, readxl (>= 1.4.2), rmarkdown, rstudioapi, sessioninfo, soundecology, testthat (>= 3.0.0), tuneR, vdiffr (>= 1.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-18 16:20:00 UTC; HopeD
Author: David Hope [aut, cre] , Steffi LaZerte [aut] , Government of Canada [cph, fnd]
Maintainer: David Hope <david.hope@ec.gc.ca>
Repository: CRAN
Date/Publication: 2024-04-18 19:32:51 UTC

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New package ADLP with initial version 0.1.0
Package: ADLP
Title: Accident and Development Period Adjusted Linear Pools for Actuarial Stochastic Reserving
Version: 0.1.0
Author: Benjamin Avanzi [aut], William Ho [aut], Yanfeng Li [aut, cre], Bernard Wong [aut], Alan Xian [aut]
Maintainer: Yanfeng Li <yanfeng.li@student.unsw.edu.au>
Description: Loss reserving generally focuses on identifying a single model that can generate superior predictive performance. However, different loss reserving models specialise in capturing different aspects of loss data. This is recognised in practice in the sense that results from different models are often considered, and sometimes combined. For instance, actuaries may take a weighted average of the prediction outcomes from various loss reserving models, often based on subjective assessments. This package allows for the use of a systematic framework to objectively combine (i.e. ensemble) multiple stochastic loss reserving models such that the strengths offered by different models can be utilised effectively. Our framework is developed in Avanzi et al. (2023). Firstly, our criteria model combination considers the full distributional properties of the ensemble and not just the central estimate - which is of particular importance in the reserving context. Secondly, our framework is that it is tai [...truncated...]
License: GPL-3
Encoding: UTF-8
URL: https://github.com/agi-lab/ADLP
BugReports: https://github.com/agi-lab/ADLP/issues
LazyData: true
Imports: methods
Suggests: knitr, tidyverse, SynthETIC (>= 1.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-04-18 07:21:50 UTC; jimli
Repository: CRAN
Date/Publication: 2024-04-18 19:23:01 UTC

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New package xlcharts with initial version 0.0.1
Package: xlcharts
Title: Create Native 'Excel' Charts and Work with Microsoft 'Excel' Files
Version: 0.0.1
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Description: An R interface to the 'OpenPyXL' 'Python' library to create native 'Excel' charts and work with Microsoft 'Excel' files.
URL: https://felixluginbuhl.com/xlcharts/
License: MIT + file LICENSE
SystemRequirements: Conda
Imports: reticulate, writexl
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-17 19:07:15 UTC; felix
Author: Felix Luginbuhl [aut, cre, cph] , Eric Gazoni [ctb, cph] ), Charlie Clark [ctb, cph] ), openpyxl authors [ctb, cph] )
Repository: CRAN
Date/Publication: 2024-04-18 18:50:02 UTC

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New package meteo with initial version 2.0-3
Package: meteo
Version: 2.0-3
Date: 2024-04-16
Encoding: UTF-8
Title: RFSI & STRK Interpolation for Meteo and Environmental Variables
Author: Milan Kilibarda [aut] , Aleksandar Sekulic [aut, cre] , Tomislav Hengl [ctb], Edzer Pebesma [ctb], Benedikt Graeler [ctb]
Maintainer: Aleksandar Sekulic <asekulic@grf.bg.ac.rs>
Depends: R (>= 4.0.0)
Description: Random Forest Spatial Interpolation (RFSI, Sekulić et al. (2020) <doi:10.3390/rs12101687>) and spatio-temporal geostatistical (spatio-temporal regression Kriging (STRK)) interpolation for meteorological (Kilibarda et al. (2014) <doi:10.1002/2013JD020803>, Sekulić et al. (2020) <doi:10.1007/s00704-019-03077-3>) and other environmental variables. Contains global spatio-temporal models calculated using publicly available data.
License: GPL (>= 2.0) | file LICENCE
URL: https://www.r-pkg.org/pkg/meteo, https://r-forge.r-project.org/projects/meteo/, https://github.com/AleksandarSekulic/Rmeteo
LazyLoad: yes
Imports: methods, utils, stats, DescTools, caret, data.table, dplyr, sp, spacetime, gstat, foreach, parallel, snowfall, doParallel, plyr, units, nabor, CAST, ranger, sf, sftime, raster, terra, jsonlite
BugReports: https://github.com/AleksandarSekulic/Rmeteo/issues
NeedsCompilation: no
Packaged: 2024-04-18 16:06:24 UTC; sekulic
Repository: CRAN
Date/Publication: 2024-04-18 18:12:48 UTC

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New package future.mirai with initial version 0.2.0
Package: future.mirai
Version: 0.2.0
Depends: future
Imports: mirai (>= 0.12.1), parallelly, utils
Suggests: future.tests, future.apply, listenv
Title: A 'Future' API for Parallel Processing using 'mirai'
Description: Implementation of the 'Future' API <doi:10.32614/RJ-2021-048> on top of the 'mirai' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local machine or across remote machines. Contrary to back-ends relying on the 'parallel' package (e.g. 'multisession') and socket connections, 'mirai_cluster' and 'mirai_multisession', provided here, can run more than 125 parallel R processes.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://future.mirai.futureverse.org, https://github.com/HenrikBengtsson/future.mirai
BugReports: https://github.com/HenrikBengtsson/future.mirai/issues
NeedsCompilation: no
Packaged: 2024-04-16 11:06:33 UTC; henrik
Author: Henrik Bengtsson [aut, cre, cph] , Charlie Gao [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2024-04-18 18:42:34 UTC

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New package spheresmooth with initial version 0.1.0
Package: spheresmooth
Title: Piecewise Geodesic Smoothing for Spherical Data
Version: 0.1.0
Description: Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: rgl, sphereplot
NeedsCompilation: no
Packaged: 2024-04-17 14:04:35 UTC; bak
Author: Seyoung Lee [aut] , Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Repository: CRAN
Date/Publication: 2024-04-18 14:32:48 UTC

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New package MethEvolSIM with initial version 0.1
Package: MethEvolSIM
Title: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies
Version: 0.1
Author: Sara Castillo Vicente [aut, cre], Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Description: DNA methylation is an epigenetic modification involved in genomic stability, gene regulation, development and disease. DNA methylation occurs mainly through the addition of a methyl group to cytosines, for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine). Tissue-specific methylation patterns lead to genomic regions with different characteristic methylation levels. E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of expressed genes tend to be unmethylated. 'MethEvolSIM' is a model-based simulation software for the generation and modification of cytosine methylation patterns along a given tree, which can be a genealogy of cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree. The simulations are based on an extension of the model of Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of the met [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: R6
Depends: R (>= 4.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-17 10:39:04 UTC; castillo
Repository: CRAN
Date/Publication: 2024-04-18 14:12:43 UTC

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New package MCCM with initial version 0.1.0
Package: MCCM
Title: Mixed Correlation Coefficient Matrix
Version: 0.1.0
Description: The IRLS (Iteratively Reweighted Least Squares) and GMM (Generalized Method of Moments) methods are applied to estimate mixed correlation coefficient matrix (Pearson, Polyseries, Polychoric), which can be estimated in pairs or simultaneously. For more information see Peng Zhang and Ben Liu (2024) <doi:10.1080/10618600.2023.2257251>; Ben Liu and Peng Zhang (2024) <doi:10.48550/arXiv.2404.06781>.
License: GPL
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
Depends: R (>= 3.5.0),
Imports: MASS, polycor, lavaan, mvtnorm
NeedsCompilation: no
Packaged: 2024-04-17 07:07:41 UTC; Administrator
Author: Ben Liu [aut, cre], Peng Zhang [ths], Xiaowei Lou [aut, dtc]
Maintainer: Ben Liu <12035024@zju.edu.cn>
Repository: CRAN
Date/Publication: 2024-04-18 14:02:52 UTC

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New package ipeaplot with initial version 0.3.1
Package: ipeaplot
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Version: 0.3.1
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Description: Convenient functions to create 'ggplot2' graphics following the editorial guidelines of the Institute for Applied Economic Research (Ipea).
License: MIT + file LICENSE
URL: https://github.com/ipeadata-lab/ipeaplot
BugReports: https://github.com/ipeadata-lab/ipeaplot/issues
Depends: R (>= 3.3.2)
Imports: checkmate, extrafont, ggplot2, grDevices, paletteer, scales, rlang, ggthemes, showtext
Suggests: abjData, data.table, dplyr, forcats, geobr, knitr, patchwork, purrr, reshape, rmarkdown, sf, sysfonts, testthat, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-17 10:36:20 UTC; caval
Author: Pedro Ferreira [aut, cre], Pedro Jorge [aut], Daniel Lima [aut], Gustavo Coelho [aut], Rafael H. M. Pereira [aut], Lucas Mation [aut], Ipea - Institue for Applied Economic Research [cph, fnd]
Repository: CRAN
Date/Publication: 2024-04-18 14:02:44 UTC

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New package CropWaterBalance with initial version 0.2.0
Package: CropWaterBalance
Title: Climate Water Balance for Irrigation Purposes
Version: 0.2.0
Description: Calculates daily climate water balance for irrigation purposes and also calculates the reference evapotranspiration (ET) using three methods, Penman and Monteith (Allen et al. 1998, ISBN:92-5-104219-5); Priestley and Taylor (1972) <doi:10/cr3qwn>; or Hargreaves and Samani (1985) <doi:10.13031/2013.26773>. Users may specify a management allowed depletion (MAD), which is used to suggest when to irrigate. The functionality allows for the use of crop and water stress coefficients as well.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.10)
LazyData: true
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Imports: PowerSDI, lubridate, stats
URL: https://github.com/gabrielblain/CropWaterBalance
BugReports: https://github.com/gabrielblain/CropWaterBalance/issues
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-17 10:17:03 UTC; Gabriel
Author: Gabriel Constantino Blain [aut, cre] , Graciela R. Sobierajski [aut] , Regina C. Matos Pires [aut] , Adam H. Sparks [aut] , Leticia L. Martins [aut]
Maintainer: Gabriel Constantino Blain <gabriel.blain@sp.gov.br>
Repository: CRAN
Date/Publication: 2024-04-18 14:02:55 UTC

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New package bagyo with initial version 0.1.1
Package: bagyo
Title: Philippine Tropical Cyclones Data
Version: 0.1.1
Description: The Philippines frequently experiences tropical cyclones (called 'bagyo' in the Filipino language) because of its geographical position. These cyclones typically bring heavy rainfall, leading to widespread flooding, as well as strong winds that cause significant damage to human life, crops, and property. Data on cyclones are collected and curated by the Philippine Atmospheric, Geophysical, and Astronomical Services Administration or 'PAGASA' and made available through its website <https://bagong.pagasa.dost.gov.ph/tropical-cyclone/publications/annual-report>. This package contains Philippine tropical cyclones data in a machine-readable format. It is hoped that this data package provides an interesting and unique dataset for data exploration and visualisation.
License: CC0
Depends: R (>= 2.10)
Suggests: dplyr, ggplot2, knitr, lubridate, pdftools, rmarkdown, spelling, testthat (>= 3.0.0), tibble, tidyr
Encoding: UTF-8
Language: en-GB
LazyData: true
URL: https://panukatan.io/bagyo/, https://github.com/panukatan/bagyo
BugReports: https://github.com/panukatan/bagyo/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-17 08:50:25 UTC; ernestguevarra
Author: Ernest Guevarra [aut, cre, cph]
Maintainer: Ernest Guevarra <ernest@guevarra.io>
Repository: CRAN
Date/Publication: 2024-04-18 14:02:48 UTC

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New package sentopics with initial version 0.7.3
Package: sentopics
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Version: 0.7.3
Date: 2024-04-17
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Description: A framework that joins topic modeling and sentiment analysis of textual data. The package implements a fast Gibbs sampling estimation of Latent Dirichlet Allocation (Griffiths and Steyvers (2004) <doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He, Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of helpers and visualizations to analyze the result of topic modeling. The framework also allows enriching topic models with dates and externally computed sentiment measures. A flexible aggregation scheme enables the creation of time series of sentiment or topical proportions from the enriched topic models. Moreover, a novel method jointly aggregates topic proportions and sentiment measures to derive time series of topical sentiment.
License: GPL (>= 3)
BugReports: https://github.com/odelmarcelle/sentopics/issues
URL: https://github.com/odelmarcelle/sentopics
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 1.0.4.6), methods, generics, quanteda (>= 3.2.0), data.table (>= 1.13.6), RcppHungarian
Suggests: ggplot2, ggridges, plotly, RColorBrewer, xts, zoo, future, future.apply, progressr, progress, testthat, covr, stm, lda, topicmodels, seededlda, keyATM, LDAvis, servr, textcat, stringr, sentometrics, spacyr, knitr, rmarkdown, webshot
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
RcppModules: model_module
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-18 10:38:58 UTC; odlmarce
Author: Olivier Delmarcelle [aut, cre] , Samuel Borms [ctb] , Chengua Lin [cph] , Yulan He [cph] , Jose Bernardo [cph] , David Robinson [cph] ), Julia Silge [cph] , <https://orcid.org/0000-0002-3671-836X>)
Repository: CRAN
Date/Publication: 2024-04-18 13:12:38 UTC

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New package glinvci with initial version 1.2.4
Package: glinvci
Title: Phylogenetic Comparative Methods with Uncertainty Estimates
Version: 1.2.4
Date: 2024-04-16
Maintainer: Woodrow Kiang <hello@hckiang.com>
Description: A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
License: GPL-3
VignetteBuilder: utils
Encoding: UTF-8
URL: https://git.sr.ht/~hckiang/glinvci, https://github.com/hckiang/glinvci
Depends: R (>= 3.3.0)
Imports: optimx, lbfgsb3c, BB, ape, numDeriv, plyr, rlang, generics, utils, stats
Suggests: testthat
NeedsCompilation: yes
Packaged: 2024-04-16 22:11:39 UTC; hckiang
Author: Woodrow Kiang [cre, aut]
Repository: CRAN
Date/Publication: 2024-04-18 10:32:44 UTC

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Wed, 17 Apr 2024

New package SpaDES with initial version 2.0.11
Package: SpaDES
Title: Develop and Run Spatially Explicit Discrete Event Simulation Models
Description: Metapackage for implementing a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models. The core simulation components (provided by 'SpaDES.core') are built upon a discrete event simulation (DES; see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>) framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules (see also 'SpaDES.tools'). Included are numerous tools to visualize rasters and other maps (via 'quickPlot'), and caching methods for reproducible simulations (via 'reproducible'). Tools for running simulation experiments are provided by 'SpaDES.experiment'. Additional functionality is provided by the 'SpaDES.addins' and 'SpaDES.shiny' packages.
URL: https://spades.predictiveecology.org, https://github.com/PredictiveEcology/SpaDES
Date: 2024-04-16
Version: 2.0.11
Depends: R (>= 4.2)
Imports: methods, quickPlot (>= 1.0.2), reproducible (>= 2.0.10), SpaDES.core (>= 2.0.3), SpaDES.tools (>= 2.0.5), utils
Suggests: covr, knitr, rmarkdown, testthat
Encoding: UTF-8
Language: en-CA
License: GPL-3
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/PredictiveEcology/SpaDES/issues
ByteCompile: yes
NeedsCompilation: no
Packaged: 2024-04-17 15:52:42 UTC; achubaty
Author: Alex M Chubaty [aut, cre] , Eliot J B McIntire [aut] , Yong Luo [ctb], Steve Cumming [ctb], His Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Repository: CRAN
Date/Publication: 2024-04-17 19:40:25 UTC

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New package TestIndVars with initial version 0.1.0
Package: TestIndVars
Title: Testing the Independence of Variables for Specific Covariance Structures
Version: 0.1.0
Maintainer: Mina Norouzirad <mina.norouzirad@gmail.com>
Description: Test the nullity of covariances, in a set of variables, using a simple univariate procedure. See Marques, Diago, Norouzirad, Bispo (2023) <doi:10.1002/mma.9130>.
License: GPL (>= 2)
URL: https://github.com/mnrzrad/TestIndVars
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: stats, matrixcalc, MASS
NeedsCompilation: no
Packaged: 2024-04-16 15:51:05 UTC; minan
Author: Filipe J. Marques [aut] , Mina Norouzirad [aut, cre] , Joana Diogo [ctb], Regina Bispo [ctb] , FCT, I.P. [fnd] )
Repository: CRAN
Date/Publication: 2024-04-17 09:50:08 UTC

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New package mapmixture with initial version 1.1.1
Package: mapmixture
Title: Spatial Visualisation of Admixture on a Projected Map
Version: 1.1.1
Description: Visualise admixture as pie charts on a projected map, admixture as traditional structure barplots or facet barplots, and scatter plots from genotype principal components analysis. A 'shiny' app allows users to create admixture maps interactively. Jenkins TL (2024) <doi:10.1111/1755-0998.13943>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: bslib (>= 0.5.0), colourpicker, dplyr, ggplot2, ggspatial, grid, htmltools, purrr, rlang, sf, shiny, shinyFeedback, shinyjs, shinyWidgets, stringr, tidyr, waiter
Suggests: shinytest2, terra, testthat (>= 3.2.0)
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2024-04-16 15:49:05 UTC; tj311
Author: Tom Jenkins [aut, cre, cph]
Maintainer: Tom Jenkins <tom.l.jenkins@outlook.com>
Repository: CRAN
Date/Publication: 2024-04-17 09:50:02 UTC

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New package gfunctions with initial version 1.0
Package: gfunctions
Title: G-Functions
Version: 1.0
Date: 2024-04-16
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Description: Modified versions of the lag() and summary() functions: glag() and gsummary(). The prefix 'g' is a reminder of who to blame if things do not work as they should.
License: GPL (>= 2)
Depends: R (>= 3.0.0), zoo, sandwich
Imports: methods, stats
NeedsCompilation: no
Packaged: 2024-04-16 16:46:17 UTC; sucarrat
Repository: CRAN
Date/Publication: 2024-04-17 10:00:02 UTC

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New package filters with initial version 0.3.1
Package: filters
Title: A "Snake_case" Filter System for R
Version: 0.3.1
Description: Enables filtering datasets by a prior specified identifiers which correspond to saved filter expressions.
Imports: magrittr, plyr, yaml
Suggests: dplyr, random.cdisc.data, testthat
License: Apache License 2.0
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-16 14:55:47 UTC; rstudio
Author: Thomas Neitman [aut] , Joe Zhu [ctb, cre], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Repository: CRAN
Date/Publication: 2024-04-17 09:50:05 UTC

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New package DataPackageR with initial version 0.15.9
Package: DataPackageR
Title: Construct Reproducible Analytic Data Sets as R Packages
Version: 0.15.9
Description: A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: digest, knitr, utils, rmarkdown, desc, yaml, purrr, roxygen2 (>= 6.0.1), devtools (>= 1.12.0), assertthat, stringr, futile.logger, rprojroot, usethis, crayon, withr
VignetteBuilder: knitr
Encoding: UTF-8
Suggests: spelling, testthat, covr, data.tree,
URL: https://github.com/ropensci/DataPackageR/, https://docs.ropensci.org/DataPackageR/
BugReports: https://github.com/ropensci/DataPackageR/issues
SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-17 00:34:02 UTC; dslager
Author: Greg Finak [aut, cph] , Paul Obrecht [ctb], Ellis Hughes [ctb] , Jimmy Fulp [ctb], Marie Vendettuoli [ctb] , Dave Slager [ctb, cre] , Jason Taylor [ctb], Kara Woo [rev] , William Landau [rev]
Maintainer: Dave Slager <dslager@scharp.org>
Repository: CRAN
Date/Publication: 2024-04-17 06:50:13 UTC

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Tue, 16 Apr 2024

New package SpaDES.core with initial version 2.0.4
Package: SpaDES.core
Title: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models
Description: Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).
URL: https://spades-core.predictiveecology.org/, https://github.com/PredictiveEcology/SpaDES.core
Date: 2024-04-10
Version: 2.0.4
Depends: R (>= 4.2), quickPlot (>= 1.0.2), reproducible (>= 2.0.9)
Imports: crayon, data.table (>= 1.11.0), fs, igraph (>= 1.0.1), lobstr, methods, qs (>= 0.21.1), Require (>= 0.3.1), stats, terra (>= 1.7-46), utils, whisker
Suggests: archive, CircStats, codetools, covr, DiagrammeR (>= 0.8.2), future, future.callr, ggplot2, ggplotify, httr, knitr, lattice, logging, magrittr, NLMR (>= 1.1.1), pkgload, png, RColorBrewer (>= 1.1-2), raster (>= 2.5-8), rmarkdown, roxygen2, RSQLite, rstudioapi, sp, SpaDES.tools (>= 2.0.0), tcltk, testthat (>= 1.0.2), withr
Additional_repositories: https://predictiveecology.r-universe.dev/
Encoding: UTF-8
Language: en-CA
License: GPL-3
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/PredictiveEcology/SpaDES.core/issues
ByteCompile: yes
NeedsCompilation: no
Packaged: 2024-04-16 00:08:31 UTC; achubaty
Author: Alex M Chubaty [aut] , Eliot J B McIntire [aut, cre] , Yong Luo [ctb], Steve Cumming [ctb], Ceres Barros [ctb] , His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Repository: CRAN
Date/Publication: 2024-04-16 20:30:02 UTC

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New package Paris2024Colours with initial version 0.1.2
Package: Paris2024Colours
Title: Color Palettes Inspired by Paris 2024 Olympic and Paralympic Games
Version: 0.1.2
Description: Palettes inspired by Paris 2024 Olympic and Paralympic Games for data visualizations. Length of color palettes is configurable.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/maximekuntz/Paris2024Colours, https://maximekuntz.github.io/Paris2024Colours/
BugReports: https://github.com/maximekuntz/Paris2024Colours/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-16 10:18:45 UTC; mkuntz
Author: Maxime Kuntz [aut, cre]
Maintainer: Maxime Kuntz <maxime.kuntz75@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-16 20:50:07 UTC

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New package CohortCharacteristics with initial version 0.1.0
Package: CohortCharacteristics
Title: Summarise and Visualise Characteristics of Patients in the OMOP CDM
Version: 0.1.0
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Description: Summarise and visualise the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model (CDM).
License: Apache License (>= 2)
Encoding: UTF-8
Suggests: covr, duckdb (>= 0.9.0), testthat (>= 3.1.5), knitr, CodelistGenerator, rmarkdown, glue, odbc, ggplot2, spelling, RPostgres, dbplyr, PaRe, here, magick, plotly, ggraph, DT, cowplot, DiagrammeRsvg, DBI, gt, flextable, tictoc, withr, scales
Imports: CDMConnector (>= 1.3.1), dplyr, tidyr, checkmate, lubridate, rlang, cli, stringr, omopgenerics (>= 0.1.2), visOmopResults (>= 0.2.0), PatientProfiles (>= 0.8.0), ggpubr, magrittr
URL: https://darwin-eu-dev.github.io/CohortCharacteristics/
BugReports: https://github.com/darwin-eu-dev/CohortCharacteristics/issues
Language: en-US
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-16 09:31:49 UTC; martics
Author: Marti Catala [aut, cre] , Yuchen Guo [aut] , Mike Du [aut] , Kim Lopez-Guell [aut] , Edward Burn [aut] , Nuria Mercade-Besora [ctb] , Marta Alcalde [aut]
Repository: CRAN
Date/Publication: 2024-04-16 20:50:11 UTC

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New package bolsec with initial version 0.1.1
Package: bolsec
Title: Bolivian Securities
Version: 0.1.1
Description: Provides data import and offers 3 daily snapshot functions from securities of varying prices traded on the Bolivian Securities Exchange, website <https://www.bbv.com.bo/>. The snapshots include a detailed list, scatter plot correlation, and descriptive statistics table for the securities.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, rvest, formattable, stats, graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-15 22:48:06 UTC; alvarotapia
Author: Alvaro Tapia [aut, cre]
Maintainer: Alvaro Tapia <alvaroignaciotapia@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-16 20:50:03 UTC

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New package mlr3resampling with initial version 2024.4.14
Package: mlr3resampling
Title: Resampling Algorithms for 'mlr3' Framework
Version: 2024.4.14
Description: A supervised learning algorithm inputs a train set, and outputs a prediction function, which can be used on a test set. If each data point belongs to a group (such as geographic region, year, etc), then how do we know if it is possible to train on one group, and predict accurately on another group? Cross-validation can be used to determine the extent to which this is possible, by first assigning fold IDs from 1 to K to all data (possibly using stratification, usually by group and label). Then we loop over test sets (group/fold combinations), train sets (same group, other groups, all groups), and compute test/prediction accuracy for each combination. Comparing test/prediction accuracy between same and other, we can determine the extent to which it is possible (perfect if same/other have similar test accuracy for each group; other is usually somewhat less accurate than same; other can be just as bad as featureless baseline when the groups have different patterns). For more information, [...truncated...]
License: GPL-3
URL: https://github.com/tdhock/mlr3resampling
BugReports: https://github.com/tdhock/mlr3resampling/issues
Imports: data.table, R6, checkmate, paradox, mlr3, mlr3misc
Suggests: animint2, mlr3tuning, lgr, future, testthat, knitr, rmarkdown, nc, rpart
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-15 21:55:40 UTC; th798
Author: Toby Hocking [aut, cre] , Michel Lang [ctb] , Bernd Bischl [ctb] , Jakob Richter [ctb] , Patrick Schratz [ctb] , Giuseppe Casalicchio [ctb] , Stefan Coors [ctb] , Quay Au [ctb] , Martin Binder [ctb], Florian Pfisterer [ctb] , Raphael Sonabend [ctb] , [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Repository: CRAN
Date/Publication: 2024-04-16 15:50:02 UTC

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New package T2DFitTailor with initial version 3.0.0
Package: T2DFitTailor
Title: Tailor the Exercise Plans and Visualize the Outcome for T2D Patients
Version: 3.0.0
Description: A system for personalized exercise plan recommendations for T2D (Type 2 Diabetes) patients based on the primary outcome of HbA1c (Glycated Hemoglobin). You provide the individual's information, and 'T2DFitTailor' details the exercise plan and predicts the intervention's effectiveness.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr,fmsb,graphics,grDevices,httr,jsonlite
NeedsCompilation: no
Packaged: 2024-04-15 08:26:28 UTC; supercheng
Author: Cheng Liu [aut, cre], Xinyu Hou [aut], Bingxiang Xu [aut], Tiemin Liu [aut], Ru Wang [aut]
Maintainer: Cheng Liu <971264017@qq.com>
Repository: CRAN
Date/Publication: 2024-04-16 14:30:02 UTC

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New package ssMutPA with initial version 0.1.0
Package: ssMutPA
Title: Single-Sample Mutation-Based Pathway Analysis
Version: 0.1.0
Description: A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: ggplot2, ggridges, grDevices, igraph, kernlab, maftools, Matrix, NbClust, parallel, pheatmap, RColorBrewer, stats, survival, utils
Suggests: knitr, qpdf, rmarkdown
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-16 01:41:36 UTC; DELL
Author: Junwei Han [aut, cre, cph], Yalan He [aut], Qian Wang [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Repository: CRAN
Date/Publication: 2024-04-16 14:50:02 UTC

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New package SPUTNIK with initial version 1.4.2
Package: SPUTNIK
Title: Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit
Version: 1.4.2
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese@outlook.com>
Description: Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) <doi:10.1093/bioinformatics/bty622>.
Depends: R (>= 3.4.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: e1071, edgeR, spatstat.explore, spatstat.geom, viridis, ggplot2, reshape, imager, methods, infotheo, parallel, irlba, doSNOW, foreach
Suggests: testthat
URL: https://github.com/paoloinglese/SPUTNIK
BugReports: https://github.com/paoloinglese/SPUTNIK/issues
NeedsCompilation: no
Packaged: 2024-04-14 17:15:33 UTC; Paolo
Repository: CRAN
Date/Publication: 2024-04-16 14:30:05 UTC

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New package spatstat.univar with initial version 2.0-2
Package: spatstat.univar
Version: 2.0-2
Date: 2024-04-16
Title: One-Dimensional Probability Distribution Support for the 'spatstat' Family
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Depends: R (>= 3.5.0), stats
Imports: spatstat.utils (>= 3.0-2)
Description: Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.
License: GPL (>= 2)
URL: http://spatstat.org/
NeedsCompilation: yes
ByteCompile: true
BugReports: https://github.com/spatstat/spatstat.univar/issues
Packaged: 2024-04-16 03:01:54 UTC; adrian
Author: Adrian Baddeley [aut, cre, cph] , Tilman M. Davies [aut, ctb, cph] , Martin L. Hazelton [aut, ctb, cph] , Ege Rubak [aut, cph] , Rolf Turner [aut, cph] , Greg McSwiggan [ctb, cph]
Repository: CRAN
Date/Publication: 2024-04-16 14:50:05 UTC

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New package PWEV with initial version 0.1.0
Package: PWEV
Title: PSO Based Weighted Ensemble Algorithm for Volatility Modelling
Version: 0.1.0
Author: Mr. Ankit Kumar Singh [aut], Dr. Ranjit Kumar Paul [aut, cre], Dr. Amrit Kumar Paul [aut], Dr. Md Yeasin [aut], Ms. Anita Sarkar [aut]
Maintainer: Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>
Description: Price volatility refers to the degree of variation in series over a certain period of time. This volatility is especially noticeable in agricultural commodities, adding uncertainty for farmers, traders, and others in the agricultural supply chain. Commonly and popularly used four volatility models viz, GARCH, Glosten Jagannatan Runkle-GARCH (GJR-GARCH) model, exponentially weighted moving average (EWMA) model and Multiplicative Error Model (MEM) are selected and implemented. PWAVE, weighted ensemble model based on particle swarm optimization (PSO) is proposed to combine the forecast obtained from all the candidate models. This package has been developed using algorithm of Paul et al. <doi:10.1007/s40009-023-01218-x> and Yeasin and Paul (2024) <doi:10.1007/s11227-023-05542-3>.
License: GPL-3
Encoding: UTF-8
Imports: stats, xts, rumidas, rugarch, WeightedEnsemble, Metrics, zoo
NeedsCompilation: no
Packaged: 2024-04-16 07:44:01 UTC; YEASIN
Repository: CRAN
Date/Publication: 2024-04-16 15:00:02 UTC

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New package newIMVC with initial version 0.1.0
Package: newIMVC
Title: A Robust Integrated Mean Variance Correlation
Version: 0.1.0
Description: Measure the dependence structure between two random variables with a new correlation coefficient and extend it to hypothesis test, feature screening and false discovery rate control.
License: GPL-3
Encoding: UTF-8
Imports: splines, quantreg, expm, CompQuadForm, GGMridge, limma, stats
Suggests: knitr, mvtnorm, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-14 04:03:04 UTC; Surface
Author: Wei Xiong [aut], Han Pan [aut, cre], Hengjian Cui [aut]
Maintainer: Han Pan <scott_pan@163.com>
Repository: CRAN
Date/Publication: 2024-04-16 14:50:13 UTC

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New package ready4 with initial version 0.1.9
Package: ready4
Title: Implement Modular and Open-Source Health Economic Models
Version: 0.1.9
Description: Programming syntax, a template model module and tools to help maintain a modular and open-source health economic model's project documentation website. These elements are the foundation for a prototype software framework to support replicable and transferable health economic models. The software framework is extended by other R libraries. For detailed documentation about the framework and how to use it visit <https://www.ready4-dev.com/>. For a background to the methodological issues that the framework is attempting to help solve, see Hamilton et al. (2024) <doi:10.48550/arXiv.2310.14138>.
License: GPL-3
URL: https://ready4-dev.github.io/ready4/, https://github.com/ready4-dev/ready4, https://www.ready4-dev.com/
Encoding: UTF-8
Suggests: devtools, Hmisc, knitr, pkgload, readr, readxl, rmarkdown, testthat, usethis, zen4R
VignetteBuilder: knitr
Imports: dataverse, dplyr, gh, kableExtra, lifecycle, magrittr, methods, piggyback, purrr, rlang, rvest, stats, stringi, stringr, tibble, tidyRSS, tidyselect, tools, utils
NeedsCompilation: no
Packaged: 2024-04-15 11:07:09 UTC; mham0053
Author: Matthew Hamilton [aut, cre, cph] , Orygen [cph, fnd], Australian Government Research Training Program [fnd], VicHealth [fnd], Victoria University [fnd]
Maintainer: Matthew Hamilton <matthew.hamilton1@monash.edu>
Repository: CRAN
Date/Publication: 2024-04-16 09:10:02 UTC

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New package yodel with initial version 1.0.0
Package: yodel
Title: A General Bayesian Model Averaging Helper
Version: 1.0.0
Description: Provides helper functions to perform Bayesian model averaging using Markov chain Monte Carlo samples from separate models. Calculates weights and obtains draws from the model-averaged posterior for quantities of interest specified by the user. Weight calculations can be done using marginal likelihoods or log-predictive likelihoods as in Ando, T., & Tsay, R. (2010) <doi:10.1016/j.ijforecast.2009.08.001>.
License: MIT + file LICENSE
URL: https://github.com/rich-payne/yodel
Imports: dplyr (>= 1.0), purrr (>= 0.3), rlang (>= 0.4)
Encoding: UTF-8
Suggests: testthat
NeedsCompilation: no
Packaged: 2024-04-12 19:12:48 UTC; c263386
Author: Richard Payne [aut, cre], Eli Lilly and Company [cph]
Maintainer: Richard Payne <paynestatistics@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-16 08:40:02 UTC

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New package vectorsurvR with initial version 0.1.0
Package: vectorsurvR
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Version: 0.1.0
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: rstudioapi, dplyr, jsonlite, kableExtra, knitr, lubridate, stringr, plotly, ggplot2, httr, tidyr, magrittr, DT
Suggests: testthat (>= 3.0.0), rmarkdown, devtools,
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-04-12 23:39:21 UTC; Christina
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Repository: CRAN
Date/Publication: 2024-04-16 08:40:05 UTC

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New package norMmix with initial version 0.1-1
Package: norMmix
Version: 0.1-1
Title: Direct MLE for Multivariate Normal Mixture Distributions
Description: Multivariate Normal (i.e. Gaussian) Mixture Models (S3) Classes. Fitting models to data using MLE (maximum likelihood estimation) for multivariate normal mixtures via smart parametrization using the LDLt (Cholesky) decomposition. McLachlan, G. and Peel, D. (2000, ISBN:9780471006268) "Finite Mixture Models". Celeux, G. and Govaert, G. (1995) <doi:10.1016/0031-3203(94)00125-6> "Gaussian parsimonious clustering models". Marron, S. and Wand, M. (1992) <doi:10.1214/aos/1176348653> "Exact Mean Integrated Squared Error".
Imports: cluster, MASS, mvtnorm, mclust, sfsmisc
Suggests: nor1mix, Matrix, testthat (>= 2.1.0), knitr, rmarkdown
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-14 22:16:55 UTC; trn
Author: Nicolas Trutmann [aut, cre], Martin Maechler [aut, ths]
Maintainer: Nicolas Trutmann <nicolas.trutmann@gmx.ch>
Repository: CRAN
Date/Publication: 2024-04-16 09:00:02 UTC

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New package cardinalR with initial version 0.1.1
Package: cardinalR
Title: Collection of Data Structures
Version: 0.1.1
Description: A collection of simple simulation datasets designed for generating Nonlinear Dimension Reduction representations techniques such as t-distributed Stochastic Neighbor Embedding, and Uniform Manifold Approximation and Projection. These datasets serve as a valuable resource for understanding the reliability of Nonlinear Dimension Reduction representations in various contexts.
License: MIT + file LICENSE
URL: https://github.com/JayaniLakshika/cardinalR
BugReports: https://github.com/JayaniLakshika/cardinalR/issues
Depends: R (>= 3.5.0)
Imports: purrr, stats
Suggests: knitr, langevitour, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-15 06:22:26 UTC; jpiy0001
Author: Jayani P.G. Lakshika [aut, cre] , Dianne Cook [aut] , Paul Harrison [aut] , Michael Lydeamore [aut] , Thiyanga S. Talagala [aut]
Maintainer: Jayani P.G. Lakshika <jayanilakshika76@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-16 09:00:06 UTC

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New package mapmisc with initial version 2.1.0
Package: mapmisc
Title: Utilities for Producing Maps
Version: 2.1.0
Date: 2024-04-15
Depends: terra, R (>= 3.5.0)
Imports: methods, grDevices, stats, utils, graphics, geosphere
Suggests: RColorBrewer, geonames, classInt, knitr
Enhances: XML, RCurl
Description: Provides a minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections. See Brown (2016) <doi:10.32614/RJ-2016-005>.
License: GPL
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-15 13:42:41 UTC; patrick
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Repository: CRAN
Date/Publication: 2024-04-16 06:20:03 UTC

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New package fastcpd with initial version 0.14.0
Package: fastcpd
Title: Fast Change Point Detection via Sequential Gradient Descent
Version: 0.14.0
Description: Implements fast change point detection algorithm based on the paper "Sequential Gradient Descent and Quasi-Newton's Method for Change-Point Analysis" by Xianyang Zhang, Trisha Dawn <https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is based on dynamic programming with pruning and sequential gradient descent. It is able to detect change points a magnitude faster than the vanilla Pruned Exact Linear Time(PELT). The package includes examples of linear regression, logistic regression, Poisson regression, penalized linear regression data, and whole lot more examples with custom cost function in case the user wants to use their own cost function.
License: GPL (>= 3)
URL: https://fastcpd.xingchi.li, https://github.com/doccstat/fastcpd
BugReports: https://github.com/doccstat/fastcpd/issues
Depends: R (>= 2.10)
Imports: fastglm, forecast, glmnet, Matrix, methods, Rcpp (>= 0.11.0), stats, tseries
Suggests: abind, breakfast, changepoint, cpm, CptNonPar, dplyr, fpop, ggplot2, gridExtra, jointseg, knitr, lubridate, matrixStats, mockthat, mvtnorm, not, numDeriv, RcppClock, reshape2, rmarkdown, segmented, stepR, testthat (>= 3.0.0), VARDetect, wbs, xml2, zoo
LinkingTo: progress, Rcpp, RcppArmadillo, RcppClock, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-15 17:47:21 UTC; doccstat
Author: Xingchi Li [aut, cre, cph] , Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li@stat.tamu.edu>
Repository: CRAN
Date/Publication: 2024-04-16 06:20:09 UTC

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Mon, 15 Apr 2024

New package SpaDES.tools with initial version 2.0.6
Package: SpaDES.tools
Title: Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for developing cellular automata, dynamic raster models, and agent based models in 'SpaDES'. Included are various methods for spatial spreading, spatial agents, GIS operations, random map generation, and others. See '?SpaDES.tools' for an categorized overview of these additional tools. The suggested package 'NLMR' can be installed from the following repository: (<https://PredictiveEcology.r-universe.dev>).
URL: https://spades-tools.predictiveecology.org, https://github.com/PredictiveEcology/SpaDES.tools
Date: 2024-04-15
Version: 2.0.6
Depends: R (>= 4.2)
Imports: backports, checkmate (>= 1.8.2), data.table (>= 1.10.4), fpCompare (>= 0.2.1), graphics, methods, parallel, Rcpp (>= 0.12.12), reproducible (>= 2.0.9), stats, terra
Suggests: animation, bit (>= 1.1-12), covr, DEoptim (>= 2.2-4), dqrng, fastmatch, knitr, NLMR (>= 1.1.1), quickPlot (>= 1.0.2), raster (>= 2.5-8), rmarkdown, sf, sp (>= 1.2-4), testthat (>= 3.0.0), tools, withr
Encoding: UTF-8
Language: en-CA
LinkingTo: Rcpp
License: GPL-3
Additional_repositories: https://predictiveecology.r-universe.dev/
BugReports: https://github.com/PredictiveEcology/SpaDES.tools/issues
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2024-04-15 20:50:20 UTC; achubaty
Author: Eliot J B McIntire [aut] , Alex M Chubaty [aut, cre] , Yong Luo [ctb], Ceres Barros [ctb] , Steve Cumming [ctb], Jean Marchal [ctb], His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Repository: CRAN
Date/Publication: 2024-04-15 21:30:11 UTC

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New package reproducible with initial version 2.0.12
Package: reproducible
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and has deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects, allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().
SystemRequirements: 'unrar' (Linux/macOS) or '7-Zip' (Windows) to work with '.rar' files.
URL: https://reproducible.predictiveecology.org, https://github.com/PredictiveEcology/reproducible
Date: 2024-04-15
Version: 2.0.12
Depends: R (>= 4.1)
Imports: data.table (>= 1.10.4), digest, filelock, fpCompare, fs, lobstr, methods, stats, utils
Suggests: covr, crayon, DBI, future, geodata, glue, googledrive, httr, knitr, parallel, qs, raster (>= 3.5-15), RCurl (>= 1.95-4.8), rlang, rmarkdown, RSQLite, sf, sp (>= 1.4-2), terra (>= 1.7-20), testthat, withr
Encoding: UTF-8
Language: en-CA
License: GPL-3
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/PredictiveEcology/reproducible/issues
ByteCompile: yes
NeedsCompilation: no
Packaged: 2024-04-15 16:06:14 UTC; emcintir
Author: Eliot J B McIntire [aut, cre] , Alex M Chubaty [aut] , Tati Micheletti [ctb] , Ceres Barros [ctb] , Ian Eddy [ctb] , His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Repository: CRAN
Date/Publication: 2024-04-15 19:10:02 UTC

More information about reproducible at CRAN
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New package zendown with initial version 0.0.2
Package: zendown
Title: Access Files from 'Zenodo' Deposits
Version: 0.0.2
Description: Access, download and locally cache files deposited on 'Zenodo' <https://zenodo.org>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: checkmate, cli, curl, fs, glue, httr2, RCurl, tibble, tidyr, tools, utils
Suggests: testthat (>= 3.0.0)
URL: https://rfsaldanha.github.io/zendown/
NeedsCompilation: no
Packaged: 2024-04-14 12:31:31 UTC; raphaelsaldanha
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Repository: CRAN
Date/Publication: 2024-04-15 16:00:02 UTC

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New package recalibratiNN with initial version 0.2.0
Package: recalibratiNN
Title: Quantile Recalibration for Regression Models
Version: 0.2.0
Description: Enables the diagnostics and enhancement of calibration of regression models. It offers both global and local visualization tools to calibration diagnostics and provides one recalibration method : Torres R, Nott DJ, Sisson SA, Rodrigues T, Reis JG, Rodrigues GS (2024) <doi:10.48550/arXiv.2403.05756>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/cmusso86/recalibratiNN, https://cmusso86.github.io/recalibratiNN/
BugReports: https://github.com/cmusso86/recalibratiNN/issues
Imports: stats(>= 4.3.0), dplyr(>= 1.0.0), ggplot2 (>= 3.0.0), purrr(>= 1.0.0), RANN(>= 2.0.0), tidyr(>= 1.0.0), tibble(>= 3.0.0), glue (>= 1.0.0), magrittr(>= 2.0.0), Hmisc (>= 5.0.0), Rdpack
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-13 12:23:41 UTC; carolinamusso
Author: Carolina Musso [aut, cre, cph] , Ricardo Torres [aut, cph] , Joao Reis [aut, cph], Guilherme Rodrigues [aut, ths, cph]
Maintainer: Carolina Musso <cmusso86@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-15 15:50:02 UTC

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New package qtlDesign with initial version 0.953
Package: qtlDesign
Title: Design of QTL (Quantitative Trait Locus) Experiments
Version: 0.953
Date: 2024-04-12
Description: Design of QTL (quantitative trait locus) experiments involves choosing which strains to cross, the type of cross, genotyping strategies, phenotyping strategies, and the number of progeny to raise and phenotype. This package provides tools to help make such choices. Sen and others (2007) <doi:10.1007/s00335-006-0090-y>.
Maintainer: Saunak Sen <sen@uthsc.edu>
Author: Saunak Sen [aut, cre], Jaya Satagopan [ctb], Karl Broman [ctb], Gary Churchill [ctb], Brian Yandell [ctb]
License: GPL-3
URL: http://www.senresearch.org
Suggests: qtl
NeedsCompilation: no
Packaged: 2024-04-13 14:45:27 UTC; sen
Repository: CRAN
Date/Publication: 2024-04-15 15:50:05 UTC

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New package bartMan with initial version 0.1.0
Package: bartMan
Title: Create Visualisations for BART Models
Version: 0.1.0
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
License: GPL (>= 2)
Imports: colorspace, cowplot, DendSer, dplyr, ggiraph, ggnewscale, ggplot2, ggraph, grid, grDevices, gtable, igraph, patchwork, purrr, rlang, rrapply, scales, stats, tidybayes, tidygraph, tidyr, tidytreatment, utils, tibble, BART, bartMachine, dbarts, rJava, cli
Suggests: ROCR, ggridges, ggforce, lvplot
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-13 14:42:50 UTC; alaninglis
Author: Alan Inglis [aut, cre], Andrew Parnell [aut], Catherine Hurley [aut], Claus Wilke [ctb]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-04-15 15:40:07 UTC

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New package phonfieldwork with initial version 0.0.13
Package: phonfieldwork
Title: Linguistic Phonetic Fieldwork Tools
Version: 0.0.13
Depends: R (>= 3.5.0)
Imports: tuneR, phonTools, grDevices, utils, graphics, rmarkdown, xml2, readr, tools, mime
Description: There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2020 <https://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity', subtitles '.srt', and 'FLEx' flextext). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). 'phonfieldwork' provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with ot [...truncated...]
License: GPL (>= 2)
SystemRequirements: pandoc (>= 1.14) - http://pandoc.org
URL: https://CRAN.R-project.org/package=phonfieldwork, https://docs.ropensci.org/phonfieldwork/
BugReports: https://github.com/ropensci/phonfieldwork/issues
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, tidyr, dplyr, DT, lingtypology, testthat, readxl
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-15 04:08:49 UTC; agricolamz
Author: George Moroz [aut, cre] , Jonathan Keane [rev] , Niko Partanen [rev] , Valeria Buntiakova [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-15 13:20:02 UTC

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Sun, 14 Apr 2024

New package longreadvqs with initial version 0.1.2
Package: longreadvqs
Title: Viral Quasispecies Comparison from Long-Read Sequencing Data
Version: 0.1.2
Description: Performs variety of viral quasispecies diversity analyses [see Gregori et al. (2016) <doi:10.1016/j.virol.2016.03.017>] based on long-read sequence alignment. Main functions include 1) sequencing error minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
License: GPL-3
URL: https://github.com/NakarinP/longreadvqs
BugReports: https://github.com/NakarinP/longreadvqs/issues
Encoding: UTF-8
Imports: ape, Biostrings, cowplot, dplyr, ggplot2, ggpubr, grDevices, magrittr, plyr, purrr, QSutils, RColorBrewer, reshape2, scales, seqinr, stats, stringdist, stringr, tibble, tidyr
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-12 18:53:33 UTC; nakarinpamornchainavakul
Author: Nakarin Pamornchainavakul [aut, cre]
Maintainer: Nakarin Pamornchainavakul <pamornakarin@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-14 19:20:02 UTC

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New package ElevDistr with initial version 1.0.8
Package: ElevDistr
Title: Calculate the Distance to the Nearest Local Treeline
Version: 1.0.8
Description: A method to calculate the distance to the climatic tree line for large data sets of coordinates (World Geodetic System 1984) with geographical uncertainty. The default thresholds and the treeline definition is based on Paulsen and Körner (2014) <doi:10.1007/s00035-014-0124-0>, users are free to decide what climate layers they would like to use.
License: MIT + file LICENSE
URL: https://github.com/LivioBaetscher/ElevDistr
BugReports: https://github.com/LivioBaetscher/ElevDistr/issues
Depends: R (>= 3.5.0)
Imports: ggmap, ggplot2, RANN, terra
Suggests: knitr, rgbif, rmarkdown, testthat (>= 3.0.0), tidyverse
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-12 16:30:12 UTC; Livio
Author: Livio Baetscher [aut, cre] , Jurriaan M. de Vos [aut]
Maintainer: Livio Baetscher <livio_999@hotmail.com>
Repository: CRAN
Date/Publication: 2024-04-14 19:10:02 UTC

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Sat, 13 Apr 2024

New package optimall with initial version 1.1.0
Package: optimall
Title: Allocate Samples Among Strata
Version: 1.1.0
Maintainer: Jasper Yang <jbyang@uw.edu>
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits.
License: GPL-3
URL: https://github.com/yangjasp/optimall
BugReports: https://github.com/yangjasp/optimall/issues
Depends: R (>= 3.5.0)
Imports: dplyr (>= 1.0.5), glue (>= 1.4.0), magrittr (>= 2.0.0), methods (>= 4.0.0), rlang (>= 0.2.2), stats (>= 4.0.2), tibble (>= 1.4.2), utils (>= 3.5.0),
Suggests: bslib (>= 0.2.4), DiagrammeR (>= 1.0.0), DT (>= 0.15), datasets, globals (>= 0.12), knitr (>= 1.28), rmarkdown (>= 2.7), shiny (>= 1.6.0), shinytest (>= 1.4.0), survey (>= 4.0), testthat (>= 3.0.2), webshot (>= 0.5)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-12 18:28:50 UTC; jasper
Author: Jasper Yang [aut, cre], Pamela Shaw [aut], Bryan Shepherd [ctb], Thomas Lumley [ctb], Gustavo Amorim [rev]
Repository: CRAN
Date/Publication: 2024-04-13 07:50:02 UTC

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Fri, 12 Apr 2024

New package konfound with initial version 0.5.1
Package: konfound
Title: Quantify the Robustness of Causal Inferences
Version: 0.5.1
Description: Statistical methods that quantify the conditions necessary to alter inferences, also known as sensitivity analysis, are becoming increasingly important to a variety of quantitative sciences. A series of recent works, including Frank (2000) <doi:10.1177/0049124100029002001> and Frank et al. (2013) <doi:10.3102/0162373713493129> extend previous sensitivity analyses by considering the characteristics of omitted variables or unobserved cases that would change an inference if such variables or cases were observed. These analyses generate statements such as "an omitted variable would have to be correlated at xx with the predictor of interest (e.g., treatment) and outcome to invalidate an inference of a treatment effect". Or "one would have to replace pp percent of the observed data with null hypothesis cases to invalidate the inference". We implement these recent developments of sensitivity analysis and provide modules to calculate these two robustness indices and generate such [...truncated...]
License: MIT + file LICENSE
URL: https://github.com/konfound-project/konfound
BugReports: https://github.com/konfound-project/konfound/issues
Depends: R (>= 2.10)
Imports: broom, broom.mixed, crayon, dplyr, ggplot2, lavaan, purrr, rlang, tidyr, lme4 (>= 1.1-35.1), tibble, ggrepel, pbkrtest
Suggests: covr, devtools, forcats, knitr, rmarkdown, mice, roxygen2, testthat, Matrix (>= 1.6-2)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-12 19:45:19 UTC; jrosenb8
Author: Joshua M Rosenberg [aut, cre], Ran Xu [ctb], Qinyun Lin [ctb], Spiro Maroulis [ctb], Sarah Narvaiz [ctb], Kenneth A Frank [ctb], Wei Wang [ctb]
Maintainer: Joshua M Rosenberg <jmrosen48@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-12 21:10:09 UTC

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New package zendown with initial version 0.0.1
Package: zendown
Title: Access Files from 'Zenodo' Deposits
Version: 0.0.1
Description: Access, download and locally cache files deposited on 'Zenodo' <https://zenodo.org>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: checkmate, cli, curl, fs, glue, httr2, rappdirs, RCurl, tibble, tidyr, tools, utils
Suggests: testthat (>= 3.0.0)
URL: https://rfsaldanha.github.io/zendown/
NeedsCompilation: no
Packaged: 2024-04-12 14:28:30 UTC; raphaelsaldanha
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Repository: CRAN
Date/Publication: 2024-04-12 15:30:02 UTC

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New package Toothnroll with initial version 1.11
Package: Toothnroll
Title: Dental Tissues Landmarking Measuring and Mapping
Version: 1.11
Description: Two- and three-dimensional morphometric maps of enamel and dentine thickness and multivariate analysis. Volume calculation of dental materials. Principal component analysis of thickness maps with associated morphometric map variations.
Imports: Arothron (>= 1.0), alphashape3d (>= 1.0), compositions(>= 2.0), morphomap (>= 1.0), stringr (>= 1.0), vegan,lattice (>= 0.2), mgcv (>= 1.8), Rvcg (>= 0.18), Morpho (>= 2.0), oce (>= 1.1), rgl (>= 0.1), geometry (>= 0.4.0), colorRamps (>= 2.3), DescTools (>= 0.99), grDevices (>= 3.5), graphics (>= 3.5)
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-12 09:27:42 UTC; anton
Author: Antonio Profico [cre, aut], Mathilde Augoyard [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-04-12 15:20:22 UTC

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New package relcircle with initial version 1.0
Package: relcircle
Title: Draw Regulatory Relationships Between Genes
Version: 1.0
Date: 2024-04-07
Description: According to the order of the loci on the chromosome, the loci can be connected according to the interrelationship between them and classified according to different locus types.
License: GPL (>= 3)
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-04-12 11:17:36 UTC; admin
Author: Ruilin Li [aut, cre]
Maintainer: Ruilin Li <2837471734@qq.com>
Repository: CRAN
Date/Publication: 2024-04-12 15:20:05 UTC

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New package heck with initial version 0.1.0
Package: heck
Title: Highly Performant String Case Converter
Version: 0.1.0
Description: Provides a case conversion between common cases like CamelCase and snake_case. Using the 'rust crate heck' <https://github.com/withoutboats/heck> as the backend for a highly performant case conversion for 'R'.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: Cargo (Rust's package manager), rustc
Suggests: spelling, testthat (>= 3.0.0)
Language: en-US
NeedsCompilation: yes
Packaged: 2024-04-12 09:15:56 UTC; dyfanjones
Author: Josiah Parry [aut] , Dyfan Jones [cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-12 15:20:10 UTC

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New package basksim with initial version 1.0.0
Package: basksim
Title: Simulation-Based Calculation of Basket Trial Operating Characteristics
Version: 1.0.0
Description: Provides a unified syntax for the simulation-based comparison of different single-stage basket trial designs with a binary endpoint and equal sample sizes in all baskets. Methods include the designs by Baumann et al. (2024) <doi:10.48550/arXiv.2309.06988>, Fujikawa et al. (2020) <doi:10.1002/bimj.201800404>, Berry et al. (2020) <doi:10.1177/1740774513497539>, Neuenschwander et al. (2016) <doi:10.1002/pst.1730> and Psioda et al. (2021) <doi:10.1093/biostatistics/kxz014>. For the latter three designs, the functions are mostly wrappers for functions provided by the packages 'bhmbasket' and 'bmabasket'.
License: GPL (>= 3)
Encoding: UTF-8
Imports: arrangements, bhmbasket, bmabasket, doFuture, extraDistr, foreach, HDInterval, progressr
Suggests: covr, testthat (>= 3.0.0)
URL: https://github.com/lbau7/basksim
BugReports: https://github.com/lbau7/basksim/issues
NeedsCompilation: no
Packaged: 2024-04-12 13:08:31 UTC; uy240
Author: Lukas Baumann [aut, cre] , Lukas Sauer [ctb]
Maintainer: Lukas Baumann <baumann@imbi.uni-heidelberg.de>
Repository: CRAN
Date/Publication: 2024-04-12 15:20:14 UTC

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New package avotrex with initial version 1.0.0
Package: avotrex
Version: 1.0.0
Title: A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder
Description: Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.
Encoding: UTF-8
Depends: R (>= 4.0.0)
LazyData: true
Imports: ape, doParallel, doSNOW, dplyr, foreach, parallel, phytools, snow, stringr, tidytree (>= 0.4.6), utils
License: GPL-3
Suggests: testthat, markdown, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-12 14:55:35 UTC; Joe
Author: Joseph Wayman [aut, cre] , Thomas J. Matthews [aut] , Paul Dufour [ctb], Ferran Sayol [ctb]
Maintainer: Joseph Wayman <j.wayman@bham.ac.uk>
Repository: CRAN
Date/Publication: 2024-04-12 15:30:05 UTC

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New package amregtest with initial version 1.0.3
Package: amregtest
Title: Runs Allelematch Regression Tests
Version: 1.0.3
Description: Automates regression testing of package 'allelematch'. Over 2500 tests covers all functions in 'allelematch', reproduces the examples from the documentation and includes negative tests. The implementation is based on 'testthat'.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: allelematch, digest, remotes, testthat (>= 3.0.0), utils, withr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-12 13:58:14 UTC; Torva
Author: Department of Wildlife, Fish and Environmental Studies at Swedish University of Agricultural Sciences [cph], Goeran Spong [cph] , Paul Galpern [ctb] , Torvald Staxler [aut, cre]
Maintainer: Torvald Staxler <torvald.staxler@telia.com>
Repository: CRAN
Date/Publication: 2024-04-12 15:30:09 UTC

More information about amregtest at CRAN
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New package smplot2 with initial version 0.1.0
Package: smplot2
Title: Creating and Annotating a Composite Plot in 'ggplot2'
Version: 0.1.0
Maintainer: Seung Hyun (Sam) Min <seung.min@mail.mcgill.ca>
Description: Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Encoding: UTF-8
License: GPL-2
Imports: ggplot2, ggpubr, cowplot, tibble, dplyr, gghalves, magrittr, utils, pwr, sdamr, stats, Hmisc, ggstance, zoo, patchwork
URL: https://smin95.github.io/dataviz/
BugReports: https://github.com/smin95/smplot2/issues
NeedsCompilation: no
Packaged: 2024-04-12 00:28:04 UTC; XPS
Author: Seung Hyun Min [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-12 09:00:02 UTC

More information about smplot2 at CRAN
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New package DIFM with initial version 1.0
Package: DIFM
Title: Dynamic ICAR Spatiotemporal Factor Models
Version: 1.0
Date: 2024-04-07
Description: Bayesian factor models are effective tools for dimension reduction. This is especially applicable to multivariate large-scale datasets. It allows researchers to understand the latent factors of the data which are the linear or non-linear combination of the variables. Dynamic Intrinsic Conditional Autocorrelative Priors (ICAR) Spatiotemporal Factor Models 'DIFM' package provides function to run Markov Chain Monte Carlo (MCMC), evaluation methods and visual plots from Shin and Ferreira (2023)<doi:10.1016/j.spasta.2023.100763>. Our method is a class of Bayesian factor model which can account for spatial and temporal correlations. By incorporating these correlations, the model can capture specific behaviors and provide predictions.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.10), Matrix, LaplacesDemon, spdep, gridExtra, sp
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-11 21:02:56 UTC; Hwasoo Shin
Author: Hwasoo Shin [aut, cre], Marco Ferreira [aut]
Maintainer: Hwasoo Shin <shwasoo@vt.edu>
Repository: CRAN
Date/Publication: 2024-04-12 08:50:03 UTC

More information about DIFM at CRAN
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Thu, 11 Apr 2024

New package mapmisc with initial version 2.0.9
Package: mapmisc
Title: Utilities for Producing Maps
Version: 2.0.9
Date: 2024-04-10
Depends: terra, R (>= 3.5.0)
Imports: methods, grDevices, stats, utils, graphics, geosphere
Suggests: RColorBrewer, geonames, classInt, knitr
Enhances: XML, RCurl
Description: Provides a minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections. See Brown (2016) <doi:10.32614/RJ-2016-005>.
License: GPL
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-11 14:23:51 UTC; patrick
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Repository: CRAN
Date/Publication: 2024-04-11 20:30:02 UTC

More information about mapmisc at CRAN
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New package AcceptReject with initial version 0.1.0
Package: AcceptReject
Title: Acceptance-Rejection Method for Generating Pseudo-Random Observations
Version: 0.1.0
Description: Provides a function that implements the acceptance-rejection method in an optimized manner to generate pseudo-random observations for discrete or continuous random variables. The function is optimized to work in parallel on Unix-based operating systems and performs well on Windows systems. The acceptance-rejection method implemented optimizes the probability of generating observations from the desired random variable, by simply providing the probability function or probability density function, in the discrete and continuous cases, respectively. Implementation is based on references CASELLA, George at al. (2004) <https://www.jstor.org/stable/4356322>, NEAL, Radford M. (2003) <https://www.jstor.org/stable/3448413> and Bishop, Christopher M. (2006, ISBN: 978-0387310732).
License: GPL (>= 3)
Encoding: UTF-8
URL: https://prdm0.github.io/AcceptReject/
BugReports: https://github.com/prdm0/AcceptReject/issues/
VignetteBuilder: knitr
Imports: cli, ggplot2, glue, lbfgs, numDeriv, pbmcapply, purrr, rlang, scales
Suggests: knitr, rmarkdown, patchwork
NeedsCompilation: no
Packaged: 2024-04-11 13:02:02 UTC; prdm0
Author: Pedro Rafael D. Marinho [aut, cre] , Vera Lucia Damasceno Tomazella [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-11 20:10:02 UTC

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New package sgboost with initial version 0.1.0
Package: sgboost
Title: Sparse-Group Boosting
Version: 0.1.0
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.
Imports: dplyr, mboost, stringr, rlang, tibble, ggplot2, ggforce
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/FabianObster/sgboost
BugReports: https://github.com/FabianObster/sgboost/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-10 20:03:03 UTC; fabia
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>
Repository: CRAN
Date/Publication: 2024-04-11 11:20:02 UTC

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New package SBI with initial version 0.1.0
Package: SBI
Title: Simple Blinding Index for Randomized Controlled Trials
Version: 0.1.0
Description: Computes a simple blinding index for randomized controlled trials introduced in the paper "A simple blinding index for randomized controlled trials" by Petroff, Bacak, Dagres, Dilk and Wachter, which has been submitted for publication.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-11 06:37:21 UTC; mir8629bac
Author: David Petroff [aut, cre, cph], Miroslav Bacak [aut, cph]
Maintainer: David Petroff <david.petroff@zks.uni-leipzig.de>
Repository: CRAN
Date/Publication: 2024-04-11 11:30:03 UTC

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New package alien with initial version 1.0.1
Package: alien
Title: Estimate Invasive and Alien Species (IAS) Introduction Rates
Version: 1.0.1
Description: Easily estimate the introduction rates of alien species given first records data. It specializes in addressing the role of sampling on the pattern of discoveries, thus providing better estimates than using Generalized Linear Models which assume perfect immediate detection of newly introduced species.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, dplyr, ggplot2, HelpersMG, rlang, stats, tidyr
Depends: R (>= 3.4.0)
LazyData: true
Suggests: BH, knitr, purrr, Rcpp, RcppEigen, RcppParallel, rmarkdown, rstan, testthat (>= 3.0.0), tibble
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-11 10:45:40 UTC; eze36
Author: Yehezkel Buba [aut, cre, cph]
Maintainer: Yehezkel Buba <hezibuba@mail.tau.ac.il>
Repository: CRAN
Date/Publication: 2024-04-11 11:50:02 UTC

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Wed, 10 Apr 2024

New package HDXBoxeR with initial version 0.0.1
Package: HDXBoxeR
Title: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data
Version: 0.0.1
Author: Maria K. Janowska [aut, cre] , Katherine Reiter [ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E. Klevit [ctb]
Maintainer: Maria K. Janowska <mka.janowska@gmail.com>
Description: A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis. It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific), automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework. Additionally, it simplifies data export, generates 'Pymol' scripts, and ensures calculations meet publication standards. 'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides, generating plots, and facilitating comparison between protein states. For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325> and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>.
License: GPL (>= 2)
Imports: dplyr, graphics, grDevices, RColorBrewer, stats, stringr, tidyr, utils, methods, wrapr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-10 18:36:44 UTC; mkaja
Repository: CRAN
Date/Publication: 2024-04-10 20:10:02 UTC

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New package WayFindR with initial version 0.1.2
Package: WayFindR
Version: 0.1.2
Date: 2024-04-09
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).
Depends: R (>= 3.5)
Imports: graphics, utils, XML, igraph
Suggests: knitr, rmarkdown, Polychrome
License: Artistic-2.0
URL: http://oompa.r-forge.r-project.org/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-09 20:36:30 UTC; kevin
Author: Kevin R. Coombes [aut, cre], Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Repository: CRAN
Date/Publication: 2024-04-10 19:50:06 UTC

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New package surveyPrev with initial version 1.0.0
Package: surveyPrev
Title: Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Version: 1.0.0
Description: Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
URL: https://github.com/richardli/surveyPrev
BugReports: https://github.com/richardli/surveyPrev/issues
Depends: R (>= 3.5)
License: GPL (>= 2)
Imports: survey, stats, ggplot2, rdhs, SUMMER, dplyr, labelled, sjlabelled, naniar, raster, sp, spdep, stringr, tidyverse, data.table, sf, matrixStats
Encoding: UTF-8
LazyData: true
Additional_repositories: https://inla.r-inla-download.org/R/testing/
Suggests: INLA, knitr, rmarkdown, R.rsp, kableExtra, geodata, patchwork, tidyr
VignetteBuilder: R.rsp, knitr
NeedsCompilation: no
Packaged: 2024-04-09 17:25:12 UTC; qianyu
Author: Qianyu Dong [cre, aut], Zehang R Li [aut], Yunhan Wu [aut], Andrea Boskovic [aut], Jon Wakefield [aut]
Maintainer: Qianyu Dong <qdong14@ucsc.edu>
Repository: CRAN
Date/Publication: 2024-04-10 19:50:02 UTC

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New package SmoothHazard with initial version 2024.04.10
Package: SmoothHazard
Title: Estimation of Smooth Hazard Models for Interval-Censored Data
Version: 2024.04.10
Description: Estimation of two-state (survival) models and irreversible illness- death models with possibly interval-censored, left-truncated and right-censored data. Proportional intensities regression models can be specified to allow for covariates effects separately for each transition. We use either a parametric approach with Weibull baseline intensities or a semi-parametric approach with M-splines approximation of baseline intensities in order to obtain smooth estimates of the hazard functions. Parameter estimates are obtained by maximum likelihood in the parametric approach and by penalized maximum likelihood in the semi-parametric approach.
Encoding: UTF-8
Copyright: See inst/COPYRIGHTS
Depends: R (>= 1.9.1), prodlim (>= 1.4.9)
Imports: lava (>= 1.4.1), mvtnorm (>= 1.0-3)
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
License: GPL (>= 2)
Packaged: 2024-04-10 14:10:36 UTC; tag
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Author: Celia Touraine [aut], Thomas Alexander Gerds [aut, cre], Pierre Joly [aut] , Cecile Proust-Lima [aut] , Helene Jacqmin-Gadda [aut] , Amadou Diakite [aut] , W.D. Cody [aut] , A.H. Morris [aut] , B.W. Brown [aut] , Robin Genuer [ctb]
Repository: CRAN
Date/Publication: 2024-04-10 20:00:08 UTC

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New package IRR2FPR with initial version 0.1
Package: IRR2FPR
Title: Computing False Positive Rate from Inter-Rater Reliability
Version: 0.1
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Description: Implements a 'Shiny Item Analysis' module and functions for computing false positive rate and other binary classification metrics from inter-rater reliability based on Bartoš & Martinková (2022) <doi:10.48550/arXiv.2207.09101>.
URL: https://github.com/FBartos/IRR2FPR
BugReports: https://github.com/FBartos/IRR2FPR/issues
License: GPL-3
Encoding: UTF-8
Imports: shiny, mvtnorm
NeedsCompilation: no
Packaged: 2024-04-10 08:42:13 UTC; fbart
Author: Frantisek Bartos [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-10 19:50:09 UTC

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New package iNEXT.4steps with initial version 1.0.0
Package: iNEXT.4steps
Title: Four-Step Biodiversity Analysis Based on 'iNEXT'
Version: 1.0.0
Author: Anne Chao [aut, cre], KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
URL: https://sites.google.com/view/chao-lab-website/software/inext-4steps/
Description: Expands 'iNEXT' to include the estimation of sample completeness and evenness. The package provides simple functions to perform the following four-step biodiversity analysis: STEP 1: Assessment of sample completeness profiles. STEP 2a: Analysis of size-based rarefaction and extrapolation sampling curves to determine whether the asymptotic diversity can be accurately estimated. STEP 2b: Comparison of the observed and the estimated asymptotic diversity profiles. STEP 3: Analysis of non-asymptotic coverage-based rarefaction and extrapolation sampling curves. STEP 4: Assessment of evenness profiles. The analyses in STEPs 2a, 2b and STEP 3 are mainly based on the previous 'iNEXT' package. Refer to the 'iNEXT' package for details. This package is mainly focusing on the computation for STEPs 1 and 4. See Chao et al. (2020) <doi:10.1111/1440-1703.12102> for statistical background.
License: GPL (>= 3)
Depends: R (>= 4.0)
Imports: ggplot2, reshape2, dplyr, stats, ggpubr, purrr, iNEXT.3D
Suggests: testthat, knitr, rmarkdown
Encoding: UTF-8
BugReports: https://github.com/KaiHsiangHu/iNEXT.4steps/issues
LazyData: true
VignetteBuilder: knitr
ByteCompile: true
NeedsCompilation: no
Packaged: 2024-04-10 15:07:43 UTC; stat-pc
Repository: CRAN
Date/Publication: 2024-04-10 20:00:05 UTC

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New package FedIRT with initial version 0.1.0
Package: FedIRT
Title: Federated Item Response Theory Models
Version: 0.1.0
Description: Integrate Item Response Theory (IRT) and Federated Learning to estimate traditional IRT models, including the 2-Parameter Logistic (2PL) and the Graded Response Models, with enhanced privacy. It allows for the estimation in a distributed manner without compromising accuracy. A user-friendly 'shiny' application is included. For more details, see Biying Zhou, Feng Ji (2024) "'FedIRT': An R package and 'shiny' app for estimating federated item response theory models" <https://github.com/Feng-Ji-Lab/FedIRT/blob/main/paper/paper.pdf>.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: purrr, pracma, shiny, httr, callr, DT, ggplot2, shinyjs,
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-10 16:50:56 UTC; zby15
Author: Biying Zhou [cre], Feng Ji [aut]
Maintainer: Biying Zhou <zby.zhou@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2024-04-10 20:00:12 UTC

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New package pctax with initial version 0.1.1
Package: pctax
Title: Professional Comprehensive Omics Data Analysis
Version: 0.1.1
Description: Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and professional omics data analysis.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
Imports: pcutils (>= 0.2.5), dplyr, ggplot2 (>= 3.2.0), vegan, magrittr, grDevices, RColorBrewer, ggrepel, reshape2, stats, tibble, utils, ggpubr, ggnewscale, ade4, scales
Suggests: picante, ggpmisc, NST, permute, aplot, pheatmap, MASS, Rtsne, mixOmics, geosphere, phyloseq, phyloseqGraphTest, plotly, umap, Hmisc, minpack.lm, bbmle, snow, foreach, doSNOW, patchwork, tidytree, ggtree, ggtreeExtra, vctrs, zoo, ape, DESeq2, limma, ALDEx2, Mfuzz, edgeR, methods, randomForest, knitr, rmarkdown, MetaNet, jsonlite, prettydoc, clipr, zetadiv, ggforce, readxl
VignetteBuilder: knitr
BugReports: https://github.com/Asa12138/pctax/issues
URL: https://github.com/Asa12138/pctax
ByteCompile: true
NeedsCompilation: no
Packaged: 2024-04-06 15:16:13 UTC; asa
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Repository: CRAN
Date/Publication: 2024-04-10 17:10:05 UTC

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New package gratis with initial version 1.0.7
Package: gratis
Title: Generating Time Series with Diverse and Controllable Characteristics
Version: 1.0.7
Description: Generates synthetic time series based on various univariate time series models including MAR and ARIMA processes. Kang, Y., Hyndman, R.J., Li, F.(2020) <doi:10.1002/sam.11461>.
License: GPL-3
URL: https://github.com/ykang/gratis
BugReports: https://github.com/ykang/gratis/issues/
Depends: R (>= 3.5.0)
Imports: doRNG, dplyr, feasts, fGarch, foreach, forecast (>= 8.16), GA, generics, magrittr, methods, mvtnorm, polynom, purrr, shiny, stats, tibble, tsfeatures, tsibble, utils
Suggests: knitr, rlang, rmarkdown, shinydashboard
VignetteBuilder: knitr
Encoding: UTF-8
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2024-04-08 01:24:01 UTC; fli
Author: Yanfei Kang [aut] , Feng Li [aut, cre] , Rob Hyndman [aut] , Mitchell O'Hara-Wild [ctb] , Bocong Zhao [ctb]
Maintainer: Feng Li <feng.li@cufe.edu.cn>
Date/Publication: 2024-04-10 17:10:20 UTC

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New package BOSO with initial version 1.0.4
Package: BOSO
Title: Bilevel Optimization Selector Operator
Version: 1.0.4
Date: 2024-04-08
Description: A novel feature selection algorithm for linear regression called BOSO (Bilevel Optimization Selector Operator). The main contribution is the use a bilevel optimization problem to select the variables in the training problem that minimize the error in the validation set. Preprint available: [Valcarcel, L. V., San Jose-Eneriz, E., Cendoya, X., Rubio, A., Agirre, X., Prosper, F., & Planes, F. J. (2020). "BOSO: a novel feature selection algorithm for linear regression with high-dimensional data." bioRxiv. <doi:10.1101/2020.11.18.388579>]. In order to run the vignette, it is recommended to install the 'bestsubset' package, using the following command: devtools::install_github(repo="ryantibs/best-subset", subdir="bestsubset"). If you do not have gurobi, run devtools::install_github(repo="lvalcarcel/best-subset", subdir="bestsubset"). Moreover, to install cplexAPI you can check <https://github.com/lvalcarcel/cplexAPI>.
SystemRequirements: IBM ILOG CPLEX (>= 12.1)
Depends: R (>= 4.0)
Imports: Matrix, MASS, methods
Suggests: cplexAPI, testthat, glmnet, knitr, rmarkdown, ggplot2, ggpubr, dplyr, kableExtra, devtools, BiocStyle, bestsubset
License: GPL-3
URL: https://github.com/lvalcarcel/BOSO
BugReports: https://github.com/lvalcarcel/BOSO/issues
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-10 11:28:18 UTC; lvalcarcel
Author: Luis V. Valcarcel [aut, cre, ctb] , Edurne San Jose-Eneriz [aut] , Xabier Cendoya [aut, ctb] , Angel Rubio [aut, ctb] , Xabier Agirre [aut] , Felipe Prosper [aut] , Francisco J. Planes [aut, ctb]
Maintainer: Luis V. Valcarcel <lvalcarcel@alumni.unav.es>
Repository: CRAN
Date/Publication: 2024-04-10 17:10:23 UTC

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New package sparseCov with initial version 0.0.1
Package: sparseCov
Title: Sparse Covariance Estimation Based on Thresholding
Version: 0.0.1
Description: A sparse covariance estimator based on different thresholding operators.
License: GPL (>= 2)
Encoding: UTF-8
Imports: Matrix, methods, mvnfast, Rfast, sparseMVN, stats
URL: https://github.com/chexjiang/sparseCov
NeedsCompilation: no
Packaged: 2024-04-10 11:43:58 UTC; chenxinjiang
Author: Chenxin Jiang [aut, cre]
Maintainer: Chenxin Jiang <cflorajiang@g.ucla.edu>
Repository: CRAN
Date/Publication: 2024-04-10 16:50:02 UTC

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New package ntranova with initial version 0.0.1
Package: ntranova
Title: Two Way Neutrosophic ANOVA
Version: 0.0.1
Description: Dealing with neutrosophic data of the form N=D+I(where N is a Neutrosophic number ,D is the determinant part of the number and I is the indeterminacy part) using the neutrosophic two way anova test keeps the type I error low. This algorithm calculates the fisher statistics when we have a neutrosophic data, also tests two hypothesizes, first is to test differences between treatments, and second is to test differences between sectors. For more information see Miari, Mahmoud; Anan, Mohamad Taher; Zeina, Mohamed Bisher(2022) <https://www.americaspg.com/articleinfo/21/show/1058>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-10 13:06:59 UTC; HP
Author: Mohamad Taher Anan [aut, cre] , Mohamad Bisher Zeina [aut], Shaza Zubeadah [aut], Mahmoud Miari [aut]
Maintainer: Mohamad Taher Anan <mtanan200988@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-10 17:00:02 UTC

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New package quadform with initial version 0.0-1
Package: quadform
Title: Efficient Evaluation of Quadratic Forms
Version: 0.0-1
Depends: R (>= 3.0.1)
Imports: mathjaxr
Suggests: testthat
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Description: A range of quadratic forms are evaluated, using efficient methods. Unnecessary transposes are not performed. Complex values are handled consistently.
License: GPL
URL: https://github.com/RobinHankin/quadform
BugReports: https://github.com/RobinHankin/quadform/issues
NeedsCompilation: no
Packaged: 2024-04-09 18:16:01 UTC; rhankin
Author: Robin K. S. Hankin [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-10 16:00:02 UTC

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New package casebase with initial version 0.10.5
Package: casebase
Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression
Version: 0.10.5
Date: 2024-04-09
Description: Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>, and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.
Depends: R (>= 3.5.0)
Imports: data.table, ggplot2 (>= 3.4.0), methods, mgcv, stats, survival, VGAM
License: MIT + file LICENSE
LazyData: TRUE
Suggests: colorspace, covr, dplyr, eha, glmnet, knitr, lubridate, progress, rmarkdown, splines, testthat (>= 3.0.0), visreg
VignetteBuilder: knitr
URL: https://sahirbhatnagar.com/casebase/
BugReports: https://github.com/sahirbhatnagar/casebase/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-09 21:23:07 UTC; maxturgeon
Author: Sahir Bhatnagar [aut, cre] , Maxime Turgeon [aut] , Jesse Islam [aut] , Olli Saarela [aut] , James Hanley [aut]
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-10 12:00:06 UTC

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Tue, 09 Apr 2024

New package SurrogateRank with initial version 1.0
Package: SurrogateRank
Title: Rank-Based Test to Evaluate a Surrogate Marker
Version: 1.0
Description: Uses a novel rank-based nonparametric approach to evaluate a surrogate marker in a small sample size setting. Details are described in Parast et al (2024) <doi:10.1093/biomtc/ujad035>.
License: GPL
Imports: stats
NeedsCompilation: no
Packaged: 2024-04-09 10:40:03 UTC; parastlm
Author: Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-04-09 16:40:09 UTC

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New package pedMermaid with initial version 1.0.2
Package: pedMermaid
Title: Pedigree Mermaid Syntax
Version: 1.0.2
Description: Generate Mermaid syntax for a pedigree flowchart from a pedigree data frame. Mermaid syntax is commonly used to generate plots, charts, diagrams, and flowcharts. It is a textual syntax for creating reproducible illustrations. This package generates Mermaid syntax from a pedigree data frame to visualize a pedigree flowchart. The Mermaid syntax can be embedded in a Markdown or R Markdown file, or viewed on Mermaid editors and renderers. Links' shape, style, and orientation can be customized via function arguments, and nodes' shapes and styles can be customized via optional columns in the pedigree data frame.
License: GPL (>= 3)
Encoding: UTF-8
Imports: grDevices, stats
Suggests: DiagrammeR, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/nilforooshan/pedMermaid
BugReports: https://github.com/nilforooshan/pedMermaid/issues
NeedsCompilation: no
Packaged: 2024-04-09 10:53:44 UTC; monil0
Author: Mohammad Ali Nilforooshan [aut, cre]
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-09 16:40:02 UTC

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