CRANberries

Fri, 26 Jul 2024

New package weatherOz with initial version 1.0.0
Package: weatherOz
Title: An API Client for Australian Weather and Climate Data Resources
Version: 1.0.0
Description: Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development ('DPIRD') of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science ('DES'). As well as the Bureau of Meteorology ('BOM') of the Australian government precis and coastal forecasts, agriculture bulletin data, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, providing access to weather station data from the 'DPIRD' weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology ('BOM') data and accessed through 'SILO' (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. 'DPIRD' data are made [...truncated...]
License: GPL (>= 3)
URL: https://github.com/ropensci/weatherOz/, https://docs.ropensci.org/weatherOz/
BugReports: https://github.com/ropensci/weatherOz/issues
Depends: R (>= 4.1.0)
Imports: apsimx, clock, crayon, crul, curl, data.table (>= 1.1.5), foreign, grDevices, jsonlite, knitr, lubridate, magick, methods, sf, stars, stats, terra, utils, xml2
Suggests: covr, dplyr, ggplot2, ggthemes, grid, gridExtra, mailR, mapproj, maps, rmarkdown, roxyglobals, spelling, testthat (>= 3.0.0), usethis, vcr (>= 0.6.0), vdiffr, withr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-22 04:53:09 UTC; dpird-mac
Author: Rodrigo Pires [aut, cre] , Anna Hepworth [aut] , Rebecca O'Leary [aut], Jonathan Carroll [aut] , James Goldie [aut] , Dean Marchiori [aut] , Paul Melloy [aut] , Mark Padgham [aut] , Hugh Parsonage [aut] , Keith Pembleton [ctb] , Maelle Salmon [ctb] ` [...truncated...]
Maintainer: Rodrigo Pires <rodrigo.pires@dpird.wa.gov.au>
Repository: CRAN
Date/Publication: 2024-07-26 19:40:02 UTC

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New package SFPL with initial version 1.0.0
Package: SFPL
Title: Sparse Fused Plackett-Luce
Imports: pracma, gtools
Version: 1.0.0
Maintainer: Sjoerd Hermes <sjoerd.hermes@wur.nl>
Description: Implements the methodological developments found in Hermes, van Heerwaarden, and Behrouzi (2024) <doi:10.48550/arXiv.2308.04325>, and allows for the statistical modeling of multi-group rank data in combination with object variables. The package also allows for the simulation of synthetic multi-group rank data.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.10)
NeedsCompilation: no
Packaged: 2024-07-22 08:58:57 UTC; sjoer
Author: Sjoerd Hermes [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-26 19:50:02 UTC

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New package SampleSizeDiagnostics with initial version 0.1.0
Package: SampleSizeDiagnostics
Title: Choosing Sample Size for Evaluating a Diagnostic Test
Version: 0.1.0
Description: Calculates the sample size needed for evaluating a diagnostic test based on sensitivity, specificity, prevalence, and desired precision. Based on Buderer (1996) <doi:10.1111/j.1553-2712.1996.tb03538.x>.
License: GPL-3
Encoding: UTF-8
Suggests: testthat, roxygen2, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-22 05:46:01 UTC; kamal
Author: Mohamed Kamal [aut, cre]
Maintainer: Mohamed Kamal <mohamedkamalhospital@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-26 19:40:07 UTC

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New package HLAtools with initial version 1.1.1
Package: HLAtools
Title: Toolkit for HLA Immunogenomics
Version: 1.1.1
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Encoding: UTF-8
Imports: DescTools, dplyr, stringr, tibble, utils, xfun, fmsb
Depends: R (>= 3.5.0)
LazyData: true
LazyDataCompression: xz
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: GPL (>= 3)
URL: <https://github.com/sjmack/HLAtools>
NeedsCompilation: no
Packaged: 2024-07-22 05:44:30 UTC; sjmack
Author: Livia Tran [aut], Ryan Nickens [aut], Leamon Crooms IV [aut], Derek Pappas [aut], Vinh Luu [ctb], Josh Bredeweg [ctb], Steven Mack [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-26 19:40:11 UTC

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New package ElectDecomp with initial version 0.0.1-1
Package: ElectDecomp
Title: Decomposition of Seats-to-Votes Distortion in Multimember Elections
Version: 0.0.1-1
Description: Decomposes the seat-to-vote distortion for every party (individual party bias or individual party deviation from proportional representation) into segments that can be attributed to separate causes for the party infra or over-representation: the electoral system effect (separating the mean and the variance effect within it) and the population effect (separating malapportionment and unequal participation effect within it). It works on (single tired) districted electoral systems with any number of seats per district. In addition, the package aggregates the individual party distortion into an index of deviation from proportionality (the Losemore-Hanby index) whose value is also decomposed into segments attributed to the major causes of deviation from proportionality (plus the interactions among them).
License: EPL
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-22 01:03:27 UTC; mariaamparo
Author: Alberto Penades [aut] , Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Repository: CRAN
Date/Publication: 2024-07-26 19:30:02 UTC

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New package AdIsMF with initial version 0.1.0
Package: AdIsMF
Title: Adsorption Isotherm Model Fitting
Version: 0.1.0
Author: Debopam Rakshit [aut, cre], Arkaprava Roy [aut], K. M. Manjaiah [aut], Siba Prasad Datta [aut], Ritwika Das [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>
Description: The Langmuir and Freundlich adsorption isotherms are pivotal in characterizing adsorption processes, essential across various scientific disciplines. Proper interpretation of adsorption isotherms involves robust fitting of data to the models, accurate estimation of parameters, and efficiency evaluation of the models, both in linear and non-linear forms. For researchers and practitioners in the fields of chemistry, environmental science, soil science, and engineering, a comprehensive package that satisfies all these requirements would be ideal for accurate and efficient analysis of adsorption data, precise model selection and validation for rigorous scientific inquiry and real-world applications. Details can be found in Langmuir (1918) <doi:10.1021/ja02242a004> and Giles (1973) <doi:10.1111/j.1478-4408.1973.tb03158.x>.
Encoding: UTF-8
License: GPL-3
Imports: AICcmodavg, ggplot2, nls2, stats
NeedsCompilation: no
Packaged: 2024-07-22 10:51:29 UTC; Debopam
Repository: CRAN
Date/Publication: 2024-07-26 20:00:06 UTC

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New package MicroSEC with initial version 2.1.3
Package: MicroSEC
Title: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples
Version: 2.1.3
Maintainer: Masachika Ikegami <ikegamitky@gmail.com>
Description: Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded samples and have many sequencing errors. We found that the majority of these errors are detected in chimeric read caused by single-strand DNA with micro-homology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in formalin-fixed and paraffin-embedded samples without over-eliminating the true mutations detected in fresh frozen samples.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Depends: R (>= 3.5.0)
LazyData: true
Imports: stringr, dplyr, Biostrings, Rsamtools, GenomeInfoDb, BiocGenerics
Suggests: BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
VignetteBuilder: knitr
URL: https://github.com/MANO-B/MicroSEC/
BugReports: https://github.com/MANO-B/MicroSEC/issues
NeedsCompilation: no
Packaged: 2024-07-26 10:14:23 UTC; ikegami
Author: Masachika Ikegami [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-26 15:00:06 UTC

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New package quickcode with initial version 0.9.1
Package: quickcode
Title: Quick and Essential 'R' Tricks for Better Scripts
Version: 0.9.1
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
License: MIT + file LICENSE
URL: https://quickcode.obi.obianom.com
BugReports: https://github.com/oobianom/quickcode
Depends: R (> 3.6)
Imports: utils, grDevices, stats, rstudioapi, tools, Polychrome, fitdistrplus
Suggests: rmarkdown, knitr, qpdf, testthat
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2024-07-25 13:43:14 UTC; in198
Author: Obinna Obianom [aut, cre], Brice Richard [aut]
Repository: CRAN
Date/Publication: 2024-07-26 12:40:02 UTC

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New package kissmig with initial version 1.0-5
Package: kissmig
Title: a Keep It Simple Species Migration Model
Version: 1.0-5
Date: 2024-07-23
Depends: R (>= 3.5.0), raster, methods
Author: Michael P. Nobis [cre, aut], Signe Normand [ctb]
Maintainer: Michael P. Nobis <michael.nobis@wsl.ch>
Description: Simulating species migration and range dynamics under stable or changing environmental conditions based on a simple, raster-based, deterministic or stochastic migration model. Kissmig runs on binary or quantitative suitability maps, which are pre-calculated with niche-based habitat suitability models (also called ecological niche models (ENMs) or species distribution models (SDMs)). Nobis & Normand (2014), <doi:10.1111/ecog.00930>.
License: GPL (>= 3)
URL: https://purl.oclc.org/wsl/kissmig
Encoding: UTF-8
LazyData: true
Imports: Rcpp
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-07-23 15:26:45 UTC; work
Repository: CRAN
Date/Publication: 2024-07-26 09:20:06 UTC

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Thu, 25 Jul 2024

New package NPRED with initial version 1.1.0
Package: NPRED
Title: Predictor Identifier: Nonparametric Prediction
Version: 1.1.0
Author: Ashish Sharma [aut] , Raj Mehrotra [aut], Sanjeev Jha [aut], Jingwan Li [aut], Ze Jiang [aut, cre]
Maintainer: Ze Jiang <ze.jiang@unsw.edu.au>
Description: Partial informational correlation (PIC) is used to identify the meaningful predictors to the response from a large set of potential predictors. Details of methodologies used in the package can be found in Sharma, A., Mehrotra, R. (2014). <doi:10.1002/2013WR013845>, Sharma, A., Mehrotra, R., Li, J., & Jha, S. (2016). <doi:10.1016/j.envsoft.2016.05.021>, and Mehrotra, R., & Sharma, A. (2006). <doi:10.1016/j.advwatres.2005.08.007>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
URL: https://github.com/zejiang-unsw/NPRED#readme
BugReports: https://github.com/zejiang-unsw/NPRED/issues
Imports: stats
Suggests: zoo, SPEI, WASP, knitr, ggplot2, synthesis, testthat, bookdown, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-25 00:31:24 UTC; z5154277
Repository: CRAN
Date/Publication: 2024-07-25 08:50:01 UTC

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Mon, 22 Jul 2024

New package trud with initial version 0.1.0
Package: trud
Title: Query the 'NHS TRUD API'
Version: 0.1.0
Description: A convenient R interface to the 'National Health Service (NHS) Technology Reference Update Distribution (TRUD) API'. Retrieve available releases for items that you are subscribed to and download these with ease. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, dplyr, httr2, magrittr, purrr, rlang, rvest, stringr, tibble, tidyselect
URL: https://rmgpanw.github.io/trud/, https://github.com/rmgpanw/trud
BugReports: https://github.com/rmgpanw/trud/issues
Suggests: testthat (>= 3.0.0), withr
NeedsCompilation: no
Packaged: 2024-07-21 14:30:14 UTC; alasdair
Author: Alasdair Warwick [aut, cre, cph] , Robert Luben [aut] , Abraham Olvera-Barrios [aut] , Chuin Ying Ung [aut]
Maintainer: Alasdair Warwick <alasdair.warwick.19@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2024-07-23 00:20:02 UTC

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New package tenm with initial version 0.5.1
Package: tenm
Version: 0.5.1
Title: Temporal Ecological Niche Models
Description: Implements methods and functions to calibrate time-specific niche models (multi-temporal calibration), letting users execute a strict calibration and selection process of niche models based on ellipsoids, as well as functions to project the potential distribution in the present and in global change scenarios.The 'tenm' package has functions to recover information that may be lost or overlooked while applying a data curation protocol. This curation involves preserving occurrences that may appear spatially redundant (occurring in the same pixel) but originate from different time periods. A novel aspect of this package is that it might reconstruct the fundamental niche more accurately than mono-calibrated approaches. The theoretical background of the package can be found in Peterson et al. (2011)<doi:10.5860/CHOICE.49-6266>.
License: GPL-3
URL: https://luismurao.github.io/tenm/
BugReports: https://github.com/luismurao/tenm/issues
Imports: MASS, terra (> 1.7.5), sf, purrr, dplyr, stringr, rgl (> 1.2), future, tidyr, furrr, lubridate, methods
Encoding: UTF-8
Depends: R (>= 4.1)
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-21 15:50:20 UTC; luis.osorio
Author: Luis Osorio-Olvera [aut, cre] , Miguel Hernandez [aut] , Rusby G. Contreras-Diaz [aut] , Xavier Chiappa-Carrara [aut] , Fernanda Rosales-Ramos [aut] , Mariana Munguia-Carrara [aut] , Oliver Lopez-Corona [aut] , Townsend Peterson [ctb] , Jorge Soberon [...truncated...]
Maintainer: Luis Osorio-Olvera <luismurao@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-23 00:30:01 UTC

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New package StuteTest with initial version 1.0.2
Package: StuteTest
Title: Stute (1997) Linearity Test
Version: 1.0.2
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Description: Non-parametric test, originally proposed by Stute (1997) <https://www.jstor.org/stable/2242560>, that the expectation of a dependent variable Y given an independent variable D is linear in D.
License: MIT + file LICENSE
VignetteBuilder: R.rsp
Imports: Rcpp (>= 1.0.12), dplyr, plm, rnames, stats
LinkingTo: Rcpp, RcppArmadillo
Author: Diego Ciccia [aut, cre], Felix Knau [aut], Doulo Sow [aut], Clement de Chaisemartin [aut], Xavier D'Haultfoeuille [aut]
Encoding: UTF-8
Suggests: R.rsp, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-07-21 11:15:23 UTC; 39380
Repository: CRAN
Date/Publication: 2024-07-23 00:20:13 UTC

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New package pastboon with initial version 0.1.0
Package: pastboon
Title: Simulation of Parameterized Stochastic Boolean Networks
Version: 0.1.0
Description: Applying stochastic noise to Boolean networks is a useful approach for representing the effects of various perturbing stimuli on complex systems. A number of methods have been developed to control noise effects on Boolean networks using parameters integrated into the update rules. This package provides functions to examine three such methods: BNp (Boolean network with perturbations), described by Trairatphisan et al. (2013) <doi:10.1186/1478-811X-11-46>, SDDS (stochastic discrete dynamical systems), proposed by Murrugarra et al. (2012) <doi:10.1186/1687-4153-2012-5>, and PEW (Boolean network with probabilistic edge weights), presented by Deritei et al. (2022) <doi:10.1371/journal.pcbi.1010536>. This package includes source code derived from the 'BoolNet' package, which is licensed under the Artistic License 2.0.
Author: Mohammad Taheri-Ledari [aut, cre, cph] , Kaveh Kavousi [ctb] , Sayed-Amir Marashi [ctb] , Authors of BoolNet [ctb] , Troy D. Hanson [ctb]
Maintainer: Mohammad Taheri-Ledari <mo.taheri@ut.ac.ir>
Depends: R (>= 3.5.0)
Suggests: BoolNet
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
BugReports: https://github.com/taherimo/pastboon/issues
Packaged: 2024-07-21 15:04:32 UTC; taheri
Repository: CRAN
Date/Publication: 2024-07-23 00:30:06 UTC

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New package bsvarSIGNs with initial version 1.0
Package: bsvarSIGNs
Title: Bayesian SVARs with Sign, Zero, and Narrative Restrictions
Version: 1.0
Date: 2024-07-19
Maintainer: Xiaolei Wang <adamwang15@gmail.com>
Description: Implements state-of-the-art algorithms for the Bayesian analysis of Structural Vector Autoregressions (SVARs) identified by sign, zero, and narrative restrictions. The core model is based on a flexible Vector Autoregression with estimated hyper-parameters of the Minnesota prior and the dummy observation priors as in Giannone, Lenza, Primiceri (2015) <doi:10.1162/REST_a_00483>. The sign restrictions are implemented employing the methods proposed by Rubio-Ramírez, Waggoner & Zha (2010) <doi:10.1111/j.1467-937X.2009.00578.x>, while identification through sign and zero restrictions follows the approach developed by Arias, Rubio-Ramírez, & Waggoner (2018) <doi:10.3982/ECTA14468>. Furthermore, our tool provides algorithms for identification via sign and narrative restrictions, in line with the methods introduced by Antolín-Díaz and Rubio-Ramírez (2018) <doi:10.1257/aer.20161852>. Users can also estimate a model with sign, zero, and narrative restrictions impos [...truncated...]
License: GPL (>= 3)
Imports: Rcpp (>= 1.0.12), RcppProgress, R6
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, bsvars
Depends: R (>= 2.10), RcppArmadillo, bsvars
Suggests: tinytest
URL: https://bsvars.github.io/bsvarSIGNs/
BugReports: https://github.com/bsvars/bsvarSIGNs/issues
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2024-07-21 12:17:36 UTC; xiaoleiwang
Author: Xiaolei Wang [aut, cre] , Tomasz Wozniak [aut]
Repository: CRAN
Date/Publication: 2024-07-23 00:20:05 UTC

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New package aka with initial version 0.1.0
Package: aka
Title: Define Aliases for R Expressions
Version: 0.1.0
Description: Create aliases for other R names or arbitrarily complex R expressions. Accessing the alias acts as-if the aliased expression were invoked instead, and continuously reflects the current value of that expression: updates to the original expression will be reflected in the alias; and updates to the alias will automatically be reflected in the original expression.
URL: https://klmr.me/aka/, https://github.com/klmr/aka
BugReports: https://github.com/klmr/aka/issues
Suggests: testthat
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-21 14:16:09 UTC; konrad
Author: Konrad Rudolph [cre, aut]
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-23 00:20:09 UTC

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New package precommit with initial version 0.4.3
Package: precommit
Title: Pre-Commit Hooks
Version: 0.4.3
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Description: Useful git hooks for R building on top of the multi-language framework 'pre-commit' for hook management. This package provides git hooks for common tasks like formatting files with 'styler' or spell checking as well as wrapper functions to access the 'pre-commit' executable.
License: GPL-3
URL: https://lorenzwalthert.github.io/precommit/, https://github.com/lorenzwalthert/precommit
Imports: cli, fs, here, magrittr, purrr, R.cache, rlang, rprojroot, withr, yaml
Suggests: desc, docopt (>= 0.7.1), git2r, glue, knitr, lintr, pkgload, pkgdown, reticulate (>= 1.16), rmarkdown, roxygen2, rstudioapi, spelling, styler, testthat (>= 2.1.0), tibble, usethis (>= 2.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
SystemRequirements: git
NeedsCompilation: no
Packaged: 2024-07-22 13:56:23 UTC; lorenz
Repository: CRAN
Date/Publication: 2024-07-22 22:20:05 UTC

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New package ssdGSA with initial version 0.1.0
Package: ssdGSA
Title: Single Sample Directional Gene Set Analysis
Version: 0.1.0
Description: A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: GSVA, dplyr, purrr, stringr, tibble, vctrs, clusterProfiler, stats, org.Hs.eg.db, tidyselect, utils
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-07-19 17:51:55 UTC; QIANQ09
Author: Xingpeng Li [aut, cre], Qi Qian [aut]
Maintainer: Xingpeng Li <xingpeng.li@pfizer.com>
Repository: CRAN
Date/Publication: 2024-07-22 17:30:02 UTC

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Sun, 21 Jul 2024

New package serocalculator with initial version 1.0.3
Package: serocalculator
Title: Estimating Infection Rates from Serological Data
Version: 1.0.3
Description: Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous 'seroincidence' package. Methods originally published in Simonsen et al. (2009) <doi:10.1002/sim.3592> and Teunis et al. (2012) <doi:10.1002/sim.5322>, and further developed in subsequent publications by de Graaf et al. (2014) <doi:10.1016/j.epidem.2014.08.002>, Teunis et al. (2016) <doi:10.1016/j.epidem.2016.04.001>, and Teunis et al. (2020) <doi:10.1002/sim.8578>.
Depends: R (>= 4.1.0)
License: GPL-3
Imports: doParallel, dplyr (>= 1.1.1), foreach, ggplot2, ggpubr, lifecycle, magrittr, mixtools, Rcpp, rlang, rngtools, scales, stats, tibble, tidyr, utils, cli
Suggests: parallel, knitr, rmarkdown, tidyverse, fs, testthat (>= 3.0.0), readr, bookdown, ggbeeswarm, DT
Encoding: UTF-8
URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/
NeedsCompilation: yes
LinkingTo: Rcpp
Language: en-US
Packaged: 2024-07-18 18:59:57 UTC; kwlai
Author: Peter Teunis [aut, cph] , Kristina Lai [aut, cre], Chris Orwa [aut], Kristen Aiemjoy [aut], Douglas Ezra Morrison [aut]
Maintainer: Kristina Lai <kwlai@ucdavis.edu>
Repository: CRAN
Date/Publication: 2024-07-21 15:40:02 UTC

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New package tetRys with initial version 1.0
Package: tetRys
Title: Game of 'tetRys'
Version: 1.0
Date: 2024-07-19
Description: A game inspired by 'Tetris'. Opens a plot window device and starts a game of 'tetRys' in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.
Depends: R (>= 3.5.0)
Imports: tcltk, grid, audio
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-19 05:06:51 UTC; ccroo
Author: Carsten Croonenbroeck [aut, cre]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Repository: CRAN
Date/Publication: 2024-07-21 11:10:02 UTC

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New package centr with initial version 0.1.0
Package: centr
Title: Weighted and Unweighted Spatial Centers
Version: 0.1.0
Description: Generate mean and median weighted or unweighted spatial centers. Functions are analogous to their identically named counterparts within 'ArcGIS Pro'. Median center methodology based off of Kuhn and Kuenne (1962) <doi:10.1111/j.1467-9787.1962.tb00902.x>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: sf
URL: https://ryanzomorrodi.github.io/centr/, https://github.com/ryanzomorrodi/centR
Suggests: testthat (>= 3.0.0)
BugReports: https://github.com/ryanzomorrodi/centR/issues
NeedsCompilation: no
Packaged: 2024-07-19 13:33:06 UTC; user
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Repository: CRAN
Date/Publication: 2024-07-21 11:20:02 UTC

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New package ResultModelManager with initial version 0.5.9
Package: ResultModelManager
Title: Result Model Manager
Version: 0.5.9
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.
URL: https://github.com/OHDSI/ResultModelManager
BugReports: https://github.com/OHDSI/ResultModelManager/issues
License: Apache License (== 2.0)
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 4.1.0), R6, DatabaseConnector (>= 6.0.0)
Imports: SqlRender, ParallelLogger, checkmate, DBI, pool, readr, zip, dplyr, dbplyr, rlang, lubridate, fastmap, withr
Suggests: testthat (>= 3.0.0), RSQLite, duckdb, RPostgres, knitr, rmarkdown, keyring, devtools, pkgdown, remotes, styler, Andromeda
NeedsCompilation: no
Packaged: 2024-07-18 23:15:45 UTC; jgilber2
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Repository: CRAN
Date/Publication: 2024-07-21 11:00:07 UTC

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New package minimapR with initial version 0.0.1.0
Package: minimapR
Title: Wrapper for 'minimap2'
Version: 0.0.1.0
Date: 2024-07-11
Maintainer: Jake Reed <hreed.ga@gmail.com>
Description: Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <me@liheng.org>. *SPECIAL NOTES 1. Examples can only be run from 'GitHub' installation. 2. If using a Windows operating system, installation of the 'MSYS2' Linux emulator is required. 3. If using a Mac operating system, installation of 'Homebrew' is required. Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".
License: MIT + file LICENSE
Depends: R (>= 4.0.0), Rsamtools, git2r, pafr
URL: https://github.com/jake-bioinfo/minimapR
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-18 16:26:22 UTC; jake
Author: Jake Reed [aut, cre] , Pradyun Pulipaka [ctb]
Repository: CRAN
Date/Publication: 2024-07-21 10:10:02 UTC

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New package infiltrodiscR with initial version 0.0.5
Package: infiltrodiscR
Title: Minidisc Infiltrometer Data Management
Version: 0.0.5
Description: A set of functions for the modeling of data derived from the Minidisc Infiltrometer device. It calculates cumulative infiltration and square root of time. Also, it calculates the A parameter based on soil physical properties.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: dplyr, tidyr, utils
Suggests: testthat (>= 3.0.0), tibble, tidyverse
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-19 00:08:38 UTC; saryace
Author: Carolina V. Giraldo [aut] , Sara E. Acevedo [aut, cre] , Carlos A. Bonilla [aut]
Maintainer: Sara E. Acevedo <seaceved@uc.cl>
Repository: CRAN
Date/Publication: 2024-07-21 11:00:01 UTC

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New package geotoolsR with initial version 1.2.1
Package: geotoolsR
Title: Tools to Improve the Use of Geostatistic
Version: 1.2.1
Author: Diogo Francisco Rossoni [aut, cre] , Vinicius Basseto Felix [aut], Ricardo Puziol de Oliveira [ctb]
Maintainer: Diogo Francisco Rossoni <dfrossoni@uem.br>
Description: The basic idea of this package is provides some tools to help the researcher to work with geostatistics. Initially, we present a collection of functions that allow the researchers to deal with spatial data using bootstrap procedure. There are five methods available and two ways to display them: bootstrap confidence interval - provides a two-sided bootstrap confidence interval; bootstrap plot - a graphic with the original variogram and each of the B bootstrap variograms.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10), geoR(>= 1.9), tidyr, dplyr, ggplot2
NeedsCompilation: no
Packaged: 2024-06-27 15:11:35 UTC; rpuzi
Repository: CRAN
Date/Publication: 2024-07-21 11:00:04 UTC

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New package COMMA with initial version 1.0.0
Package: COMMA
Title: Correcting Misclassified Mediation Analysis
Version: 1.0.0
Author: Kimberly Webb [aut, cre]
Maintainer: Kimberly Webb <kah343@cornell.edu>
Description: Use three methods to estimate parameters from a mediation analysis with a binary misclassified mediator. These methods correct for the problem of "label switching" using Youden's J criteria. A detailed description of the analysis methods is available in Webb and Wells (2024), "Effect estimation in the presence of a misclassified binary mediator" <doi:10.48550/arXiv.2407.06970>.
Depends: R (>= 4.2.0)
Imports: Matrix (> 1.4-1), turboEM (>= 2021.1)
Suggests: knitr (>= 1.40), kableExtra (>= 1.3.4), ggplot2 (>= 3.5.0), dplyr (>= 1.1.4), markdown (>= 1.13), stats (>= 4.3.1), svglite (>= 2.1.3)
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-18 15:37:41 UTC; kimho
Repository: CRAN
Date/Publication: 2024-07-21 10:10:05 UTC

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New package bodycompref with initial version 2.0.1
Package: bodycompref
Title: Reference Values for CT-Assessed Body Composition
Version: 2.0.1
Maintainer: J. Peter Marquardt <peter@kmarquardt.de>
Description: Get z-scores, percentiles, absolute values, and percent of predicted of a reference cohort. Functionality requires installing the data packages 'adiposerefdata' and 'musclerefdata'. For more information on the underlying research, please visit our website which also includes a graphical interface. The models and underlying data are described in Marquardt JP et al.(planned publication 2025; reserved doi 10.1097/RLI.0000000000001104), "Subcutaneous and Visceral adipose tissue Reference Values from Framingham Heart Study Thoracic and Abdominal CT", *Investigative Radiology* and Tonnesen PE et al. (2023), "Muscle Reference Values from Thoracic and Abdominal CT for Sarcopenia Assessment [column] The Framingham Heart Study", *Investigative Radiology*, <doi:10.1097/RLI.0000000000001012>.
URL: https://bodycomp-metrics.mgh.harvard.edu, https://github.com/p-mq/bodycompref
Depends: R (>= 4.0.0)
Imports: assertthat, gamlss, stats, sae
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), usethis, adiposerefdata, musclerefdata, knitr, rmarkdown
Additional_repositories: https://p-mq.github.io/drat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-18 18:20:28 UTC; petem
Author: J. Peter Marquardt [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-21 10:20:01 UTC

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New package SumcaVer1 with initial version 0.1.0
Package: SumcaVer1
Title: Mean Square Prediction Error Estimation in Small Area Estimation
Version: 0.1.0
Maintainer: Mahmoud Torabi <mahmoud.torabi@umanitoba.ca>
Description: Estimation of mean squared prediction error of a small area predictor is provided. In particular, the recent method of Simple, Unified, Monte-Carlo Assisted approach for the mean squared prediction error estimation of small area predictor is provided. We also provide other existing methods of mean squared prediction error estimation such as jackknife method for the mixed logistic model.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: lme4, psych, stats
NeedsCompilation: no
Packaged: 2024-07-18 14:04:05 UTC; ruwan
Author: Mahmoud Torabi [aut, cre], Jiming Jiang [ctb]
Repository: CRAN
Date/Publication: 2024-07-21 10:00:02 UTC

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New package moc.gapbk with initial version 0.1.1
Package: moc.gapbk
Title: Multi-Objective Clustering Algorithm Guided by a-Priori Biological Knowledge
Version: 0.1.1
Date: 2024-07-15
Author: Jorge Parraga-Alava [aut, cre]
Maintainer: Jorge Parraga-Alava <jorge.parraga@usach.cl>
Description: Implements the Multi-Objective Clustering Algorithm Guided by a-Priori Biological Knowledge (MOC-GaPBK) which was proposed by Parraga-Alava, J. et. al. (2018) <doi:10.1186/s13040-018-0178-4>. It was designed for clustering genes based on co-expression, biological coherence, compactness, and separation criteria. However, its flexible design allows it to be applied to cluster data of various types and domains. The algorithm optimizes object relationships based on two objective functions using cluster quality indexes, incorporating intensification and diversification strategies to enhance the search process.
Depends: R (>= 3.2.5)
License: GPL-2
Encoding: UTF-8
Imports: stats, amap, nsga2R, foreach, parallel, doParallel, utils, doSNOW, doMPI
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-07-18 01:05:00 UTC; UTM
Repository: CRAN
Date/Publication: 2024-07-21 09:10:02 UTC

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New package MLE with initial version 1.0
Package: MLE
Title: Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions
Version: 1.0
Date: 2024-07-18
Author: Michail Tsagris [aut, cre], Sofia Piperaki [aut], Muhammad Imran [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: BGFD, bivpois, Compositional, Directional, geppe, gp, MN, Rfast, Rfast2, skellam
Suggests: mvcauchy
Description: Maximum likelihood estimation of various univariate and multivariate distributions. The list includes univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-07-18 10:16:19 UTC; mtsag
Repository: CRAN
Date/Publication: 2024-07-21 09:40:02 UTC

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New package mimdo with initial version 0.1.0
Package: mimdo
Title: Multivariate Imputation by Mahalanobis Distance Optimization
Version: 0.1.0
Author: Geovert John Labita [aut, cre]
Maintainer: Geovert John Labita <geovertjohn.labita@ustp.edu.ph>
Description: Imputes missing values of an incomplete data matrix by minimizing the Mahalanobis distance of each sample from the overall mean [Labita, GJ.D. and Tubo, B.F. (2024) <doi:10.24412/1932-2321-2024-278-115-123>].
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-18 04:15:05 UTC; pc
Repository: CRAN
Date/Publication: 2024-07-21 09:20:02 UTC

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New package trdist with initial version 1.0.1
Package: trdist
Title: Univariate Proability Distributions with Truncation
Version: 1.0.1
Date: 2024-07-17
Author: Jared Studyvin [aut, cre]
Depends: R (>= 3.6.0)
Imports:
Maintainer: Jared Studyvin <studyvinstat@gmail.com>
Description: Truncation of univariate probability distributions. The probability distribution can come from other packages so long as the function names follow the standard d, p, q, r naming format. Also other univariate probability distributions are included.
License: GNU General Public License
NeedsCompilation: no
Packaged: 2024-07-17 17:15:27 UTC; jaredstudyvin
Repository: CRAN
Date/Publication: 2024-07-21 09:00:02 UTC

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New package ROCsurf with initial version 0.1.0
Package: ROCsurf
Title: ROC Surface Analysis Under the Three-Class Problems
Version: 0.1.0
Maintainer: Ertan Akgenc <statistician.ertan@gmail.com>
Description: Receiver Operating Characteristic (ROC) analysis is performed assuming samples are from the proposed distributions. In addition, the volume under the ROC surface and true positive fractions values are evaluated by ROC surface analysis.
License: GPL-3
URL: https://github.com/ErtanSU/ROCsurf, https://ertansu.github.io/ROCsurf/
BugReports: https://github.com/ErtanSU/ROCsurf/issues
Imports: plotly, pracma, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-07-17 16:12:34 UTC; stati
Author: Ertan Akgenc [cre, aut, cph] , Coskun Kus [aut, ctb]
Repository: CRAN
Date/Publication: 2024-07-21 09:00:05 UTC

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New package poldis with initial version 0.1.1
Package: poldis
Title: Analyse Political Texts
Version: 0.1.1
Date: 2024-07-17
Maintainer: Henrique Sposito <henrique.sposito@graduateinstitute.ch>
Description: Wrangle and annotate different types of political texts. It also introduces Urgency Analysis, a new method for the analysis of urgency in political texts.
URL: http://henriquesposito.com/poldis/
BugReports: https://github.com/henriquesposito/poldis/issues
License: MIT + file LICENSE
Imports: dplyr, stringr, purrr, stringi, quanteda, spacyr, textstem, tidyr, stringdist
Suggests: rmarkdown, testthat, tesseract, quanteda.textstats, keyATM, messydates, pdftools, fmsb, ggplot2, tm
Encoding: UTF-8
LazyData: True
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-07-17 15:47:40 UTC; henriquesposito
Author: Henrique Sposito [cre, aut, ctb] , James Hollway [ctb] , Jael Tan [ctb]
Repository: CRAN
Date/Publication: 2024-07-21 08:50:02 UTC

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New package kpcaIG with initial version 1.0
Package: kpcaIG
Title: Variables Interpretability with Kernel PCA
Version: 1.0
Maintainer: Mitja Briscik <mitja.briscik@math.univ-toulouse.fr>
Description: The kernelized version of principal component analysis (KPCA) has proven to be a valid nonlinear alternative for tackling the nonlinearity of biological sample spaces. However, it poses new challenges in terms of the interpretability of the original variables. 'kpcaIG' aims to provide a tool to select the most relevant variables based on the kernel PCA representation of the data as in Briscik et al. (2023) <doi:10.1186/s12859-023-05404-y>. It also includes functions for 2D and 3D visualization of the original variables (as arrows) into the kernel principal components axes, highlighting the contribution of the most important ones.
License: GPL-3
Encoding: UTF-8
Imports: grDevices, rgl, kernlab, ggplot2, stats, progress, viridis, WallomicsData
NeedsCompilation: no
Packaged: 2024-07-17 15:29:03 UTC; mbriscik
Author: Mitja Briscik [aut, cre], Mohamed Heimida [aut], Sebastien Dejean [aut]
Repository: CRAN
Date/Publication: 2024-07-21 08:50:05 UTC

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Sat, 20 Jul 2024

New package WASP with initial version 1.4.4
Package: WASP
Title: Wavelet System Prediction
Version: 1.4.4
Author: Ze Jiang [aut, cre] , Md. Mamunur Rashid [aut] , Ashish Sharma [aut] , Fiona Johnson [aut]
Maintainer: Ze Jiang <ze.jiang@unsw.edu.au>
Description: The wavelet-based variance transformation method is used for system modelling and prediction. It refines predictor spectral representation using Wavelet Theory, which leads to improved model specifications and prediction accuracy. Details of methodologies used in the package can be found in Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962>, Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>, and Jiang, Z., Sharma, A., & Johnson, F. (2021) <doi:10.1016/J.JHYDROL.2021.126816>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.6.0)
URL: https://github.com/zejiang-unsw/WASP#readme
BugReports: https://github.com/zejiang-unsw/WASP/issues
Imports: waveslim, stats, tidyr, readr, ggplot2, sp, zoo, fitdistrplus
Suggests: FNN, SPEI, knitr, dplyr, cowplot, gridGraphics, bookdown, rmarkdown, synthesis, kableExtra, devtools, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-20 05:07:40 UTC; z5154277
Repository: CRAN
Date/Publication: 2024-07-20 06:40:02 UTC

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New package fdaconcur with initial version 0.1.3
Package: fdaconcur
Title: Concurrent Regression and History Index Models for Functional Data
URL: https://github.com/functionaldata/tFDAconcur
BugReports: https://github.com/functionaldata/tFDAconcur/issues
Version: 0.1.3
Encoding: UTF-8
Date: 2024-07-16
Maintainer: Su I Iao <siao@ucdavis.edu>
Description: Provides an implementation of concurrent or varying coefficient regression methods for functional data. The implementations are done for both dense and sparsely observed functional data. Pointwise confidence bands can be constructed for each case. Further, the influence of past predictor values are modeled by a smooth history index function, while the effects on the response are described by smooth varying coefficient functions, which are very useful in analyzing real data such as COVID data. References: Yao, F., Müller, H.G., Wang, J.L. (2005) <doi:10.1214/009053605000000660>. Sentürk, D., Müller, H.G. (2010) <doi:10.1198/jasa.2010.tm09228>.
License: BSD_3_clause + file LICENSE
Imports: Rcpp (>= 0.11.5), fdapace (>= 0.6.0), stats
LinkingTo: Rcpp, RcppEigen
Suggests: MASS, Matrix, pracma, numDeriv, testthat
NeedsCompilation: yes
Packaged: 2024-07-19 21:32:01 UTC; suiiao
Author: Su I Iao [aut, cre], Satarupa Bhattacharjee [aut], Yaqing Chen [aut], Changbo Zhu [aut], Han Chen [aut], Yidong Zhou [aut], Alvaro Gajardo [aut], Poorbita Kundu [aut], Hang Zhou [aut], Hans-Georg Mueller [cph, ths, aut]
Repository: CRAN
Date/Publication: 2024-07-20 06:30:02 UTC

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Fri, 19 Jul 2024

New package modeltime.ensemble with initial version 1.0.4
Package: modeltime.ensemble
Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Version: 1.0.4
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging, weighted averaging, and stacking. These techniques are popular methods to improve forecast accuracy and stability.
URL: https://business-science.github.io/modeltime.ensemble/, https://github.com/business-science/modeltime.ensemble
BugReports: https://github.com/business-science/modeltime.ensemble/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: modeltime (>= 1.2.3), modeltime.resample (>= 0.2.1), R (>= 3.5)
Imports: tune (>= 0.1.2), rsample, yardstick, workflows (>= 0.2.1), recipes (>= 0.1.15), timetk (>= 2.5.0), tibble, dplyr (>= 1.0.0), tidyr, purrr, stringr, rlang (>= 0.1.2), cli, generics, magrittr, tictoc, parallel, doParallel, foreach, glmnet
Suggests: gt, dials, utils, earth, testthat, tidymodels, xgboost, lubridate, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-16 21:37:51 UTC; mdancho
Author: Matt Dancho [aut, cre], Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Repository: CRAN
Date/Publication: 2024-07-19 15:30:02 UTC

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New package iC10 with initial version 2.0.2
Package: iC10
Title: A Copy Number and Expression-Based Classifier for Breast Tumours
Version: 2.0.2
Date: 2024-07-16
Maintainer: Oscar M Rueda <Oscar.Rueda@mrc-bsu.cam.ac.uk>
Description: Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.
License: GPL-3
Imports: pamr, impute, iC10TrainingData
Packaged: 2024-07-19 06:32:13 UTC; oscar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2024-07-19 09:00:26 UTC
Author: Oscar M Rueda [aut, cre]

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Thu, 18 Jul 2024

New package tidydelta with initial version 0.1.0
Package: tidydelta
Title: Estimation of Standard Errors using Delta Method
Version: 0.1.0
Description: Delta Method implementation to estimate standard errors with known asymptotic properties within the 'tidyverse' workflow. The Delta Method is a statistical tool that approximates an estimator’s behaviour using a Taylor Expansion. For a comprehensive explanation, please refer to Chapter 3 of van der Vaart (1998, ISBN: 9780511802256).
License: MIT + file LICENSE
Imports: dplyr, numDeriv, purrr, rlang, tibble, cli
Suggests: testthat (>= 3.0.0), tidyverse
Encoding: UTF-8
URL: https://github.com/JavierMtzRdz/tidydelta
BugReports: https://github.com/JavierMtzRdz/tidydelta/issues
NeedsCompilation: no
Packaged: 2024-07-16 13:58:31 UTC; javiermtz
Author: Javier Martinez-Rodriguez [aut, cre, cph]
Maintainer: Javier Martinez-Rodriguez <javier.matz.rdz@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-18 23:20:02 UTC

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New package piecenorms with initial version 1.0.0
Package: piecenorms
Title: Calculate a Piecewise Normalised Score Using Class Intervals
Version: 1.0.0
Author: David Hammond [aut, cre]
URL: https://github.com/david-hammond/piecenorms
BugReports: https://github.com/david-hammond/piecenorms/issues
Maintainer: David Hammond <anotherdavidhammond@gmail.com>
Description: Provides an implementation of piecewise normalisation techniques useful when dealing with the communication of skewed and highly skewed data.
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Imports: dplyr, rlang, scales
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-07-16 09:25:16 UTC; david
Repository: CRAN
Date/Publication: 2024-07-18 23:10:02 UTC

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New package LMPdata with initial version 0.1.0
Package: LMPdata
Title: Easy Import of the EU Labour Market Policy Data
Version: 0.1.0
Author: Aleksander Rutkowski [aut, cre]
Maintainer: Aleksander Rutkowski <alek.rutkowski@gmail.com>
Description: European Commission's Labour Market Policy (LMP) database (<https://webgate.ec.europa.eu/empl/redisstat/databrowser/explore/all/lmp?lang=en&display=card&sort=category>) provides information on labour market interventions, which are government actions to help and support the unemployed and other disadvantaged groups in the transition from unemployment or inactivity to work. It covers the EU countries and Norway. This package provides functions for downloading and importing the LMP data and metadata (codelists).
License: MIT + file LICENSE
Encoding: UTF-8
Imports: magrittr, data.table
URL: https://github.com/alekrutkowski/LMPdata
NeedsCompilation: no
Packaged: 2024-07-16 07:30:38 UTC; alekr
Repository: CRAN
Date/Publication: 2024-07-18 23:10:10 UTC

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New package EWOC.Comb with initial version 1.0
Package: EWOC.Comb
Title: Escalation with Overdose Control using 2 Drug Combinations
Version: 1.0
Date: 2024-07-01
Maintainer: Yujie Cui <yujie.cui@cshs.org>
Description: Implements Escalation With Overdose Control trial designs using two drug combinations described by this paper <doi:10.1002/sim.6961>(Tighiouart et al., 2016). It calculates the recommended dose for next cohorts and perform simulations to obtain operating characteristics.
License: GPL (>= 2)
Depends: rjags
Imports: MASS
NeedsCompilation: no
Packaged: 2024-07-16 16:22:02 UTC; CuiY
Repository: CRAN
Date/Publication: 2024-07-18 23:30:02 UTC
SystemRequirements: JAGS (>= 4.0.0). For installation instructions, see http://mcmc-jags.sourceforge.net/
Author: Yujie Cui [aut, cre], Quanlin Li [aut], Mourad Tighiouart [aut]

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New package cooltools with initial version 2.4
Package: cooltools
Title: Practical Tools for Scientific Computations and Visualizations
Version: 2.4
Description: Collection of routines for efficient scientific computations in physics and astrophysics. These routines include utility functions, numerical computation tools, as well as visualisation tools. They can be used, for example, for generating random numbers from spherical and custom distributions, information and entropy analysis, special Fourier transforms, two-point correlation estimation (e.g. as in Landy & Szalay (1993) <doi:10.1086/172900>), binning & gridding of point sets, 2D interpolation, Monte Carlo integration, vector arithmetic and coordinate transformations. Also included is a non-exhaustive list of important constants and cosmological conversion functions. The graphics routines can be used to produce and export publication-ready scientific plots and movies, e.g. as used in Obreschkow et al. (2020, MNRAS Vol 493, Issue 3, Pages 4551–4569). These routines include special color scales, projection functions, and bitmap handling routines.
Imports: plotrix, celestial, data.table, pracma, utils, png, jpeg, MASS, raster, sp, cubature, bit64, randtoolbox, Rcpp, FNN
Suggests: EBImage
LinkingTo: Rcpp
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2024-07-16 08:19:46 UTC; 00077389
Author: Danail Obreschkow [aut, cre]
Maintainer: Danail Obreschkow <danail.obreschkow@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-18 23:10:05 UTC

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New package adass with initial version 1.0.1
Package: adass
Title: Adaptive Smoothing Spline (AdaSS) Estimator for the Function-on-Function Linear Regression
Version: 1.0.1
Description: Implements the adaptive smoothing spline estimator for the function-on-function linear regression model described in Centofanti et al. (2023) <doi:10.1007/s00180-022-01223-6>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: fda, parallel, matrixcalc, SparseM, mvtnorm, Rfast, plot3D
URL: https://github.com/unina-sfere/adass
BugReports: https://github.com/unina-sfere/adass
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2024-07-17 15:34:03 UTC; fabio
Author: Fabio Centofanti [cre, aut], Antonio Lepore [aut], Alessandra Menafoglio [aut], Biagio Palumbo [aut], Simone Vantini [aut]
Maintainer: Fabio Centofanti <fabio.centofanti@unina.it>
Repository: CRAN
Date/Publication: 2024-07-18 13:30:06 UTC

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Wed, 17 Jul 2024

New package rplanes with initial version 0.1.0
Package: rplanes
Title: Plausibility Analysis of Epidemiological Signals
Version: 0.1.0
Description: Provides functionality to prepare data and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausibility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score.
License: MIT + file LICENSE
URL: https://signaturescience.github.io/rplanes/
Depends: R (>= 2.10)
Imports: dplyr, dtw, ecp, lubridate, magrittr, purrr, readr, rlang, stringr, tibble, tidyr, utils
Suggests: DT, ggplot2, markdown, knitr, MMWRweek, rmarkdown, shiny, shinyjs, shinyWidgets, shinycssloaders, testthat (>= 3.0.0), tools
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-15 16:28:47 UTC; vpnagraj
Author: VP Nagraj [aut, cre] , Desiree Williams [aut], Amy Benefield [aut]
Maintainer: VP Nagraj <nagraj@nagraj.net>
Repository: CRAN
Date/Publication: 2024-07-17 10:50:02 UTC

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New package kmeRs with initial version 2.1.0
Package: kmeRs
Title: K-Mers Similarity Score Matrix and HeatMap
Version: 2.1.0
Description: Similarity Score Matrix and HeatMap for nucleic and amino acid k-mers. Similarity score is evaluated by Point Accepted Mutation (PAM) and BLOcks SUbstitution Matrix (BLOSUM). The 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM and BLOSUM, respectively. Alignment is evaluated by local and global alignment.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/urniaz/kmeRs
BugReports: https://github.com/urniaz/kmeRs/issues
Imports: utils, stats, Biostrings, BiocGenerics, pwalign
Suggests: RColorBrewer, knitr, rmarkdown, unittest, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-16 00:04:12 UTC; urniaz
Author: Rafal Urniaz [aut, cre] , Jason Lin [ctb]
Maintainer: Rafal Urniaz <rafal.urniaz@cantab.net>
Repository: CRAN
Date/Publication: 2024-07-17 11:00:02 UTC

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New package charlesschwabapi with initial version 1.0.2
Package: charlesschwabapi
Title: Wrapper Functions Around 'Charles Schwab Individual Trader API'
Version: 1.0.2
Description: For those wishing to interact with the 'Charles Schwab Individual Trader API' (<https://developer.schwab.com/products/trader-api--individual>) with R in a simplified manner, this package offers wrapper functions around authentication and the available API calls to streamline the process.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, lubridate, stringr, purrr, tidyr, anytime, dplyr, openssl
Suggests: testthat (>= 3.0.0), covr
NeedsCompilation: no
Packaged: 2024-07-16 00:43:48 UTC; njbul
Author: Nick Bultman [aut, cre, cph]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-17 11:00:05 UTC

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Tue, 16 Jul 2024

New package r311 with initial version 0.3.7
Package: r311
Title: Interface to the 'open311' Standard
Version: 0.3.7
Maintainer: Jonas Lieth <jonas.lieth@gesis.org>
Description: Access and handle APIs that use the international 'open311' 'GeoReport v2' standard for civic issue tracking <https://wiki.open311.org/GeoReport_v2/>. Retrieve civic service types and request data. Select and add available 'open311' endpoints and jurisdictions. Implicitly supports custom queries and 'open311' extensions. Requires a minimal number of hard dependencies while still allowing the integration in common R formats ('xml2', 'tibble', 'sf').
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: utils, tools, curl, jsonlite
Suggests: httptest2, testthat (>= 3.0.0), knitr, tibble, sf, xml2, xmlconvert, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/jslth/r311, https://jslth.github.io/r311/, https://github.com/JsLth/r311
BugReports: https://github.com/JsLth/r311/issues
NeedsCompilation: no
Packaged: 2024-07-16 10:49:19 UTC; PC
Author: Jonas Lieth [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-07-16 21:20:02 UTC

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New package clrng with initial version 0.0.5
Package: clrng
Title: Parallel Random Number Generation on GPU
Description: Builds on 'gpuR' and utilizes the 'clRNG' ('OpenCL') library to provide efficient tools to generate independent random numbers in parallel on a GPU and save the results as 'R' objects, ensuring high-quality random numbers even when 'R' is used interactively or in an ad-hoc manner. Includes Fisher's simulation method adapted from Patefield, William M (1981) <doi:10.2307/2346669> and 'MRG31k3p' Random Number Generator from 'clRNG' library by Advanced Micro Devices, Inc. (2015) <https://github.com/clMathLibraries/clRNG>.
Version: 0.0.5
Date: 2024-07-11
Maintainer: Ruoyong Xu <ruoyong.xu@mail.utoronto.ca>
License: GPL-3
Encoding: UTF-8
NeedsCompilation: yes
Depends: R (>= 3.5.0), gpuR
Suggests: knitr
LinkingTo: RViennaCL, Rcpp, gpuR, RcppEigen
OS_type: unix
VignetteBuilder: knitr
Packaged: 2024-07-12 15:56:59 UTC; ruoyong
Author: Ruoyong Xu [cre, aut, ctb] , Patrick Brown [aut, ctb] , Advanced Micro Devices, Inc. [cph]
Repository: CRAN
Date/Publication: 2024-07-16 09:00:02 UTC

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Mon, 15 Jul 2024

New package xrnet with initial version 1.0.0
Package: xrnet
Title: Hierarchical Regularized Regression
Version: 1.0.0
URL: https://github.com/USCbiostats/xrnet, https://uscbiostats.github.io/xrnet/
Description: Fits hierarchical regularized regression models to incorporate potentially informative external data, Weaver and Lewinger (2019) <doi:10.21105/joss.01761>. Utilizes coordinate descent to efficiently fit regularized regression models both with and without external information with the most common penalties used in practice (i.e. ridge, lasso, elastic net). Support for standard R matrices, sparse matrices and big.matrix objects.
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat, Matrix, doParallel
LinkingTo: Rcpp, RcppEigen, BH, bigmemory
Imports: Rcpp (>= 0.12.19), foreach, bigmemory, methods
Depends: R (>= 4.0)
BugReports: https://github.com/USCbiostats/xrnet/issues
NeedsCompilation: yes
Packaged: 2024-07-15 04:54:39 UTC; garrett.weaver
Author: Garrett Weaver [aut, cre] , Dixin Shen [aut], Juan Pablo Lewinger [ctb, ths]
Maintainer: Garrett Weaver <gmweaver.usc@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-16 00:40:02 UTC

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New package databraryr with initial version 0.6.6
Package: databraryr
Title: Interact with the 'Databrary.org' API
Version: 0.6.6
Maintainer: Rick O. Gilmore <rog1@psu.edu>
Description: 'Databrary.org' is a restricted access repository for research data, especially video and audio. This package provides commands to interact with the data stored on 'Databrary.org'.
License: MIT + file LICENSE
URL: https://databrary.github.io/databraryr/, https://github.com/databrary/databraryr
BugReports: https://github.com/databrary/databraryr/issues
Imports: assertthat (>= 0.2.1), dplyr (>= 1.1.4), getPass (>= 0.2.4), httr2 (>= 1.0.0), keyring (>= 1.3.2), lifecycle (>= 1.0.4), magick (>= 2.8.2), magrittr, methods (>= 4.3.2), options (>= 0.2.0), purrr (>= 1.0.2), stringr (>= 1.5.1), tibble (>= 3.2.1), xfun (>= 0.41)
Suggests: av (>= 0.9.0), ggplot2, knitr, openssl, readr, rmarkdown (>= 2.26), testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-09 15:01:58 UTC; rog1
Author: Rick O. Gilmore [aut, cre, cph], Jeffrey Spies [aut], National Science Foundation OAC-2032713 [fnd], National Institutes of Health R01HD094830 [fnd]
Repository: CRAN
Date/Publication: 2024-07-15 18:40:02 UTC

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New package holi with initial version 0.1.0
Package: holi
Title: Higher Order Likelihood Inference Web Applications
Version: 0.1.0
Description: Higher order likelihood inference is a promising approach for analyzing small sample size data. The 'holi' package provides web applications for higher order likelihood inference. It currently supports linear, logistic, and Poisson generalized linear models through the rstar_glm() function, based on Pierce and Bellio (2017) <doi:10.1111/insr.12232> and 'likelihoodAsy'. The package offers two main features: LA_rstar(), which launches an interactive 'shiny' application allowing users to fit models with rstar_glm() through their web browser, and sim_rstar_glm_pgsql(), which streamlines the process of launching a web-based 'shiny' simulation application that saves results to a user-created 'PostgreSQL' database.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/mightymetrika/holi
BugReports: https://github.com/mightymetrika/holi/issues
Suggests: testthat (>= 3.0.0)
Imports: DT, ggplot2, likelihoodAsy, MASS, pool, RPostgres, shiny, shinythemes, sn
NeedsCompilation: no
Packaged: 2024-07-14 15:59:28 UTC; Administrator
Author: Mackson Ncube [aut, cre], mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-15 07:40:02 UTC

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Sun, 14 Jul 2024

New package zippeR with initial version 0.1.0
Package: zippeR
Title: Working with United States ZIP Code and ZIP Code Tabulation Area Data
Version: 0.1.0
Description: Provides a set of functions for working with American postal codes, which are known as ZIP Codes. These include accessing ZIP Code to ZIP Code Tabulation Area (ZCTA) crosswalks, retrieving demographic data for ZCTAs, and tabulating demographic data for three-digit ZCTAs.
Depends: R (>= 3.5)
License: Apache License (>= 2)
URL: https://github.com/pfizer-opensource/zippeR
BugReports: https://github.com/pfizer-opensource/zippeR/issues
Encoding: UTF-8
LazyData: true
Imports: datasets, dplyr, httr, jsonlite, purrr, readr, sf, spatstat.univar, stats, stringr, tibble, tidycensus, tidyr, tigris
Suggests: covr, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-12 15:44:37 UTC; prenec
Author: Christopher Prener [aut, cre] , Timothy Wiemken [aut] , Angela Cook [aut]
Maintainer: Christopher Prener <Christopher.Prener@pfizer.com>
Repository: CRAN
Date/Publication: 2024-07-14 12:40:02 UTC

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New package modisfast with initial version 0.9.1
Package: modisfast
Title: Fast and Efficient Access to MODIS Earth Observation Data
Version: 0.9.1
Description: Programmatic interface to several NASA Earth Observation 'OPeNDAP' servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).
License: GPL (>= 3)
URL: https://github.com/ptaconet/modisfast
BugReports: https://github.com/ptaconet/modisfast/issues
Depends: R (>= 2.10)
Imports: curl, dplyr, httr, lubridate, magrittr, parallel, purrr, rvest, sf, stats, stringr, terra, xml2
Suggests: ggplot2, knitr, mapview, rmarkdown, spelling, testthat
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2024-07-12 12:08:40 UTC; ptaconet
Author: Paul Taconet [aut, cre, cph] , Nicolas Moiroux [fnd] , French National Research Institute for Sustainable Development, IRD [fnd]
Maintainer: Paul Taconet <paul.taconet@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-14 12:10:02 UTC

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New package mig with initial version 1.0
Package: mig
Title: Multivariate Inverse Gaussian Distribution
Version: 1.0
Description: Provides utilities for estimation for the multivariate inverse Gaussian distribution of Minami (2003) <doi:10.1081/STA-120025379>, including random vector generation and explicit estimators of the location vector and scale matrix. The package implements kernel density estimators discussed in Belzile, Desgagnes, Genest and Ouimet (2024) <doi:10.48550/arXiv.2209.04757> for smoothing multivariate data on half-spaces.
BugReports: https://github.com/lbelzile/mig/issues
Imports: statmod, TruncatedNormal (>= 2.3), Rcpp (>= 1.0.12)
Depends: R (>= 2.10)
Suggests: numDeriv, tinytest, knitr, rmarkdown, minqa
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
LazyData: true
License: MIT + file LICENSE
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-07-12 13:32:47 UTC; lbelzile
Author: Frederic Ouimet [aut] , Leo Belzile [aut, cre]
Maintainer: Leo Belzile <belzilel@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-14 12:30:02 UTC

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New package EEML with initial version 0.1.0
Package: EEML
Title: Ensemble Explainable Machine Learning Models
Version: 0.1.0
Author: Dr. Md Yeasin [aut, cre], Dr. Ranjit Kumar Paul [aut], Dr. Dipanwita Haldar [aut], Dr. Suresh Kumar [aut]
Maintainer: Dr. Md Yeasin <yeasin.iasri@gmail.com>
Description: We introduced a novel ensemble-based explainable machine learning model using Model Confidence Set (MCS) and two stage Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) algorithm. The model combined the predictive capabilities of different machine-learning models and integrates the interpretability of explainability methods. To develop the proposed algorithm, a two-stage Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) framework was employed. The package has been developed using the 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, MCS, WeightedEnsemble, topsis
NeedsCompilation: no
Packaged: 2024-07-12 20:22:54 UTC; YEASIN
Repository: CRAN
Date/Publication: 2024-07-14 12:50:02 UTC

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New package ChangePointTaylor with initial version 0.3
Package: ChangePointTaylor
Title: Identify Changes in Mean
Version: 0.3
Date: 2024-07-12
Maintainer: Michael Marks <michaelmarks@analyticaconsulting.com>
Description: A basic implementation of the change in mean detection method outlined in: Taylor, Wayne A. (2000) <https://variation.com/wp-content/uploads/change-point-analyzer/change-point-analysis-a-powerful-new-tool-for-detecting-changes.pdf>. The package recursively uses the mean-squared error change point calculation to identify candidate change points. The candidate change points are then re-estimated and Taylor's backwards elimination process is then employed to come up with a final set of change points. Many of the underlying functions are written in C++ for improved performance.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.4), dplyr, purrr, tidyr, magrittr, rlang
LinkingTo: Rcpp
LazyData: true
Suggests: knitr, rmarkdown, ggplot2, bench
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-07-12 20:39:00 UTC; mmark
Author: Michael Marks [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-07-14 13:00:02 UTC

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New package BATSS with initial version 0.7.14
Package: BATSS
Title: Bayesian Adaptive Trial Simulator Software (BATSS) for Generalised Linear Models
Version: 0.7.14
Description: Defines operating characteristics of Bayesian Adaptive Trials considering a generalised linear model response via Monte Carlo simulations of Bayesian GLM fitted via integrated Laplace approximations (INLA).
URL: https://batss-dev.github.io/BATSS/
License: GPL-2
Encoding: UTF-8
Suggests: INLA
Imports: parallel, methods, stats, grDevices, abind, plyr, rlang, R.utils, cli
Additional_repositories: https://inla.r-inla-download.org/R/testing
NeedsCompilation: no
Packaged: 2024-07-12 14:50:23 UTC; research
Author: Dominique-Laurent Couturier [aut, cre] , Liz Ryan [aut] , Rainer Puhr [aut], Thomas Jaki [aut] , Stephane Heritier [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Repository: CRAN
Date/Publication: 2024-07-14 12:40:06 UTC

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New package iPRISM with initial version 0.1.1
Package: iPRISM
Title: Intelligent Predicting Response to Cancer Immunotherapy Through Systematic Modeling
Version: 0.1.1
Maintainer: Junwei Han <hanjunwei1981@163.com>
Description: Immunotherapy has revolutionized cancer treatment, but predicting patient response remains challenging. Here, we presented Intelligent Predicting Response to cancer Immunotherapy through Systematic Modeling (iPRISM), a novel network-based model that integrates multiple data types to predict immunotherapy outcomes. It incorporates gene expression, biological functional network, tumor microenvironment characteristics, immune-related pathways, and clinical data to provide a comprehensive view of factors influencing immunotherapy efficacy. By identifying key genetic and immunological factors, it provides an insight for more personalized treatment strategies and combination therapies to overcome resistance mechanisms.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1.0)
Imports: ggplot2, Hmisc, tidyr, igraph, pbapply, Matrix, methods
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-12 06:27:46 UTC; syc
Author: Junwei Han [aut, cre, ctb], Yinchun Su [aut], Siyuan Li [aut]
Repository: CRAN
Date/Publication: 2024-07-14 12:00:02 UTC

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New package HonestDiD with initial version 0.2.6
Package: HonestDiD
Title: Robust Inference in Difference-in-Differences and Event Study Designs
Version: 0.2.6
Depends: R (>= 3.6.0)
Imports: stats, rlang, foreach (>= 1.4.7), matrixStats (>= 0.63.0), CVXR (>= 0.99-6), latex2exp (>= 0.4.0), lpSolveAPI (>= 5.5.2.0-17), Matrix (>= 1.2-17), pracma (>= 2.2.5), purrr (>= 0.3.4), tibble (>= 1.3.4), dplyr (>= 0.7.4), ggplot2 (>= 2.2.1), Rglpk (>= 0.6-4), mvtnorm (>= 1.1-3), TruncatedNormal (>= 1.0)
Suggests: knitr, testthat, haven, lfe, rmarkdown
Description: Provides functions to conduct robust inference in difference-in-differences and event study designs by implementing the methods developed in Rambachan & Roth (2023) <doi:10.1093/restud/rdad018>, "A More Credible Approach to Parallel Trends" [Previously titled "An Honest Approach..."]. Inference is conducted under a weaker version of the parallel trends assumption. Uniformly valid confidence sets are constructed based upon conditional confidence sets, fixed-length confidence sets and hybridized confidence sets.
Encoding: UTF-8
LazyData: true
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2024-07-12 00:19:14 UTC; asheshr
Author: Ashesh Rambachan [aut, cph, cre], Jonathan Roth [aut, cph]
Maintainer: Ashesh Rambachan <ashesh.a.rambachan@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-14 11:40:02 UTC

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New package hedgedrf with initial version 0.0.1
Package: hedgedrf
Title: An Implementation of the Hedged Random Forest Algorithm
Version: 0.0.1
Description: This algorithm is described in detail in the paper "Hedging Forecast Combinations With an Application to the Random Forest" by Beck et al. (2023) <doi:10.48550/arXiv.2308.15384>. The package provides a function hedgedrf() that can be used to train a Hedged Random Forest model on a dataset, and a function predict.hedgedrf() that can be used to make predictions with the model.
License: GPL-3
Imports: ranger, CVXR
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-12 06:41:08 UTC; ubuntu
Author: Elliot Beck [aut, cre]
Maintainer: Elliot Beck <elliot.beck@bf.uzh.ch>
Repository: CRAN
Date/Publication: 2024-07-14 12:00:05 UTC

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New package closeloop with initial version 0.1.0
Package: closeloop
Title: Integrate Single-Arm Observational Data in Network Meta Analysis
Version: 0.1.0
Date: 2024-08-07
Maintainer: Shubhram Pandey <shubhram1992@gmail.com>
Description: Calculate the distance between single-arm observational studies using covariate information to remove heterogeneity in Network Meta-Analysis (NMA) of randomized clinical trials. Facilitate the inclusion of observational data in NMA, enhancing the comprehensiveness and robustness of comparative effectiveness research. Schmitz (2018) <doi:10.1186/s12874-018-0509-7>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: combinat
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/heorlytics/closeloop
NeedsCompilation: no
Packaged: 2024-07-12 12:00:18 UTC; ShubhramPandey
Author: Supreet Kaur [ctb], Akanksha Sharma [ctb], Shubhram Pandey [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-14 12:00:09 UTC

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Sat, 13 Jul 2024

New package vol2birdR with initial version 1.0.3
Package: vol2birdR
Title: Vertical Profiles of Biological Signals in Weather Radar Data
Version: 1.0.3
Date: 2024-07-10
Description: 'R' implementation of the 'vol2bird' software for generating vertical profiles of birds and other biological signals in weather radar data. See Dokter et al. (2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
License: LGPL (>= 3)
Language: en-US
URL: https://github.com/adokter/vol2birdR/, https://adriaandokter.com/vol2bird/
BugReports: https://github.com/adokter/vol2birdR/issues
Imports: assertthat, methods, pkgbuild, Rcpp (>= 1.0.4), rlang, utils, withr
LinkingTo: Rcpp, RcppGSL
VignetteBuilder: knitr
SystemRequirements: GNU make, GSL, HDF5, PROJ
NeedsCompilation: yes
RcppModules: RaveIO, PolarVolume, Vol2Bird, Vol2BirdConfig
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Copyright: file COPYRIGHTS
Encoding: UTF-8
Packaged: 2024-07-10 20:45:07 UTC; at744
Author: Anders Henja [aut] , Adriaan M. Dokter [aut, cre] , Alexander Tedeschi [ctb] , Tsung-Yu Lin [ctb] , Subranshu Maji [ctb] , Daniel Sheldon [ctb] , Bart Kranstauber [ctb] , Jurriaan H. Spaaks [ctb] , Lourens Veen [ctb] , Iwan Holleman [ctb] , Hidde Lei [...truncated...]
Maintainer: Adriaan M. Dokter <vol2birdr@cornell.edu>
Repository: CRAN
Date/Publication: 2024-07-13 12:30:02 UTC

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New package graphicalMCP with initial version 0.2.5

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Fri, 12 Jul 2024

New package SmithWilsonYieldCurve with initial version 1.1.1
Package: SmithWilsonYieldCurve
Title: Smith-Wilson Yield Curve Construction
Version: 1.1.1
Date: 2024-07-11
Description: Constructs a yield curve by the Smith-Wilson method from a table of libor and swap rates. Now updated to take bond coupons and prices in the same table.
License: GPL-3
Suggests: testthat
Packaged: 2024-07-11 06:53:34 UTC; philj
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2024-07-12 15:20:05 UTC
Author: Phil Joubert [aut, cre]
Maintainer: Phil Joubert <phil.joubert@gmail.com>

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New package SCIntRuler with initial version 0.99.6
Package: SCIntRuler
Title: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets
Version: 0.99.6
Maintainer: Yue Lyu <yuelyu0521@gmail.com>
Description: The accumulation of single-cell RNA-seq ('scRNA-seq') studies highlights the potential benefits of integrating multiple datasets. By augmenting sample sizes and enhancing analytical robustness, integration can lead to more insightful biological conclusions. However, challenges arise due to the inherent diversity and batch discrepancies within and across studies. 'SCIntRuler', a novel R package, addresses these challenges by guiding the integration of multiple 'scRNA-seq' datasets.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Rcpp, Matrix, batchelor, base, Seurat, SeuratObject, MatrixGenerics, SingleCellExperiment, SummarizedExperiment, dplyr, coin, harmony, ggplot2, gridExtra, cowplot, magrittr, stats
LinkingTo: Rcpp
URL: https://github.com/yuelyu21/SCIntRuler, https://yuelyu21.github.io/SCIntRuler/
BugReports: https://github.com/yuelyu21/SCIntRuler/issues
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 4.3.0)
LazyData: true
LazyDataCompression: xz
NeedsCompilation: yes
Packaged: 2024-07-11 06:55:10 UTC; a98455
Author: Yue Lyu [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-12 15:20:08 UTC

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New package governor with initial version 0.1.2
Package: governor
Title: Speed Limiter to Control Rate of Execution of Loops
Version: 0.1.2
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Description: Speed limiter for controlling rate of execution of loops. It can be necessary to limit the rate of execution of a loop or repeated function call e.g. to show or gather data only at particular intervals. This package includes two methods for limiting this execution rate; speed governors and timers. A speed governor will insert pauses during execution to meet a user-specified loop time. Timers are alarm clocks which will indicate whether a certain time has passed. These mechanisms are implemented in 'C' to minimize processing overhead.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/coolbutuseless/governor
BugReports: https://github.com/coolbutuseless/governor/issues
NeedsCompilation: yes
Packaged: 2024-07-11 08:01:15 UTC; mike
Author: Mike Cheng [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-07-12 15:20:01 UTC

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New package WES with initial version 1.0.0
Package: WES
Title: Tools for Analyzing Wastewater and Environmental Sampling Data
Version: 1.0.0
Date: 2024-07-03
Description: Provides reproducible functions for collating and analyzing data from environmental sampling studies. Environmental Sampling (ES) of infectious diseases involves collecting samples from various sources (such as sewage, water, air, soil, or surfaces) to monitor the presence of pathogens in the environment. Analysis of ES data often requires the calculation of Real-Time Quantitative PCR (qPCR) variables, normalizing ES observations, and analyzing sampling site characteristics. To help reduce the complexity of these analyses we have implemented tools that assist with establishing standardized ES data formats, absolute and relative quantification of qPCR data, estimation of qPCR amplification efficiency, and collating open-source spatial data for sampling sites.
URL: https://www.r-wes.com/
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
Imports: glue, foreach, data.table, dplyr, HDInterval, zoo, openmeteo, chirps, whitebox, exactextractr, elevatr, raster, sp, sf, rworldmap, stars, RCurl, XML, httr, jsonlite
Depends: R (>= 4.1.1), stats, graphics, grDevices, utils
Suggests: rmarkdown, rworldxtra, progress
NeedsCompilation: no
Packaged: 2024-07-11 02:31:38 UTC; johngiles
Author: John R Giles [aut, cre]
Maintainer: John R Giles <john.giles@gatesfoundation.org>
Repository: CRAN
Date/Publication: 2024-07-12 14:00:06 UTC

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New package tidygate with initial version 1.0.13
Package: tidygate
Title: Interactively Gate Points
Version: 1.0.13
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Description: Interactively gate points on a scatter plot. Interactively drawn gates are recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is based on the package gatepoints by Wajid Jawaid (who is also an author of this package).
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: utils, graphics, lifecycle, scales, magrittr, tibble, dplyr, purrr, rlang, tidyr, viridis, grDevices, RColorBrewer, stringr, shiny, plotly, ggplot2
Suggests: testthat, markdown, knitr, readr
VignetteBuilder: knitr
Biarch: true
URL: https://github.com/stemangiola/tidygate
BugReports: https://github.com/stemangiola/tidygate/issues
NeedsCompilation: no
Packaged: 2024-07-11 00:17:21 UTC; mangiola.s
Author: Stefano Mangiola [aut, cre], Wajid Jawaid [ctb], William Hutchison [aut]
Repository: CRAN
Date/Publication: 2024-07-12 13:30:01 UTC

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New package sdtmchecks with initial version 1.0.0
Package: sdtmchecks
Title: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets
Version: 1.0.0
Description: A series of checks to identify common issues in Study Data Tabulation Model (SDTM) datasets. These checks are intended to be generalizable, actionable, and meaningful for analysis.
License: Apache License (>= 2)
Encoding: UTF-8
Language: en-US
LazyData: true
Imports: dplyr (>= 1.1.1), tidyselect, openxlsx
Suggests: knitr, rmarkdown (>= 2.7), testthat, DT
VignetteBuilder: knitr
URL: https://pharmaverse.github.io/sdtmchecks/, https://github.com/pharmaverse/sdtmchecks
BugReports: https://github.com/pharmaverse/sdtmchecks/issues
Repository: CRAN
NeedsCompilation: no
Packaged: 2024-07-11 01:33:03 UTC; harric17
Author: Will Harris [aut, cre], Sara Bodach [aut], Edgar Manukyan [aut], Adrian Waddell [aut], Ross Farrugia [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Will Harris <harric17@gene.com>
Date/Publication: 2024-07-12 13:50:02 UTC

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New package sampcompR with initial version 0.2.0
Package: sampcompR
Title: Comparing and Visualizing Differences Between Surveys
Version: 0.2.0
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). „Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Non-Probability Surveys with [...truncated...]
License: GPL-3
Encoding: UTF-8
Imports: boot, boot.pval, data.table, dplyr, forcats, furrr, future, ggplot2, Hmisc, lmtest, magrittr, psych, purrr, readr, reshape2, sandwich, stats, survey, svrep, tibble, tidyr,
Suggests: testthat (>= 3.0.0), wooldridge, jtools, utils, parallel
NeedsCompilation: no
Packaged: 2024-07-10 08:27:27 UTC; rohrbn
Author: Bjoern Rohr [aut, cre, cph]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Repository: CRAN
Date/Publication: 2024-07-12 11:20:03 UTC

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New package mergenstudio with initial version 1.0
Package: mergenstudio
Title: 'Mergen' Studio: An 'RStudio' Addin Wrapper for the 'Mergen' Package
Version: 1.0
Maintainer: Jacqueline Jansen <jacqueline-98@hotmail.com>
Description: An 'RStudio' Addin wrapper for the 'mergen' package. This package employs artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. This package makes it easier to use Large Language Models in your development environment by providing a chat-like interface, while also allowing you to inspect and execute the returned code.
License: MIT + file LICENSE
Depends: R (>= 4.0)
Imports: mergen, assertthat, bslib (>= 0.4.2), cli, colorspace, fontawesome, glue, grDevices, htmltools, htmlwidgets, httr2, ids, jsonlite, magrittr, purrr, rlang, rstudioapi (>= 0.12), shiny, shiny.i18n, shinyjs, shinyFiles, fs, stringr (>= 1.5.0), rvest, utils, waiter, yaml, rmarkdown, methods
Encoding: UTF-8
Language: en-US
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-07-10 11:35:56 UTC; jacquelinejansen
Author: Jacqueline Jansen [aut, cre], Artuer Manukyan [aut], Nour Alkhoury [aut], Altuna Akalin [aut]
Repository: CRAN
Date/Publication: 2024-07-12 11:30:02 UTC

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New package drglm with initial version 1.0
Package: drglm
Title: Fitting Linear and Generalized Linear Models in "Divide and Recombine" Approach to Large Data Sets
Version: 1.0
Maintainer: Md. Mahadi Hassan Nayem <mhnayem.cu.stat@outlook.com>
Depends: R (>= 3.5.0)
Imports: nnet, speedglm, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Description: To overcome the memory limitations for fitting linear (LM) and Generalized Linear Models (GLMs) to large data sets, this package implements the Divide and Recombine (D&R) strategy. It basically divides the entire large data set into suitable subsets manageable in size and then fits model to each subset. Finally, results from each subset are aggregated to obtain the final estimate. This package also supports fitting GLMs to data sets that cannot fit into memory and provides methods for fitting GLMs under linear regression, binomial regression, Poisson regression, and multinomial logistic regression settings. Respective models are fitted using different D&R strategies as described by: Xi, Lin, and Chen (2009) <doi:10.1109/TKDE.2008.186>, Xi, Lin and Chen (2006) <doi:10.1109/TKDE.2006.196>, Zuo and Li (2018) <doi:10.4236/ojs.2018.81003>, Karim, M.R., Islam, M.A. (2019) <doi:10.1007/978-981-13-9776-9>.
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://nayemmh.github.io/drglm/
NeedsCompilation: no
Packaged: 2024-07-10 14:27:38 UTC; mhnay
Author: Md. Mahadi Hassan Nayem [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-12 11:40:02 UTC

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New package docket with initial version 1.33
Package: docket
Title: Insert R Data into 'Word' Documents
Version: 1.33
Description: Populate data from an R environment into '.doc' and '.docx' templates. Create a template document in a program such as 'Word', and add strings encased in guillemet characters to create flags («example»). Use getDictionary() to create a dictionary of flags and replacement values, then call docket() to generate a populated document.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stringr, XML, xml2, zip
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/JonathanConrad98/docket
BugReports: https://github.com/JonathanConrad98/docket/issues
NeedsCompilation: no
Packaged: 2024-07-10 20:48:35 UTC; Jonra
Author: Jonathan Conrad [aut, cre], Ian Conrad [ctb]
Maintainer: Jonathan Conrad <JonathanGConrad@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-12 11:50:02 UTC

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New package CPoptim with initial version 0.1.0
Package: CPoptim
Title: Convex Partition Optimisation
Version: 0.1.0
Author: Erick G.G. de Paz [aut, cre] , Humberto Vaquera Huerta [aut] , Francisco Javier Albores Velasco [aut] , John R. Bauer Mengelberg [aut] , Juan Manuel Romero Padilla [aut]
Maintainer: Erick G.G. de Paz <giles.erick@colpos.mx>
Description: Convex Partition is a black-box optimisation algorithm for single objective real-parameters functions. The basic principle is to progressively estimate and exploit a regression tree similar to a CART (Classification and Regression Tree) of the objective function. For more details see 'de Paz' (2024) <doi:10.1007/978-3-031-62836-8_3> and 'Loh' (2011) <doi:10.1002/widm.8> .
License: GPL-2
Encoding: UTF-8
NeedsCompilation: yes
Repository: CRAN
Date: 2024-07-07
Depends: R (>= 2.10.0)
Packaged: 2024-07-10 00:04:28 UTC; erickdepaz
Date/Publication: 2024-07-12 11:10:02 UTC

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Thu, 11 Jul 2024

New package quantspec with initial version 1.2-4
Package: quantspec
Version: 1.2-4
Encoding: UTF-8
Date: 2024-07-10
Title: Quantile-Based Spectral Analysis of Time Series
Depends: R (>= 3.0.0), stats4
Suggests: testthat
Imports: methods, graphics, quantreg, abind, zoo, snowfall, Rcpp (>= 0.11.0)
Description: Methods to determine, smooth and plot quantile periodograms for univariate and multivariate time series. See Kley (2016) <doi:10.18637/jss.v070.i03> for a description and tutorial.
License: GPL (>= 2)
URL: https://github.com/tobiaskley/quantspec
BugReports: https://github.com/tobiaskley/quantspec/issues
LazyData: TRUE
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-07-10 13:05:01 UTC; tkley
Author: Tobias Kley [aut, cre], Stefan Birr [ctb]
Maintainer: Tobias Kley <tobias.kley@uni-goettingen.de>
Repository: CRAN
Date/Publication: 2024-07-11 12:50:02 UTC

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Wed, 10 Jul 2024

New package rnaCrosslinkOO with initial version 0.1.4
Package: rnaCrosslinkOO
Title: Analysis of RNA Crosslinking Data
Version: 0.1.4
Maintainer: Jonathan Price <jlp76@cam.ac.uk>
Description: Analysis of RNA crosslinking data for RNA structure prediction. The package is suitable for the analysis of RNA structure cross-linking data and chemical probing data.
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/JLP-BioInf/rnaCrosslinkOO/issues
Depends: seqinr, GenomicRanges, stats
Imports: ggplot2, reshape2, MASS, mixtools, utils, S4Vectors, patchwork, doParallel, igraph, R4RNA, RColorBrewer, IRanges, foreach,grDevices, heatmap3, TopDom, tidyverse, RRNA, ggrepel, methods, parallel, ClassDiscovery
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-10 15:59:22 UTC; jp
Author: Jonathan Price [aut, cre] , Andrew Lim [ctb]
Repository: CRAN
Date/Publication: 2024-07-10 23:40:02 UTC

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New package PurpleAir with initial version 1.0.0
Package: PurpleAir
Title: Query the 'PurpleAir' Application Programming Interface
Version: 1.0.0
Description: Send requests to the 'PurpleAir' Application Programming Interface (API; <https://community.purpleair.com/c/data/api/18>). Check a 'PurpleAir' API key and get information about the related organization. Download real-time data from a single 'PurpleAir' sensor or many sensors by sensor identifier, geographical bounding box, or time since modified. Download historical data from a single sensor.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: sf, testthat (>= 3.0.0)
URL: https://github.com/cole-brokamp/PurpleAir
BugReports: https://github.com/cole-brokamp/PurpleAir/issues
Imports: httr2, purrr, tibble, rlang, cli, dplyr, glue
NeedsCompilation: no
Packaged: 2024-07-09 18:27:07 UTC; cole
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Repository: CRAN
Date/Publication: 2024-07-10 16:50:05 UTC

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New package exams.forge with initial version 1.0.10
Package: exams.forge
Title: Support for Compiling Examination Tasks using the 'exams' Package
Version: 1.0.10
Date: 2024-07-08
Description: The main aim is to further facilitate the creation of exercises based on the package 'exams' by Grün, B., and Zeileis, A. (2009) <doi:10.18637/jss.v029.i10>. Creating effective student exercises involves challenges such as creating appropriate data sets and ensuring access to intermediate values for accurate explanation of solutions. The functionality includes the generation of univariate and bivariate data including simple time series, functions for theoretical distributions and their approximation, statistical and mathematical calculations for tasks in basic statistics courses as well as general tasks such as string manipulation, LaTeX/HTML formatting and the editing of XML task files for 'Moodle'.
License: GPL-3
LazyData: true
Depends: R (>= 3.5.0), tools, polynom
Imports: base64enc, extraDistr, exams, knitr, MASS, methods, magrittr, psych, rjson, rstudioapi, spelling, stringdist, stringr, stranslate, tinytex, utils, xml2, xtable, yaml
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: rmarkdown
NeedsCompilation: no
Packaged: 2024-07-09 09:29:52 UTC; sigbert
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Repository: CRAN
Date/Publication: 2024-07-10 16:40:02 UTC

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New package checked with initial version 0.1.0
Package: checked
Title: Systematically Run R CMD Checks
Version: 0.1.0
Description: Systematically Run R checks against multiple packages. Checks are run in parallel with strategies to minimize dependency installation. Provides out of the box interface for running reverse dependency check.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: callr, cli, igraph, jsonlite, R6, rcmdcheck, utils (>= 3.6.2), tools
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-07-08 23:38:16 UTC; maksymis
Author: Szymon Maksymiuk [cre, aut] , Doug Kelkhoff [aut] , F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-10 16:30:02 UTC

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New package amscorer with initial version 0.1.0
Package: amscorer
Title: Clinical Scores Calculator for Healthcare
Version: 0.1.0
Description: Provides functions to compute various clinical scores used in healthcare. These include the Charlson Comorbidity Index (CCI), predicting 10-year survival in patients with multiple comorbidities; the EPICES score, an individual indicator of precariousness considering its multidimensional nature; the MELD score for chronic liver disease severity; the Alternative Fistula Risk Score (a-FRS) for postoperative pancreatic fistula risk; and the Distal Pancreatectomy Fistula Risk Score (D-FRS) for risk following distal pancreatectomy. For detailed methodology, refer to Charlson et al. (1987) <doi:10.1016/0021-9681(87)90171-8> , Sass et al. (2006) <doi:10.1007/s10332-006-0131-5>, Kamath et al. (2001) <doi:10.1053/jhep.2001.22172>, Kim et al. (2008) <doi:10.1056/NEJMoa0801209> Kim et al. (2021) <doi:10.1053/j.gastro.2021.08.050>, Mungroop et al. (2019) <doi:10.1097/SLA.0000000000002620>, and de Pastena et al. (2023) <doi:10.1097/SLA.0000000000005497>..
Imports: stats
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-09 15:54:24 UTC; amadousow
Author: Amadou Khalilou Sow [aut, cre]
Maintainer: Amadou Khalilou Sow <kkhalilou.sow@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-10 16:50:02 UTC

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Tue, 09 Jul 2024

New package FVDDPpkg with initial version 0.1.2
Package: FVDDPpkg
Title: Implement Fleming-Viot-Dependent Dirichlet Processes
Version: 0.1.2
Description: A Bayesian Nonparametric model for the study of time-evolving frequencies, which has become renowned in the study of population genetics. The model consists of a Hidden Markov Model (HMM) in which the latent signal is a distribution-valued stochastic process that takes the form of a finite mixture of Dirichlet Processes, indexed by vectors that count how many times each value is observed in the population. The package implements methodologies presented in Ascolani, Lijoi and Ruggiero (2021) <doi:10.1214/20-BA1206> and Ascolani, Lijoi and Ruggiero (2023) <doi:10.3150/22-BEJ1504> that make it possible to study the process at the time of data collection or to predict its evolution in future or in the past.
License: LGPL (>= 3)
Encoding: UTF-8
Imports: Rcpp, Rdpack
LinkingTo: Rcpp
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-07-08 15:42:52 UTC; stefano.damato
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefano.damato@idsia.ch>
Repository: CRAN
Date/Publication: 2024-07-09 16:10:12 UTC

More information about FVDDPpkg at CRAN
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New package decp with initial version 0.1.0
Package: decp
Title: Complete Change Point Analysis
Version: 0.1.0
Description: Provides a comprehensive approach for identifying and estimating change points in multivariate time series through various statistical methods. Implements the multiple change point detection methodology from Ryan & Killick (2023) <doi:10.1080/00401706.2023.2183261> and a novel estimation methodology from Fotopoulos et al. (2023) <doi:10.1007/s00362-023-01495-0> generalized to fit the detection methodologies. Performs both detection and estimation of change points, providing visualization and summary information of the estimation process for each detected change point.
Depends: R (>= 3.1)
License: GPL-3
Encoding: UTF-8
Imports: geigen, ggplot2, magrittr, matrixcalc, purrr, rlang, stats
Maintainer: Vasileios Pavlopoulos <vasileios.pavlopoulos@uah.edu>
NeedsCompilation: no
Packaged: 2024-07-08 19:19:16 UTC; Business
Author: Vasileios Pavlopoulos [cre, aut], Hieu Pham [aut, ctb], Paras Bhatt [aut, ctb], Yi Tan [aut, ctb], Ravi Patnayakuni [aut, ctb]
Repository: CRAN
Date/Publication: 2024-07-09 16:10:02 UTC

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New package dapper with initial version 1.0.0
Package: dapper
Title: Data Augmentation for Private Posterior Estimation
Version: 1.0.0
Description: A data augmentation based sampler for conducting privacy-aware Bayesian inference. The dapper_sample() function takes an existing sampler as input and automatically constructs a privacy-aware sampler. The process of constructing a sampler is simplified through the specification of four independent modules, allowing for easy comparison between different privacy mechanisms by only swapping out the relevant modules. Probability mass functions for the discrete Gaussian and discrete Laplacian are provided to facilitate analyses dealing with privatized count data. The output of dapper_sample() can be analyzed using many of the same tools from the `rstan` ecosystem. For methodological details on the sampler see Ju et al. (2022) <doi:10.48550/arXiv.2206.00710>, and for details on the discrete Gaussian and discrete Laplacian distributions see Canonne et al. (2020) <doi:10.48550/arXiv.2004.00010>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/mango-empire/dapper
BugReports: https://github.com/mango-empire/dapper/issues
Suggests: testthat (>= 3.0.0)
Imports: bayesplot, checkmate, furrr, memoise, posterior, progressr, stats
NeedsCompilation: no
Packaged: 2024-07-08 15:30:25 UTC; kevin
Author: Kevin Eng [aut, cre, cph]
Maintainer: Kevin Eng <kevine1221@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-09 16:10:05 UTC

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New package syrup with initial version 0.1.0
Package: syrup
Title: Measure Memory and CPU Usage for Parallel R Code
Version: 0.1.0
Description: Measures memory and CPU usage of R code by regularly taking snapshots of calls to the system command 'ps'. The package provides an entry point (albeit coarse) to profile usage of system resources by R code run in parallel.
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Depends: bench
Imports: callr, dplyr, ps, purrr, rlang, tibble, vctrs, withr
URL: https://github.com/simonpcouch/syrup, https://simonpcouch.github.io/syrup/
BugReports: https://github.com/simonpcouch/syrup/issues
NeedsCompilation: no
Packaged: 2024-07-08 17:11:18 UTC; simoncouch
Author: Simon Couch [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Repository: CRAN
Date/Publication: 2024-07-09 15:50:02 UTC

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New package somaticflags with initial version 0.1.0
Package: somaticflags
Title: Database of Somatic Flags
Version: 0.1.0
Description: Database of genes which frequently sustain somatic mutations, but are unlikely to drive cancer.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: usethis, devtools
URL: https://github.com/CCICB/somaticflags
BugReports: https://github.com/CCICB/somaticflags/issues
NeedsCompilation: no
Packaged: 2024-07-07 23:04:50 UTC; selkamand
Author: Sam El-Kamand [aut, cre] , Children's Cancer Institute Australia [cph]
Maintainer: Sam El-Kamand <selkamand@ccia.org.au>
Repository: CRAN
Date/Publication: 2024-07-09 15:50:06 UTC

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New package rank with initial version 0.1.0
Package: rank
Title: Customisable Ranking of Numerical and Categorical Data
Version: 0.1.0
Description: Provides a flexible alternative to the built-in rank() function called smartrank(). Optionally rank categorical variables by frequency (instead of in alphabetical order), and control whether ranking is based on descending/ascending order. smartrank() is suitable for both numerical and categorical data.
License: MIT + file LICENSE
Suggests: covr, testthat (>= 3.0.0)
Encoding: UTF-8
URL: https://github.com/selkamand/rank, https://selkamand.github.io/rank/
BugReports: https://github.com/selkamand/rank/issues
NeedsCompilation: no
Packaged: 2024-07-07 05:14:16 UTC; selkamand
Author: Sam El-Kamand [aut, cre, cph]
Maintainer: Sam El-Kamand <sam.elkamand@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-09 15:30:02 UTC

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New package pEPA with initial version 1.0
Package: pEPA
Title: Tests of Equal Predictive Accuracy for Panels of Forecasts
Version: 1.0
Depends: R (>= 2.10)
Date: 2024-07-07
Author: Krzysztof Drachal [aut, cre]
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Description: Allows to perform the tests of equal predictive accuracy for panels of forecasts. Main references: Qu et al. (2024) <doi:10.1016/j.ijforecast.2023.08.001> and Akgun et al. (2024) <doi:10.1016/j.ijforecast.2023.02.001>.
License: GPL-3
LazyData: TRUE
URL: https://CRAN.R-project.org/package=pEPA
Note: Research funded by the grant of the National Science Centre, Poland, under the contract number DEC-2018/31/B/HS4/02021.
NeedsCompilation: no
Packaged: 2024-07-07 13:49:30 UTC; Krzysiek
Repository: CRAN
Date/Publication: 2024-07-09 15:50:14 UTC

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New package paramDemo with initial version 1.0.1
Package: paramDemo
Title: Parametric and Non-Parametric Demographic Functions and Applications
Version: 1.0.1
Date: 2024-07-03
Depends: R (>= 2.10)
Description: Calculate parametric mortality and Fertility models, following packages 'BaSTA' in Colchero, Jones and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and 'BaFTA' <https://github.com/fercol/BaFTA>, summary statistics (e.g. ageing rates, life expectancy, lifespan equality, etc.), life table and product limit estimators from census data.
License: GPL
BugReports: https://github.com/fercol/paramDemo/issues
NeedsCompilation: no
Packaged: 2024-07-08 08:26:27 UTC; fernando_colchero
Author: Fernando Colchero [aut, cre]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Repository: CRAN
Date/Publication: 2024-07-09 15:50:10 UTC

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New package nascaR.data with initial version 1.0.0
Package: nascaR.data
Title: NASCAR Race Data
Version: 1.0.0
Description: A collection of NASCAR race, driver, owner and manufacturer data across the three major NASCAR divisions: NASCAR Cup Series, NASCAR Xfinity Series, and NASCAR Craftsman Truck Series. The curated data begins with the 1949 season and extends through the end of the 2023 season. Data was sourced with permission from DriverAverages.com.
LazyData: true
License: CC BY 4.0
Depends: R (>= 3.5.0)
Encoding: UTF-8
Suggests: conflicted, ggtext, glue, gtsummary, here, knitr, quarto (>= 1.3.12), rmarkdown, roxygen2, rUM, scales, tidyverse
VignetteBuilder: quarto
URL: https://github.com/kyleGrealis/nascaR.data/, https://kylegrealis.github.io/nascaR.data/
BugReports: https://github.com/kyleGrealis/nascaR.data/issues
NeedsCompilation: no
Packaged: 2024-07-06 15:16:39 UTC; kxg679
Author: Kyle Grealis [aut, cre] , Gabriel Odom [ctb]
Maintainer: Kyle Grealis <kylegrealis@icloud.com>
Repository: CRAN
Date/Publication: 2024-07-09 15:20:02 UTC

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New package glam with initial version 1.0.2
Package: glam
Title: Generalized Additive and Linear Models (GLAM)
Version: 1.0.2
Description: Contains methods for fitting Generalized Linear Models (GLMs) and Generalized Additive Models (GAMs). Generalized regression models are common methods for handling data for which assuming Gaussian-distributed errors is not appropriate. For instance, if the response of interest is binary, count, or proportion data, one can instead model the expectation of the response based on an appropriate data-generating distribution. This package provides methods for fitting GLMs and GAMs under Beta regression, Poisson regression, Gamma regression, and Binomial regression (currently GLM only) settings. Models are fit using local scoring algorithms described in Hastie and Tibshirani (1990) <doi:10.1214/ss/1177013604>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: gam, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-07 18:11:43 UTC; Andy
Author: Andrew Cooper [aut, cre, cph]
Maintainer: Andrew Cooper <ahcooper@vt.edu>
Repository: CRAN
Date/Publication: 2024-07-09 15:40:02 UTC

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New package GDILM.ME with initial version 1.2.1
Package: GDILM.ME
Title: Spatial Modeling of Infectious Diseases with Co-Variate Error
Version: 1.2.1
Description: Provides tools for simulating from spatial modeling of individual level of infectious disease transmission when co-variates measured with error, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based model within Susceptible-Infectious-Removed (SIR) compartmental frameworks.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: MASS, corpcor, mvtnorm, ngspatial, numDeriv, stats, psych
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-06 14:41:34 UTC; ruwan
Author: Ruwani Herath [aut, cre], Leila Amiri [ctb], Mahmoud Torabi [ctb]
Maintainer: Ruwani Herath <ruwanirasanjalih@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-09 15:20:06 UTC

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New package FastUtils with initial version 0.1.1
Package: FastUtils
Title: Fast, Readable Utility Functions
Version: 0.1.1
Date: 2024-06-21
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Description: A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible.
BugReports: https://github.com/Qile0317/FastUtils/issues/
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Imports: assertthat, BiocManager, devtools, dplyr, ggplot2, hash, lifecycle, methods, Rcpp (>= 1.0.12), rlang, testthat, tools, usethis
LinkingTo: Rcpp
Suggests: covr, knitr, rmarkdown, spelling
VignetteBuilder: knitr
URL: https://github.com/Qile0317/FastUtils, https://qile0317.github.io/FastUtils/
NeedsCompilation: yes
Packaged: 2024-07-07 21:12:07 UTC; qile
Author: Qile Yang [cre, aut, cph]
Repository: CRAN
Date/Publication: 2024-07-09 15:40:06 UTC

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New package FAfA with initial version 0.2
Package: FAfA
Title: Factor Analysis for All
Version: 0.2
Description: This Shiny application offers researchers a comprehensive tool for performing factor analysis. Users can upload datasets, validate assumptions, manage missing and outlier data, split data for different analyses, and run exploratory and confirmatory factor analyses ("EFA" and "CFA"). The software also offers reliability analysis, exploratory graph analysis, and item weighting. With a user-friendly interface, this tool simplifies the EFA and CFA processes. The main features are data submission and simple data inspection. Data manipulation (excluding variables, splitting data, checking for outliers), assumption checking (Tabachnik & Fidell (2012) <ISBN:978-0-205-84957-4> and Field (2009) <ISBN:978-1-84787-906-6>) for factor analysis, exploratory factor analysis (with various factor number determination methods (Lorenzo-Seva & Ferrando (2021) <doi:10.5964/meth.7185>)), confirmatory factor analysis (model definition and modification suggestions (Kline (2011) <IS [...truncated...]
License: GPL-3
Imports: shiny, shinydashboard, utils, shinycssloaders, golem, magrittr, lavaan, dplyr, psych
Suggests: knitr, rmarkdown, spelling, testthat, EFA.MRFA, EFA.dimensions, EFAtools, EGAnet, MBESS, config, energy, ggcorrplot, mctest, moments, mvnormalTest, pastecs, psychometric, semPlot, semTools, sirt, stats
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-07-08 08:11:37 UTC; Faruk
Author: Abdullah Faruk KILIC [cre, aut]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Repository: CRAN
Date/Publication: 2024-07-09 15:50:25 UTC

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New package boomer with initial version 0.2.0
Package: boomer
Title: Debugging Tools to Inspect the Intermediate Steps of a Call
Version: 0.2.0
Description: Provides debugging tools that let you inspect the intermediate results of a call. The output looks as if we explode a call into its parts hence the package name.
License: GPL-3
URL: https://github.com/moodymudskipper/boomer
BugReports: https://github.com/moodymudskipper/boomer/issues
Imports: crayon, methods, pryr, rlang, rstudioapi, styler, withr
Suggests: flow, knitr, lobstr, magrittr, rmarkdown, shiny, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en
NeedsCompilation: no
Packaged: 2024-07-07 16:13:26 UTC; Antoine
Author: Antoine Fabri [aut, cre]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-09 15:50:17 UTC

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New package aLBI with initial version 0.1.4
Package: aLBI
Title: Estimating Length-Based Indicators for Fish Stock
Version: 0.1.4
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include: CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt). FishPar(): Calculates length-based indicators (LBIs) proposed by Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> such as the percentage of mature fish (Pmat), percentage of optimal length fish (Popt), percentage of mega spawners (Pmega), and the sum of these as Pobj. This function also estimates confidence intervals for different lengths, visualizes length frequency distributions, a [...truncated...]
Depends: R (>= 3.5.0)
Suggests: testthat, knitr, rmarkdown, devtools, readxl
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/Ataher76/aLBI
BugReports: https://github.com/Ataher76/aLBI/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-08 07:50:43 UTC; User
Author: Ataher Ali [aut, cre], Alam Mohammed Shahidul [aut]
Repository: CRAN
Date/Publication: 2024-07-09 15:50:21 UTC

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Mon, 08 Jul 2024

New package BaSTA with initial version 2.0.0
Package: BaSTA
Title: Age-Specific Bayesian Survival Trajectory Analysis from Incomplete Census or Capture-Recapture/Recovery Data
Version: 2.0.0
Date: 2024-07-05
Depends: R (>= 3.5.0)
Imports: snowfall (>= 1.84-6-2)
Description: Estimates survival and mortality with covariates from census or capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots, as described in Colchero, Jones, and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and Colchero et al. (2021) <doi:10.1038/s41467-021-23894-3>.
License: GPL (>= 3)
LazyData: yes
NeedsCompilation: no
Packaged: 2024-07-08 08:47:00 UTC; fernando_colchero
Author: Fernando Colchero [aut, cre], Owen Jones [ctb]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Repository: CRAN
Date/Publication: 2024-07-08 11:00:09 UTC

More information about BaSTA at CRAN
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New package translit.uk with initial version 1.0.0
Package: translit.uk
Title: Ukrainian to Latin Transliteration
Version: 1.0.0
Description: Provides a robust and user-friendly solution for transliterating Ukrainian strings into Latin symbols.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/Amice13/translit.uk
BugReports: https://github.com/Amice13/translit.uk/issues
NeedsCompilation: no
Packaged: 2024-07-04 14:49:17 UTC; kiril
Author: Kyrylo Zakharov [aut, cre]
Maintainer: Kyrylo Zakharov <kirillzakharov13@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-08 05:10:02 UTC

More information about translit.uk at CRAN
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New package taxnames with initial version 0.1.0
Package: taxnames
Version: 0.1.0
Encoding: UTF-8
Title: Formatting Taxonomic Names in Markdown
Depends: R (>= 4.3.0)
Imports: taxlist (>= 0.3.0)
Suggests: testthat (>= 3.0.0)
Description: A collection of functions used to format taxonomic names in Markdown documents. Those functions work with data structured according to Alvarez and Luebert (2018) <doi:10.3897/bdj.6.e23635>.
License: GPL-3
URL: https://github.com/kamapu/taxnames
BugReports: https://github.com/kamapu/taxnames/issues
NeedsCompilation: no
Packaged: 2024-07-05 11:19:11 UTC; miguel
Author: Miguel Alvarez [aut, cre]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-08 05:10:05 UTC

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New package Rdune with initial version 1.0.2
Package: Rdune
Title: 'Creates Color Palettes Inspired by Dune'
Version: 1.0.2
Maintainer: Nicholas Vietto <nicholasvietto@gmail.com>
Description: Enables the use of color palettes inspired by the 'Dune' movies. These palettes are compatible with 'ggplot2'. See Wickham (2016) <doi:10.1007/978-3-319-24277-4> for more details on 'ggplot2'.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, graphics, grDevices
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/nvietto/Rdune
BugReports: https://github.com/nvietto/Rdune/issues
NeedsCompilation: no
Packaged: 2024-07-05 14:06:08 UTC; nicholasvietto
Author: Nicholas Vietto [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-07-08 05:30:05 UTC

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New package PCAPAM50 with initial version 1.0.0
Package: PCAPAM50
Title: Enhanced 'PAM50' Subtyping of Breast Cancer
Version: 1.0.0
Maintainer: Praveen-Kumar Raj-Kumar <p.rajkumar@wriwindber.org>
Description: Accurate classification of breast cancer tumors based on gene expression data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier, which uses 50 gene centroid correlation distances to classify tumors, faces challenges with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50' package leverages principal component analysis and iterative 'PAM50' calls to create a gene expression-based ER-balanced subset for gene centering, avoiding the use of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.
License: GPL (>= 3)
Copyright: 2024 Windber Research Institute, Windber, PA - 15963. All Rights Reserved.
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown
Imports: Biobase, lattice, ComplexHeatmap, impute
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-05 13:26:08 UTC; praveen
Author: Praveen-Kumar Raj-Kumar [aut, cre, cph], Jianfang Liu [aut], Jeffrey A. Hooke [aut], Albert J. Kovatich [aut], Leonid Kvecher [aut], Craig D. Shriver [aut], Hai Hu [aut, cph]
Repository: CRAN
Date/Publication: 2024-07-08 05:30:11 UTC

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New package mlr3torch with initial version 0.1.0
Package: mlr3torch
Title: Deep Learning with 'mlr3'
Version: 0.1.0
Description: Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.
License: LGPL (>= 3)
Depends: mlr3 (>= 0.20.0), mlr3pipelines (>= 0.6.0), torch (>= 0.13.0), R (>= 3.5.0)
Imports: backports, checkmate (>= 2.2.0), data.table, lgr, methods, mlr3misc (>= 0.14.0), paradox (>= 1.0.0), R6, withr
Suggests: callr, future, ggplot2, igraph, jsonlite, knitr, magick, mlr3tuning (>= 1.0.0), progress, rmarkdown, rpart, viridis, visNetwork, testthat (>= 3.0.0), torchvision (>= 0.6.0), waldo
NeedsCompilation: no
ByteCompile: no
Encoding: UTF-8
Packaged: 2024-07-06 07:40:01 UTC; sebi
Author: Sebastian Fischer [cre, aut] , Bernd Bischl [ctb] , Lukas Burk [ctb] , Martin Binder [aut], Florian Pfisterer [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-08 05:40:02 UTC

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New package aelab with initial version 0.4.0
Package: aelab
Title: Calculation of Greenhouse Gas Flux
Version: 0.4.0
Maintainer: Zhao-Jun Yong <nuannuan0425@gmail.com>
Description: Facilitate the analysis of data related to ecology, specifically the establishment of carbon budget. Currently, the package allows the below analysis. (i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024). (ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010). Lin et al. (2024) <doi:10.1016/j.scitotenv.2024.170768>. Staehr et al. (2024) <doi:10.4319/lom.2010.8.0628>.
Imports: tibble, lubridate, stats, dplyr, openxlsx, readxl, ggplot2, readr, tidyr
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 2.10)
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-05 15:18:24 UTC; yangshaojun
Author: Zhao-Jun Yong [cre, aut]
Repository: CRAN
Date/Publication: 2024-07-08 05:30:02 UTC

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New package rkriging with initial version 1.0
Package: rkriging
Title: Kriging Modeling
Version: 1.0
Description: An 'Eigen'-based computationally efficient 'C++' implementation for fitting various kriging models to data. This research is supported by U.S. National Science Foundation grant DMS-2310637.
License: GPL (>= 2)
Depends: R (>= 3.0.2)
Imports: Rcpp, nloptr (>= 1.2.0), methods, stats
LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0), BH (>= 1.75.0.0), nloptr (>= 1.2.0)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-07-04 19:08:48 UTC; billhuang
Author: Chaofan Huang [aut, cre], V. Roshan Joseph [aut]
Maintainer: Chaofan Huang <10billhuang01@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-08 05:00:02 UTC

More information about rkriging at CRAN
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New package covtracer with initial version 0.0.1
Package: covtracer
Title: Contextualizing Tests
Version: 0.0.1
Description: Dissects a package environment or 'covr' coverage object in order to cross reference tested code with the lines that are evaluated, as well as linking those evaluated lines to the documentation that they are described within. Connecting these three pieces of information provides a mechanism of linking tests to documented behaviors.
URL: https://github.com/genentech/covtracer
BugReports: https://github.com/genentech/covtracer/issues
Depends: R (>= 3.2.0)
Imports: tools, stats, methods
Suggests: testthat, covr (>= 3.5.2), withr, R6, cli, dplyr, igraph, knitr, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-04 17:10:53 UTC; root
Author: Doug Kelkhoff [cre, aut] , Szymon Maksymiuk [aut] , Andrew McNeil [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-08 05:00:07 UTC

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Sun, 07 Jul 2024

New package frailtypack with initial version 3.6.2
Package: frailtypack
Version: 3.6.2
Date: 2024-07-04
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Depends: R (>= 3.5.0), survival, boot, MASS, survC1, doBy
Imports: statmod, nlme, shiny, rootSolve, splines
LazyLoad: no
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested fra [...truncated...]
License: GPL (>= 2.0)
URL: https://virginie1rondeau.wixsite.com/virginierondeau/software-frailtypack https://frailtypack-pkg.shinyapps.io/shiny_frailtypack/
Suggests: knitr, testthat, rmarkdown, markdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2024-07-07 16:10:02 UTC
Packaged: 2024-07-05 18:00:27 UTC; Quent
NeedsCompilation: yes
Author: Virginie Rondeau [aut, cre] , Juan R. Gonzalez [aut], Yassin Mazroui [aut], Audrey Mauguen [aut], Amadou Diakite [aut], Alexandre Laurent [aut], Myriam Lopez [aut], Agnieszka Krol [aut], Casimir L. Sofeu [aut], Julien Dumerc [aut], Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>

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New package synthesis with initial version 1.2.5
Package: synthesis
Title: Generate Synthetic Data from Statistical Models
Version: 1.2.5
Author: Ze Jiang [aut, cre]
Maintainer: Ze Jiang <ze.jiang@unsw.edu.au>
Description: Generate synthetic time series from commonly used statistical models, including linear, nonlinear and chaotic systems. Applications to testing methods can be found in Jiang, Z., Sharma, A., & Johnson, F. (2019) <doi:10.1016/j.advwatres.2019.103430> and Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962> associated with an open-source tool by Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/zejiang-unsw/synthesis#readme
BugReports: https://github.com/zejiang-unsw/synthesis/issues
Imports: stats, MASS, graphics
Suggests: zoo, knitr, rmarkdown, testthat, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-28 22:28:48 UTC; ze
Repository: CRAN
Date/Publication: 2024-07-07 15:10:02 UTC

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Sat, 06 Jul 2024

New package emIRT with initial version 0.0.14
Package: emIRT
Title: EM Algorithms for Estimating Item Response Theory Models
Version: 0.0.14
Date: 2024-06-23
Author: Kosuke Imai <imai@harvard.edu>, James Lo <jameslo989@gmail.com>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: Kosuke Imai <imai@harvard.edu>
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory (IRT) models. The package includes IRT models for binary and ordinal responses, along with dynamic and hierarchical IRT models with binary responses. The latter two models are fitted using variational EM. The package also includes variational network and text scaling models. The algorithms are described in Imai, Lo, and Olmsted (2016) <DOI:10.1017/S000305541600037X>.
License: GPL (>= 3)
Depends: R (>= 2.10), pscl (>= 1.0.0), Rcpp (>= 0.10.6)
Suggests: MCMCpack
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-07-05 08:47:18 UTC; kosukeimai
Repository: CRAN
Date/Publication: 2024-07-06 15:22:03 UTC

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Fri, 05 Jul 2024

New package angstromATE with initial version 0.1.2
Package: angstromATE
Title: Imports Log Files from Angstrom Engineering Thermal Evaporator
Version: 0.1.2
Author: Thomas Gredig [aut, cre]
Maintainer: Thomas Gredig <tgredig@csulb.edu>
Description: Opens and imports log files from Angstrom Engineering Thermal Evaporator and extracts basic characteristics, such as base pressure, time of the evaporation. It can visualize the deposition observables for review.
License: GPL (>= 3)
BugReports: https://github.com/thomasgredig/angstromATE/issues
Encoding: UTF-8
Imports: utils, XML
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-07-04 21:55:25 UTC; gredigcsulb
Repository: CRAN
Date/Publication: 2024-07-05 08:10:02 UTC

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Thu, 04 Jul 2024

New package wTO with initial version 2.1
Package: wTO
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Version: 2.1
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <doi:10.1186/s12859-018-2351-7>.
License: GPL-2
LazyData: TRUE
Imports: data.table, igraph, magrittr, plyr, parallel, som, visNetwork, reshape2, Rfast, HiClimR, methods
Suggests: knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-04 19:54:14 UTC; deisygysi
Repository: CRAN
Date/Publication: 2024-07-04 22:40:01 UTC

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New package FLightR with initial version 0.5.5
Package: FLightR
Title: Reconstruct Animal Paths from Solar Geolocation Loggers Data
Version: 0.5.5
Date: 2024-06-28
Description: Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.
URL: https://CRAN.R-project.org/package=FLightR
BugReports: https://github.com/eldarrak/FLightR/issues
Depends: R (>= 4.1.0)
Imports: bit, geosphere, ggmap, ggplot2, CircStats, circular, fields, maps, mgcv, nlme, parallel, RcppArmadillo, sf, suntools, truncnorm
License: GPL-3
ByteCompile: true
Encoding: UTF-8
Suggests: covr, testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-04 11:15:15 UTC; eldar
Author: Eldar Rakhimberdiev [aut, cre], Anatoly Saveliev [aut], Julia Karagicheva [aut], Simeon Lisovski [ctb], Johannes de Groeve [ctb]
Maintainer: Eldar Rakhimberdiev <eldar.rakhimberdiev@uva.nl>
Repository: CRAN
Date/Publication: 2024-07-04 17:10:06 UTC

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New package circhelp with initial version 1.1
Package: circhelp
Title: Circular Analyses Helper Functions
Version: 1.1
Description: Light-weight functions for computing descriptive statistics in different circular spaces (e.g., 2pi, 180, or 360 degrees), to handle angle-dependent biases, pad circular data, and more. Specifically aimed for psychologists and neuroscientists analyzing circular data. Basic methods are based on Jammalamadaka and SenGupta (2001) <doi:10.1142/4031>, removal of cardinal biases is based on the approach introduced in van Bergen, Ma, Pratte, & Jehee (2015) <doi:10.1038/nn.4150> and Chetverikov and Jehee (2023) <doi:10.1038/s41467-023-43251-w>.
URL: https://achetverikov.github.io/circhelp/index.html, https://github.com/achetverikov/circhelp
BugReports: https://github.com/achetverikov/circhelp/issues
License: CC0
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), circular, knitr, rmarkdown, BAMBI, mgcv, ragg
Imports: gamlss, MASS, mathjaxr, patchwork
Depends: stats, data.table, ggplot2, R (>= 2.10)
VignetteBuilder: knitr, patchwork, ggplot2, MASS, gamlss, mgcv, ragg
NeedsCompilation: no
Packaged: 2024-07-04 11:36:14 UTC; anche7026
Author: Andrey Chetverikov [aut, cre] , Eline Van Geert [ctb]
Maintainer: Andrey Chetverikov <andrey.chetverikov@uib.no>
Repository: CRAN
Date/Publication: 2024-07-04 17:10:02 UTC

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New package LightLogR with initial version 0.3.8
Package: LightLogR
Title: Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
Version: 0.3.8
Description: Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/tscnlab/LightLogR, https://tscnlab.github.io/LightLogR/, https://zenodo.org/doi/10.5281/zenodo.11562600
BugReports: https://github.com/tscnlab/LightLogR/issues
Imports: cowplot, dplyr, flextable, ggplot2, ggsci, ggtext, hms, lubridate, magrittr, pkgload, plotly, purrr, readr, rlang, rsconnect, scales, slider, stats, stringr, tibble, tidyr, utils
Depends: R (>= 2.10)
LazyData: true
Suggests: covr, gghighlight, gt, gtsummary, knitr, patchwork, rmarkdown, testthat (>= 3.0.0), tidyverse
NeedsCompilation: no
Packaged: 2024-07-04 09:38:03 UTC; zauner
Author: Johannes Zauner [aut, cre] , Manuel Spitschan [aut] , Steffen Hartmeyer [aut] , MeLiDos [fnd], EURAMET [fnd] has received funding from the European Partnership on Metrology, co-financed from the European Union’s Horizon Europe Research and Innovatio [...truncated...]
Maintainer: Johannes Zauner <johannes.zauner@tum.de>
Repository: CRAN
Date/Publication: 2024-07-04 17:00:02 UTC

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New package ctxR with initial version 1.0.0
Package: ctxR
Title: Utilities for Interacting with the 'CTX' APIs
Version: 1.0.0
Description: Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://api-ccte.epa.gov/docs/>. 'ctxR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.
License: GPL (>= 3)
Imports: cli, data.table, httr, jsonlite, purrr, rlang, stringr, tidyr, tibble, urltools
Encoding: UTF-8
LazyData: true
Suggests: countcolors, devtools, DT, ggplot2, gridExtra, httptest, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0), XML
URL: https://github.com/USEPA/ctxR
BugReports: https://github.com/USEPA/ctxR/issues
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-07-03 12:20:29 UTC; PKRUSE
Author: Paul Kruse [aut, cre] , Caroline Ring [aut] , Madison Feshuk [ctb] , Carter Thunes [ctb], Jason Brown [ctb]
Maintainer: Paul Kruse <kruse.paul@epa.gov>
Repository: CRAN
Date/Publication: 2024-07-04 16:40:02 UTC

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New package ACSSpack with initial version 0.0.1.4
Package: ACSSpack
Title: ACSS, Corresponding ACSS, and GLP Algorithm
Version: 0.0.1.4
Date: 2024-06-30
Description: Allow user to run the Adaptive Correlated Spike and Slab (ACSS) algorithm, corresponding INdependent Spike and Slab (INSS) algorithm, and Giannone, Lenza and Primiceri (GLP) algorithm with adaptive burn-in. All of the three algorithms are used to fit high dimensional data set with either sparse structure, or dense structure with smaller contributions from all predictors. The state-of-the-art GLP algorithm is in Giannone, D., Lenza, M., & Primiceri, G. E. (2021, ISBN:978-92-899-4542-4) "Economic predictions with big data: The illusion of sparsity". The two new algorithms, ACSS algorithm and INSS algorithm, and the discussion on their performance can be seen in Yang, Z., Khare, K., & Michailidis, G. (2024, preprint) "Bayesian methodology for adaptive sparsity and shrinkage in regression".
License: GPL-3
Encoding: UTF-8
Imports: stats, HDCI (>= 1.0-2), MASS (>= 7.3-60), extraDistr (>= 1.4-4)
LinkingTo: Rcpp (>= 1.0.11), RcppArmadillo (>= 0.12.6.3.0)
Depends: R (>= 3.0.2)
LazyData: true
NeedsCompilation: yes
Packaged: 2024-07-03 23:35:18 UTC; yangt
Author: Ziqian Yang [cre, aut], Kshitij Khare [aut], George Michailidis [aut]
Maintainer: Ziqian Yang <zi.yang@ufl.edu>
Repository: CRAN
Date/Publication: 2024-07-04 16:40:08 UTC

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New package cubar with initial version 0.6.0
Package: cubar
Title: Codon Usage Bias Analysis
Version: 0.6.0
Description: A suite of functions for rapid and flexible analysis of codon usage bias. It provides in-depth analysis at the codon level, including relative synonymous codon usage (RSCU), tRNA weight calculations, machine learning predictions for optimal or preferred codons, and visualization of codon-anticodon pairing. Additionally, it can calculate various gene- specific codon indices such as codon adaptation index (CAI), effective number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation index (tAI), mean codon stabilization coefficients (CSCg), and GC contents (GC/GC3s/GC4d). It also supports both standard and non-standard genetic code tables found in NCBI, as well as custom genetic code tables.
License: MIT + file LICENSE
URL: https://github.com/mt1022/cubar, https://mt1022.github.io/cubar/
BugReports: https://github.com/mt1022/cubar/issues
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
Imports: Biostrings (>= 2.60.0), IRanges (>= 2.34.0), data.table (>= 1.14.0), ggplot2 (>= 3.3.5), rlang (>= 0.4.11)
Depends: R (>= 4.1.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-04 11:13:49 UTC; mt1022
Author: Hong Zhang [aut, cre] , Bu Zi [aut]
Maintainer: Hong Zhang <mt1022.dev@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-04 12:50:06 UTC

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New package ReturnCurves with initial version 1.0
Package: ReturnCurves
Title: Estimation of Return Curves
Version: 1.0
Date: 2024-06-24
Maintainer: Lidia Andre <l.andre@lancaster.ac.uk>
Description: Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: evd, ismev, Rdpack, mathjaxr, ggplot2 (>= 3.4.4), gridExtra, methods, stats, shiny, tools, DT, shinydashboard, openair
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-03 17:40:21 UTC; andrel
Author: Lidia Andre [aut, cre], Callum Murphy-Barltrop [aut]
Repository: CRAN
Date/Publication: 2024-07-04 11:30:02 UTC

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New package hidradenitis with initial version 1.0.0
Package: hidradenitis
Title: Calculate Clinical Scores for Hidradenitis Suppurativa (HS), a Dermatologic Disease
Version: 1.0.0
Description: Calculate clinical scores for hidradenitis suppurativa (HS), a dermatologic disease. The scores are typically used for evaluation of efficacy in clinical trials. The scores are not commonly used in clinical practice. The specific scores implemented are Hidradenitis Suppurativa Clinical Response (HiSCR) (Kimball, et al. (2015) <doi:10.1111/jdv.13216>), Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb, et al. (2020) <doi:10.1111/bjd.19565>), hidradenitis suppurativa Physician Global Assessment (HS PGA) (Marzano, et al. (2020) <doi:10.1111/jdv.16328>), and the International Hidradenitis Suppurativa Severity Score System (IHS4) (Zouboulis, et al. (2017) <doi:10.1111/bjd.15748>).
License: GPL (>= 3)
Encoding: UTF-8
Suggests: spelling, testthat (>= 3.0.0)
URL: https://billdenney.github.io/hidradenitis/
Language: en-US
Imports: checkmate
NeedsCompilation: no
Packaged: 2024-07-03 13:29:28 UTC; bill
Author: Bill Denney [aut, cre] , Devon Bartlett [aut]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Repository: CRAN
Date/Publication: 2024-07-04 08:20:02 UTC

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New package SOMnmR with initial version 0.3.0
Package: SOMnmR
Title: Analysis of Soil Organic Matter using Nuclear Magnetic Resonance
Version: 0.3.0
Description: Integrates the 13C nuclear magnetic resonance spectra using different integration ranges. Output depends on the method chosen. For the Molecular Mixing Model, a measurement of the fitting quality is given by its R-factor. For more details see: <doi:10.5281/zenodo.10137768>.
URL: https://github.com/LuisCol8/SOMnmR/
Encoding: UTF-8
LazyData: true
Imports: pracma, minpack.lm, quadprog, IntervalSurgeon, dplyr, ggplot2, rlang
Depends: data.table, R (>= 2.10)
Suggests: testthat (>= 3.0.0)
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2024-07-03 11:28:45 UTC; zak69953
Author: Luis Colocho [aut, cre]
Maintainer: Luis Colocho <lucacol8@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-04 07:50:05 UTC

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New package pmev with initial version 0.0.2
Package: pmev
Title: Calculates Earned Value for a Project Schedule
Version: 0.0.2
Author: David Hammond [aut, cre]
URL: https://github.com/david-hammond/pmev
BugReports: https://github.com/david-hammond/pmev
Maintainer: David Hammond <anotherdavidhammond@gmail.com>
Description: Given a project schedule and associated costs, this package calculates the earned value to date. It is an implementation of Project Management Body of Knowledge (PMBOK) methodologies (reference Project Management Institute. (2021). A guide to the Project Management Body of Knowledge (PMBOK guide) (7th ed.). Project Management Institute, Newtown Square, PA, ISBN 9781628256673 (pdf)).
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Imports: dplyr, lubridate, magrittr, zoo, rlang
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-03 11:02:17 UTC; david
Repository: CRAN
Date/Publication: 2024-07-04 07:50:02 UTC

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Wed, 03 Jul 2024

New package SILFS with initial version 0.1.0
Package: SILFS
Title: Subgroup Identification with Latent Factor Structure
Version: 0.1.0
Author: Yong He [aut], Dong Liu [aut], Fuxin Wang [aut, cre], Mingjuan Zhang [aut], Wenxin Zhou [aut]
Maintainer: Fuxin Wang <wangfuxin2001@163.com>
Description: In various domains, many datasets exhibit both high variable dependency and group structures, which necessitates their simultaneous estimation. This package provides functions for two subgroup identification methods based on penalized functions, both of which utilize factor model structures to adapt to data with cross-sectional dependency. The first method is the Subgroup Identification with Latent Factor Structure Method (SILFSM) we proposed. By employing Center-Augmented Regularization and factor structures, the SILFSM effectively eliminates data dependencies while identifying subgroups within datasets. For this model, we offer optimization functions based on two different methods: Coordinate Descent and our newly developed Difference of Convex-Alternating Direction Method of Multipliers (DC-ADMM) algorithms; the latter can be applied to cases where the distance function in Center-Augmented Regularization takes L1 and L2 forms. The other method is the Factor-Adjusted Pairwise Fusion [...truncated...]
License: GPL-2 | GPL-3
Encoding: UTF-8
Imports: MASS, glmnet, stats, Ckmeans.1d.dp
NeedsCompilation: no
Packaged: 2024-07-03 07:37:39 UTC; 王福鑫
Repository: CRAN
Date/Publication: 2024-07-03 16:20:06 UTC

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New package dropR with initial version 1.0.3
Package: dropR
Version: 1.0.3
Title: Dropout Analysis by Condition
Description: Analysis and visualization of dropout between conditions in surveys and (online) experiments. Features include computation of dropout statistics, comparing dropout between conditions (e.g. Chi square), analyzing survival (e.g. Kaplan-Meier estimation), comparing conditions with the most different rates of dropout (Kolmogorov-Smirnov) and visualizing the result of each in designated plotting functions. Sources: Andrea Frick, Marie-Terese Baechtiger & Ulf-Dietrich Reips (2001) <https://www.researchgate.net/publication/223956222_Financial_incentives_personal_information_and_drop-out_in_online_studies>; Ulf-Dietrich Reips (2002) "Standards for Internet-Based Experimenting" <doi:10.1027//1618-3169.49.4.243>.
Depends: R (>= 3.0.0)
Imports: shiny, ggplot2, data.table, survival, lifecycle
Suggests: DT, shinydashboard, knitr, rmarkdown, kableExtra
Date: 2024-06-24
License: GPL (>= 3)
LazyData: true
URL: https://iscience-kn.github.io/dropR/, https://github.com/iscience-kn/dropR
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-03 09:38:39 UTC; Admin
Author: Annika Tave Overlander [aut, cre], Matthias Bannert [aut], Ulf-Dietrich Reips [ctb]
Maintainer: Annika Tave Overlander <annika-tave.overlander@uni.kn>
Repository: CRAN
Date/Publication: 2024-07-03 16:20:02 UTC

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New package rmstBayespara with initial version 0.1.0
Package: rmstBayespara
Title: Bayesian Restricted Mean Survival Time for Cluster Effect
Version: 0.1.0
Description: The parametric Bayes analysis for the restricted mean survival time (RMST) with cluster effect, as described in Hanada and Kojima (2024) <doi:10.48550/arXiv.2406.06071>. Bayes estimation with random-effect and frailty-effect can be applied to several parametric models useful in survival time analysis. The RMST under these parametric models can be computed from the obtained posterior samples.
License: GPL (>= 3)
Depends: R (>= 3.4.0)
Imports: brms (>= 2.21.0), crayon (>= 1.5.0), loo (>= 2.7.0), methods, rstan (>= 2.32.0), stats (>= 4.3.0), zipfR (>= 0.6.7)
Biarch: true
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-07-03 00:22:44 UTC; keihb
Author: Keisuke Hanada [aut, cre] , Masahiro Kojima [aut]
Maintainer: Keisuke Hanada <keisuke.hanada.87@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-03 16:00:02 UTC

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New package ntsDatasets with initial version 0.1.0
Package: ntsDatasets
Title: Neutrosophic Data Sets
Version: 0.1.0
Maintainer: Amin Roshani <roshani.amin@gmail.com>
Description: Provides a collection of datasets related to neutrosophic sets for statistical modeling and analysis.
License: GPL-3
URL: https://github.com/a-roshani/ntsDatasets
Encoding: UTF-8
LazyData: false
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2024-07-02 17:03:21 UTC; minan
Author: Amin Roshani [aut, cre] , Mina Norouzirad [aut] , Danial Mazarei [aut] , FCT, I.P. [fnd] )
Repository: CRAN
Date/Publication: 2024-07-03 16:00:05 UTC

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New package nonsmooth with initial version 1.0.0
Package: nonsmooth
Title: Nonparametric Methods for Smoothing Nonsmooth Data
Version: 1.0.0
Imports: stats, np, graphics, reshape2
Maintainer: John R.J. Thompson <john.thompson@ubc.ca>
Description: Nonparametric methods for smoothing regression function data with change-points, utilizing range kernels for iterative and anisotropic smoothing methods. For further details, see the paper by John R.J. Thompson (2024) <doi:10.1080/02664763.2024.2352759>.
License: CC BY 4.0
URL: https://github.com/jrjthompson/R-package-nonsmooth/
BugReports: https://github.com/jrjthompson/R-package-nonsmooth/issues
Depends: R (>= 3.5.0)
Repository: CRAN
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-07-02 22:10:34 UTC; jthomp14
Author: John R.J. Thompson [aut, cre]
Date/Publication: 2024-07-03 16:00:09 UTC

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New package neuroimaGene with initial version 0.1.0
Package: neuroimaGene
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Version: 0.1.0
Maintainer: Xavier Bledsoe <xavier.bledsoe@vanderbilt.edu>
Description: Contains functions to query and visualize the Neuroimaging features associated with genetically regulated gene expression (GReX). The primary utility, neuroimaGene(), relies on a list of user-defined genes and returns a table of neuroimaging features (NIDPs) associated with each gene. This resource is designed to assist in the interpretation of genome-wide and transcriptome-wide association studies that evaluate brain related traits. Bledsoe (2024) <doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization functions that generate summary plots and 2-dimensional visualizations of regional brain measures. Mowinckel (2020).
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: data.table, ggplot2, DBI, stringr, ggseg, RSQLite
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-02 16:43:17 UTC; xbledsoe
Author: Xavier Bledsoe [aut, cre] , Eric Gamazon [aut]
Repository: CRAN
Date/Publication: 2024-07-03 15:50:02 UTC

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New package scellpam with initial version 1.4.6.1
Package: scellpam
Title: Applying Partitioning Around Medoids to Single Cell Data with High Number of Cells
Version: 1.4.6.1
Date: 2024-07-01
Author: Juan Domingo [aut, cre] , Guillermo Ayala [ctb] , Spanish Ministry of Science and Innovation, MCIN/AEI <doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Description: PAM (Partitioning Around Medoids) algorithm application to samples of single cell sequencing techniques with a high number of cells (as many as the computer memory allows). The package uses a binary format to store matrices (either full, sparse or symmetric) in files written in the disk that can contain any data type (not just double) which allows its manipulation when memory is sufficient to load them as int or float, but not as double. The PAM implementation is done in parallel, using several/all the cores of the machine, if it has them. This package shares a great part of its code with packages 'jmatrix' and 'parallelpam' but their functionality is included here so there is no need to install them.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.8), memuse (>= 4.2.1), cluster (>= 2.1.4)
LinkingTo: Rcpp
Encoding: UTF-8
Suggests: rmarkdown, knitr, scater, splatter
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-07-01 21:31:29 UTC; jdomingo
Repository: CRAN
Date/Publication: 2024-07-03 12:30:02 UTC

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New package metajam with initial version 0.3.0
Package: metajam
Title: Easily Download Data and Metadata from 'DataONE'
Version: 0.3.0
Date: 2024-07-02
Maintainer: Julien Brun <julien.brun@alumni.duke.edu>
Description: A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.
License: Apache License (== 2.0)
Encoding: UTF-8
Language: en-US
SystemRequirements: Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>= 1.0.14)
URL: https://nceas.github.io/metajam/
BugReports: https://github.com/nceas/metajam/issues
Depends: R (>= 3.6.0)
Imports: dataone, dplyr, EML, emld, lubridate, purrr, readr, stats, stringr, tibble, tidyr, XML
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-02 22:45:13 UTC; jb160-local
Author: Julien Brun [cre, aut] , Irene Steves [aut] , Mitchell Maier [aut] , Kristen Peach [aut] , Nicholas Lyon [aut] , Nathan Hwangbo [ctb] , Derek Strong [ctb] , Colin Smith [ctb] , Regents of the University of California [cph]
Repository: CRAN
Date/Publication: 2024-07-03 07:20:05 UTC

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Tue, 02 Jul 2024

New package PRA with initial version 0.2.0
Package: PRA
Title: Project Risk Analysis
Version: 0.2.0
Description: Data analysis for Project Risk Management via the Second Moment Method, Monte Carlo Simulation, Bayesian methods, Design Structure Matrices, and more.
Imports: mc2d, minpack.lm, stats
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://paulgovan.github.io/PRA/, https://github.com/paulgovan/PRA
BugReports: https://github.com/paulgovan/PRA/issues
Suggests: ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-01 19:10:44 UTC; paulgovan
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-02 15:20:05 UTC

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New package ppRank with initial version 0.1.0
Package: ppRank
Title: Classification of Algorithms
Version: 0.1.0
Maintainer: Tiago Costa Soares <tiagocsoares22@gmail.com>
Description: Implements the Bi-objective Lexicographical Classification method and Performance Assessment Ratio at 10% metric for algorithm classification. Constructs matrices representing algorithm performance under multiple criteria, facilitating decision-making in algorithm selection and evaluation. Analyzes and compares algorithm performance based on various metrics to identify the most suitable algorithms for specific tasks. This package includes methods for algorithm classification and evaluation, with examples provided in the documentation. Carvalho (2019) presents a statistical evaluation of algorithmic computational experimentation with infeasible solutions <doi:10.48550/arXiv.1902.00101>. Moreira and Carvalho (2023) analyze power in preprocessing methodologies for datasets with missing values <doi:10.1080/03610918.2023.2234683>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-01 18:34:27 UTC; tiago
Author: Tiago Costa Soares [aut, cre], Pedro Augusto Mendes [aut]
Repository: CRAN
Date/Publication: 2024-07-02 15:10:02 UTC

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New package mcODE with initial version 1.1
Package: mcODE
Title: Monte Carlo Solution of First Order Differential Equations
Version: 1.1
Date: 2024-07-01
Description: Two functions for simulating the solution of initial value problems of the form g'(x) = G(x, g) with g(x0) = g0. One is an acceptance-rejection method. The other is a method based on the Mean Value Theorem.
LazyLoad: true
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-07-01 21:41:28 UTC; johbraun
Author: W.J. Braun [aut, cre]
Maintainer: W.J. Braun <john.braun@ubc.ca>
Repository: CRAN
Date/Publication: 2024-07-02 15:20:02 UTC

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New package matrixmodp with initial version 0.2.0
Package: matrixmodp
Title: Working with Matrices over Finite Prime Fields
Version: 0.2.0
Description: Provides functions for row-reducing and inverting matrices with entries in many of the finite fields (those with a prime number of elements). With this package, users will be able to find the reduced row echelon form (RREF) of a matrix and calculate the inverse of a (square, invertible) matrix.
License: GPL (>= 2)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
URL: https://github.com/rhigginbottom/matrixmodp, https://rhigginbottom.github.io/matrixmodp/
BugReports: https://github.com/rhigginbottom/matrixmodp/issues
NeedsCompilation: no
Packaged: 2024-07-01 15:46:42 UTC; rhigginbottom
Author: Ryan Higginbottom [aut, cre, cph]
Maintainer: Ryan Higginbottom <rhigginbottom@washjeff.edu>
Repository: CRAN
Date/Publication: 2024-07-02 15:10:05 UTC

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New package jlme with initial version 0.1.0
Package: jlme
Title: Regression Modelling with 'GLM.jl' and 'MixedModels.jl' in 'Julia'
Version: 0.1.0
Description: Bindings to 'Julia' packages 'GLM.jl' <doi:10.5281/zenodo.3376013> and 'MixedModels.jl' <doi:10.5281/zenodo.12575371>, powered by 'JuliaConnectoR'. Fits (generalized) linear (mixed-effects) regression models in 'Julia' using familiar model fitting syntax from R. Offers 'broom'-style data frame summary functionalities for 'Julia' regression models.
License: MIT + file LICENSE
URL: https://yjunechoe.github.io/jlme/
Depends: R (>= 4.1)
Imports: generics, JuliaConnectoR, JuliaFormulae, MASS, stats, utils
Suggests: broom, broom.mixed, lme4, testthat (>= 3.0.0)
Encoding: UTF-8
SystemRequirements: Julia (>= 1.8)
NeedsCompilation: no
Packaged: 2024-07-02 10:00:19 UTC; jchoe
Author: June Choe [aut, cre]
Maintainer: June Choe <jchoe001@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-02 15:50:02 UTC

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New package CBPE with initial version 0.1.0
Package: CBPE
Title: Correlation-Based Penalized Estimators
Version: 0.1.0
Maintainer: Mina Norouzirad <mina.norouzirad@gmail.com>
Description: Provides correlation-based penalty estimators for both linear and logistic regression models by implementing a new regularization method that incorporates correlation structures within the data. This method encourages a grouping effect where strongly correlated predictors tend to be in or out of the model together. See Tutz and Ulbricht (2009) <doi:10.1007/s11222-008-9088-5> and Algamal and Lee (2015) <doi:10.1016/j.eswa.2015.08.016>.
License: GPL (>= 2)
URL: https://github.com/mnrzrad/CBPE
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: stats
NeedsCompilation: no
Packaged: 2024-07-02 07:23:55 UTC; minan
Author: Mohammad Arashi [ctb] , Mahdi Rahimi [ctb], Mina Norouzirad [aut, cre, cph] , FCT, I.P. [fnd] )
Repository: CRAN
Date/Publication: 2024-07-02 15:30:02 UTC

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New package worldbank with initial version 0.1.0
Package: worldbank
Title: Client for the 'World Bank Indicators API'
Version: 0.1.0
Description: Download and search data from the 'World Bank Indicators API', which provides access to nearly 16,000 time series indicators. See <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation> for further details about the API.
License: MIT + file LICENSE
URL: https://m-muecke.github.io/worldbank/, https://github.com/m-muecke/worldbank
BugReports: https://github.com/m-muecke/worldbank/issues
Depends: R (>= 4.1.0)
Imports: httr2
Suggests: ggplot2, scales, testthat (>= 3.0.0), tibble
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-07-01 10:30:47 UTC; mmuecke
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Repository: CRAN
Date/Publication: 2024-07-02 14:50:02 UTC

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New package CPCAT with initial version 1.0.0
Package: CPCAT
Title: The Closure Principle Computational Approach Test
Version: 1.0.0
Description: P-values and no/lowest observed (adverse) effect concentration values derived from the closure principle computational approach test (Lehmann, R. et al. (2015) <doi:10.1007/s00477-015-1079-4>) are provided. The package contains functions to generate intersection hypotheses according to the closure principle (Bretz, F., Hothorn, T., Westfall, P. (2010) <doi:10.1201/9781420010909>), an implementation of the computational approach test (Ching-Hui, C., Nabendu, P., Jyh-Jiuan, L. (2010) <doi:10.1080/03610918.2010.508860>) and the combination of both, that is, the closure principle computational approach test.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-07-01 10:59:59 UTC; René Lehmann
Author: Rene Lehmann [aut, cre]
Maintainer: Rene Lehmann <rene.lehmann82@t-online.de>
Repository: CRAN
Date/Publication: 2024-07-02 15:00:06 UTC

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New package uncertainUCDP with initial version 0.5.2
Package: uncertainUCDP
Title: Parametric Mixture Models for Uncertainty Estimation of Fatalities in UCDP Conflict Data
Version: 0.5.2
Description: Provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, mistr, rlang, tibble
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-07-01 08:45:16 UTC; david
Author: David Randahl [cre, aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Repository: CRAN
Date/Publication: 2024-07-02 06:30:02 UTC

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New package sundialr with initial version 0.1.4.2
Package: sundialr
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
Version: 0.1.4.2
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
URL: https://github.com/sn248/sundialr
BugReports: https://github.com/sn248/sundialr/issues
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
License: BSD_3_clause + file LICENSE
Copyright: file COPYRIGHTS
Imports: Rcpp (>= 1.0.12)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat
SystemRequirements: GNU make
NeedsCompilation: yes
VignetteBuilder: knitr
Packaged: 2024-06-30 13:27:11 UTC; nayaks16
Author: Satyaprakash Nayak [aut, cre, cph] , Lawrence Livermore National Security [cph], Southern Methodist University [cph]
Repository: CRAN
Date/Publication: 2024-07-02 06:10:02 UTC

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New package icpack with initial version 0.1.0
Package: icpack
Date: 2024-06-21
Title: Survival Analysis of Interval-Censored Data
Version: 0.1.0
Depends: R (>= 4.1.0), survival (>= 3.1)
Imports: methods, rlang, gridExtra, checkmate, matrixStats, dplyr, reshape2, ggplot2
Suggests: testthat, flexsurv, lemon, knitr, markdown
Description: Survival analysis of interval-censored data with proportional hazards, and an explicit smooth estimate of the baseline log-hazard with P-splines.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-07-01 07:44:24 UTC; hputter
Author: Hein Putter [aut, cre], Paul Eilers [aut]
Maintainer: Hein Putter <h.putter@lumc.nl>
Repository: CRAN
Date/Publication: 2024-07-02 06:30:05 UTC

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New package ecode with initial version 0.1.0
Package: ecode
Title: Ordinary Differential Equation Systems in Ecology
Version: 0.1.0
Description: A framework to simulate ecosystem dynamics through ordinary differential equations (ODEs). You create an ODE model, tells 'ecode' to explore its behaviour, and perform numerical simulations on the model. 'ecode' also allows you to fit model parameters by machine learning algorithms. Potential users include researchers who are interested in the dynamics of ecological community and biogeochemical cycles.
Imports: ggplot2, cowplot, rlang, stringr
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/HaoranPopEvo/ecode/issues
URL: https://github.com/HaoranPopEvo/ecode
NeedsCompilation: no
Packaged: 2024-06-30 14:55:42 UTC; asa
Author: Haoran Wu [aut, cre] , Chen Peng [aut]
Maintainer: Haoran Wu <haoran.wu@wolfson.ox.ac.uk>
Repository: CRAN
Date/Publication: 2024-07-02 06:20:02 UTC

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New package aqfig with initial version 0.9
Package: aqfig
Version: 0.9
Date: 2024-06-27
Title: Display Air Quality Model Output and Monitoring Data
Imports: graphics, grDevices, stats, geoR
Suggests: maps
Description: Display air quality model output and monitoring data using scatterplots, grids, and legends.
License: Unlimited
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-30 21:15:56 UTC; jenise
Author: Jenise Swall [aut, cre], Kristen Foley [ctb]
Maintainer: Jenise Swall <jswall@vcu.edu>
Repository: CRAN
Date/Publication: 2024-07-02 06:20:10 UTC

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Mon, 01 Jul 2024

New package vse4ts with initial version 1.0.0
Package: vse4ts
Title: Identify Memory Patterns in Time Series Using Variance Scale Exponent
Version: 1.0.0
Description: Methods for calculating the variance scale exponent to identify memory patterns in time series data. Includes tests for white noise, short memory, and long memory. See Fu, H. et al. (2018) <doi:10.1016/j.physa.2018.06.092>.
License: MIT + file LICENSE
URL: https://z-my-cn.github.io/vse4ts/
BugReports: https://github.com/z-my-cn/vse4ts/issues
Imports: stats
Suggests: pracma
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-29 09:27:23 UTC; Dream
Author: Mengyang Zheng [aut, cre], Hui Fu [aut]
Maintainer: Mengyang Zheng <mengyang.zheng@outlook.com>
Repository: CRAN
Date/Publication: 2024-07-01 10:20:03 UTC

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New package simdata with initial version 0.4.0
Package: simdata
Title: Generate Simulated Datasets
Version: 0.4.0
Maintainer: Michael Kammer <michael.kammer@meduniwien.ac.at>
Description: Generate simulated datasets from an initial underlying distribution and apply transformations to obtain realistic data. Implements the 'NORTA' (Normal-to-anything) approach from Cario and Nelson (1997) and other data generating mechanisms. Simple network visualization tools are provided to facilitate communicating the simulation setup.
License: GPL-3
Imports: Matrix, mvtnorm, igraph (>= 1.2.1)
Suggests: doParallel, doRNG, dplyr, fitdistrplus, forcats, ggplot2, GGally, ggcorrplot, knitr, nhanesA, patchwork, purrr, reshape2, rmarkdown, testthat (>= 2.1.0)
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://matherealize.github.io/simdata/, https://github.com/matherealize/simdata
BugReports: https://github.com/matherealize/simdata/issues
NeedsCompilation: no
Packaged: 2024-06-29 09:44:13 UTC; MichaelK
Author: Michael Kammer [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-01 10:20:20 UTC

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New package LSEbootLS with initial version 0.1.0
Package: LSEbootLS
Date: 2024-06-28
Title: Bootstrap Methods for Regression Models with Locally Stationary Errors
Version: 0.1.0
Maintainer: Nicolas Loyola <nloyola2016@udec.cl>
Description: Implements bootstrap methods for linear regression models with errors following a time-varying process, focusing on approximating the distribution of the least-squares estimator for regression models with locally stationary errors. It enables the construction of bootstrap and classical confidence intervals for regression coefficients, leveraging intensive simulation studies and real data analysis.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: TRUE
Depends: doParallel, R (>= 2.10)
Imports: foreach, doRNG, stats, parallel, LSTS, tibble, iterators, rlecuyer
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-06-29 04:35:05 UTC; nicol
Author: Guillermo Ferreira [aut], Joel Munoz [aut], Nicolas Loyola [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-01 10:10:03 UTC

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New package orbital with initial version 0.1.0
Package: orbital
Title: Predict with 'tidymodels' Workflows in Databases
Version: 0.1.0
Description: Turn 'tidymodels' workflows into objects containing the sufficient sequential equations to perform predictions. These smaller objects allow for low dependency prediction locally or directly in databases.
License: MIT + file LICENSE
URL: https://github.com/tidymodels/orbital
BugReports: https://github.com/tidymodels/orbital/issues
Imports: cli, rlang
Suggests: dbplyr, dplyr, dtplyr, jsonlite, kknn, parsnip, recipes, testthat (>= 3.0.0), tidypredict, workflows
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-28 20:11:07 UTC; emilhvitfeldt
Author: Emil Hvitfeldt [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Repository: CRAN
Date/Publication: 2024-07-01 10:00:02 UTC

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New package EIEntropy with initial version 0.0.1
Package: EIEntropy
Title: Ecological Inference Applying Entropy
Version: 0.0.1
Depends: R (>= 3.5.0)
Maintainer: Silvia Maria Franco Anaya <sfrana@unileon.es>
Description: Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, magrittr
Suggests: devtools, knitr, rmarkdown, here
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-06-28 17:10:49 UTC; pc
Author: Alberto Diaz-Dapena [aut, cph], Silvia Maria Franco Anaya [aut, cre, cph], Esteban Fernandez-Vazquez [aut, cph]
Repository: CRAN
Date/Publication: 2024-07-01 09:40:02 UTC

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Sat, 29 Jun 2024

New package PDXpower with initial version 1.0.2
Package: PDXpower
Title: Time to Event Outcome in Experimental Designs of Pre-Clinical Studies
Version: 1.0.2
Date: 2024-06-27
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Description: Conduct simulation-based customized power calculation for clustered time to event data in a mixed crossed/nested design, where a number of cell lines and a number of mice within each cell line are considered to achieve a desired statistical power, motivated by Eckel-Passow and colleagues (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2024) <doi:10.48550/arXiv.2404.08927>. This package provides two commonly used models for powering a design, linear mixed effects and Cox frailty model. Both models account for within-subject (cell line) correlation while holding different distributional assumptions about the outcome. Alternatively, the counterparts of fixed effects model are also available, which produces similar estimates of statistical power.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.5.0),survival,stats,parallel
Imports: nlme,frailtypack,ggplot2,ggpubr
Suggests: testthat (>= 3.0.0), spelling
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-28 15:41:02 UTC; shanpengli
Author: Shanpeng Li [aut, cre], Gang Li [ctb]
Repository: CRAN
Date/Publication: 2024-06-29 07:00:02 UTC

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Fri, 28 Jun 2024

New package osmapiR with initial version 0.1.0
Package: osmapiR
Title: 'OpenStreetMap' API
Version: 0.1.0
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Description: Interface to 'OpenStreetMap API' for fetching and saving data from/to the 'OpenStreetMap' database (<https://wiki.openstreetmap.org/wiki/API_v0.6>).
License: GPL (>= 3)
URL: https://jmaspons.github.io/osmapiR/, https://github.com/jmaspons/osmapiR
BugReports: https://github.com/jmaspons/osmapiR/issues
Imports: curl, httr2, xml2
Suggests: httptest2, httpuv, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-27 10:11:16 UTC; joan
Author: Joan Maspons [aut, cre, cph] , Jon Harmon [rev] , Carlos Camara [rev]
Repository: CRAN
Date/Publication: 2024-06-28 14:40:04 UTC

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New package convertBCD with initial version 1.0
Package: convertBCD
Title: Convert Decimal to Binary-Coded Decimal (BCD) Form and Vice Versa
Version: 1.0
Date: 2024-06-24
Description: Convert BCD (raw bytes) to decimal numbers and vice versa. BCD format is used to preserve decimals exactly, as opposed to the binary rounding errors inherent in "numeric" or "floating-point" formats.
License: LGPL-3
Imports: Rmpfr, gmp, methods
NeedsCompilation: no
Packaged: 2024-06-28 11:50:35 UTC; cgw
Author: Carl Witthoft [aut, cre]
Maintainer: Carl Witthoft <cellocgw@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-28 15:00:02 UTC

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New package clap with initial version 0.1.0
Package: clap
Title: Detecting Class Overlapping Regions in Multidimensional Data
Version: 0.1.0
Description: The issue of overlapping regions in multidimensional data arises when different classes or clusters share similar feature representations, making it challenging to delineate distinct boundaries between them accurately. This package provides methods for detecting and visualizing these overlapping regions using partitional clustering techniques based on nearest neighbor distances.
License: GPL-3
Encoding: UTF-8
Imports: mclust, FNN, dplyr, stats, rlang
Suggests: ggplot2
URL: https://github.com/pridiltal/clap
BugReports: https://github.com/pridiltal/clap/issues
NeedsCompilation: no
Packaged: 2024-06-28 10:25:59 UTC; User
Author: Priyanga Dilini Talagala [aut, cre, cph]
Maintainer: Priyanga Dilini Talagala <pritalagala@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-28 14:50:06 UTC

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New package cartographr with initial version 0.2.2
Package: cartographr
Title: Crafting Print-Ready Maps and Layered Visualizations
Version: 0.2.2
Description: Simplifying the creation of print-ready maps, this package offers a user-friendly interface derived from 'ggplot2' for handling OpenStreetMap data. It streamlines the map-making process, allowing users to focus on the story their maps tell. Transforming raw geospatial data into informative visualizations is made easy with simple features 'sf' geometries. Whether for urban planning, environmental studies, or impactful public presentations, this tool facilitates straightforward and effective map creation. Enhance the dissemination of spatial information with high-quality, narrative-driven visualizations!
License: GPL (>= 3)
URL: https://da-wi.github.io/cartographr/, https://github.com/da-wi/cartographr
BugReports: https://github.com/da-wi/cartographr/issues
Depends: R (>= 3.6)
Imports: cli, crayon, osmdata, ggplot2, grid, showtext, sysfonts, sf, utils
Suggests: dplyr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-06-28 10:12:36 UTC; David.Willinger
Author: David Willinger [aut, cre, cph]
Maintainer: David Willinger <david.willinger@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-28 14:50:09 UTC

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New package poweRbal with initial version 0.0.0.3
Package: poweRbal
Title: Phylogenetic Tree Models and the Power of Tree Shape Statistics
Version: 0.0.0.3
Author: Sophie Kersting [aut, cre] , Kristina Wicke [aut] , Mareike Fischer [aut]
Maintainer: Sophie Kersting <sophie_kersting@gmx.de>
Description: The first goal of this package is to provide a multitude of tree models, i.e., functions that generate rooted binary trees with a given number of leaves. Second, the package allows for an easy evaluation and comparison of tree shape statistics by estimating their power to differentiate between different tree models. Please note that this R package was developed alongside the manuscript "Tree balance in phylogenetic models" by S. J. Kersting, K. Wicke, and M. Fischer (2024) <doi:10.48550/arXiv.2406.05185>, which provides further background and the respective mathematical definitions. This project was supported by the project ArtIGROW, which is a part of the WIR!-Alliance ArtIFARM – Artificial Intelligence in Farming funded by the German Federal Ministry of Education and Research (No. 03WIR4805).
License: GPL (>= 3)
Depends: R (>= 3.5.0)
Imports: ape, scales, phytools, treebalance, R.utils, diversitree
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-27 07:43:47 UTC; Maus
Repository: CRAN
Date/Publication: 2024-06-28 09:20:02 UTC

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New package mgi.report.reader with initial version 0.0.1
Package: mgi.report.reader
Title: Read Mouse Genome Informatics Reports
Version: 0.0.1
Description: Provides readers for easy and consistent importing of Mouse Genome Informatics (MGI) report files: <https://www.informatics.jax.org/downloads/reports/index.html>. These data are provided by Baldarelli RM, Smith CL, Ringwald M, Richardson JE, Bult CJ, Mouse Genome Informatics Group. (2024) <doi:10.1093/genetics/iyae031>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Imports: data.table, dplyr, rlang, stringr, tibble, vroom
URL: https://www.pattern.institute/mgi.report.reader/, https://github.com/patterninstitute/mgi.report.reader/
BugReports: https://github.com/patterninstitute/mgi.report.reader/issues
NeedsCompilation: no
Packaged: 2024-06-27 14:52:13 UTC; rmagno
Author: Ramiro Magno [aut, cre] , Isabel Duarte [aut] , Ismail Gbadamosi [aut] , Ali Jawaid [aut] , Nencki Institute of Experimental Biology [fnd], University of Algarve [fnd], Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-06-28 09:40:01 UTC

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New package LogisticCopula with initial version 0.1.0
Package: LogisticCopula
Title: A Copula Based Extension of Logistic Regression
Version: 0.1.0
Maintainer: Simon Boge Brant <simbrant91@gmail.com>
Description: An implementation of a method of extending a logistic regression model beyond linear effects of the co-variates. The extension in is constructed by first equating the logistic regression model to a naive Bayes model where all the margins are specified to follow natural exponential distributions conditional on Y, that is, a model for Y given X that is specified through the distribution of X given Y, where the columns of X are assumed to be mutually independent conditional on Y. Subsequently, the model is expanded by adding vine - copulas to relax the assumption of mutual independence, where pair-copulas are added in a stage-wise, forward selection manner. Some heuristics are employed during the process of selecting edges, as well as the families of pair-copula models. After each component is added, the parameters are updated by a (smaller) number of gradient steps to maximise the likelihood. When the algorithm has stopped adding edges, based the criterion that a new edge should improve [...truncated...]
License: MIT + file LICENSE
Imports: VineCopula (>= 2.5.0), rvinecopulib (>= 0.6.3.1.1), igraph (>= 2.0.3), numDeriv (>= 8-1.1), stringr (>= 1.5.1)
Depends: R (>= 3.5.0), brglm2 (>= 0.9)
Encoding: UTF-8
LazyData: true
Author: Simon Boge Brant [aut, cre], Ingrid Hobaek Haff [aut]
NeedsCompilation: no
Packaged: 2024-06-27 09:44:30 UTC; simbr
Repository: CRAN
Date/Publication: 2024-06-28 09:20:06 UTC

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New package gggenomes with initial version 1.0.0
Package: gggenomes
Title: A Grammar of Graphics for Comparative Genomics
Version: 1.0.0
Description: An extension of 'ggplot2' for creating complex genomic maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It implements a layout concept inspired by 'ggraph' and introduces tracks to bring tidiness to the mess that is genomics data.
License: MIT + file LICENSE
URL: https://github.com/thackl/gggenomes
BugReports: https://github.com/thackl/gggenomes/issues
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Depends: R (>= 3.4.2), ggplot2 (>= 3.5.0),
Imports: vctrs, rlang, dplyr, tidyr, readr (>= 2.0.0), purrr, tibble, stringr, grid, jsonlite, snakecase, magrittr, scales, tidyselect, colorspace, methods, utils, ellipsis
Suggests: testthat, ggtree, patchwork, Hmisc, knitr, ggrepel, IRanges,
NeedsCompilation: no
Packaged: 2024-06-27 07:06:49 UTC; iimog
Author: Thomas Hackl [aut, cre], Markus J. Ankenbrand [aut], Bart van Adrichem [aut], Kristina Haslinger [ctb, sad]
Maintainer: Thomas Hackl <t.hackl@rug.nl>
Repository: CRAN
Date/Publication: 2024-06-28 09:30:06 UTC

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New package fullRankMatrix with initial version 0.1.0
Package: fullRankMatrix
Title: Generation of Full Rank Design Matrix
Version: 0.1.0
Description: Creates a full rank matrix out of a given matrix. The intended use is for one-hot encoded design matrices that should be used in linear models to ensure that significant associations can be correctly interpreted. However, 'fullRankMatrix' can be applied to any matrix to make it full rank. It removes columns with only 0's, merges duplicated columns and discovers linearly dependent columns and replaces them with linearly independent columns that span the space of the original columns. Columns are renamed to reflect those modifications. This results in a full rank matrix that can be used as a design matrix in linear models. The algorithm and some functions are inspired by Kuhn, M. (2008) <doi:10.18637/jss.v028.i05>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, igraph, testthat (>= 3.0.0), WeightIt, caret, plm, spelling
VignetteBuilder: knitr
URL: https://github.com/Pweidemueller/fullRankMatrix
BugReports: https://github.com/Pweidemueller/fullRankMatrix/issues
Language: en-US
NeedsCompilation: no
Packaged: 2024-06-26 21:45:03 UTC; pweide
Author: Paula Weidemueller [aut, cre, cph] , Constantin Ahlmann-Eltze [aut]
Maintainer: Paula Weidemueller <paulahw3214@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-28 09:10:02 UTC

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New package evitaicossa with initial version 0.0-1
Package: evitaicossa
Title: Antiassociative Algebra
Version: 0.0-1
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Description: Methods to deal with the free antiassociative algebra over the reals with an arbitrary number of indeterminates. Antiassociativity means that (xy)z = -x(yz). Antiassociative algebras are nilpotent with nilindex four (Remm, 2022, <doi:10.48550/arXiv.2202.10812>) and this drives the design and philosophy of the package. Methods are defined to create and manipulate arbitrary elements of the antiassociative algebra, and to extract and replace coefficients. A vignette is provided.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Suggests: knitr, markdown, rmarkdown, testthat, mvtnorm, covr
VignetteBuilder: knitr
Imports: Rcpp (>= 1.0-7), disordR (>= 0.9-8-2), methods, Rdpack
LinkingTo: Rcpp
URL: https://github.com/RobinHankin/evitaicossa
BugReports: https://github.com/RobinHankin/evitaicossa/issues
NeedsCompilation: yes
Packaged: 2024-06-26 19:36:19 UTC; rhankin
Author: Robin K. S. Hankin [aut, cre]
Repository: CRAN
Date/Publication: 2024-06-28 09:10:06 UTC

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New package epiCo with initial version 1.0.0
Package: epiCo
Title: Statistical and Viz Tools for Vector-Borne Diseases in Colombia
Version: 1.0.0
Description: Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
License: MIT + file LICENSE
URL: https://epiverse-trace.github.io/epiCo/, https://github.com/epiverse-trace/epiCo
BugReports: https://github.com/epiverse-trace/epiCo/issues
Depends: R (>= 3.5.0)
Imports: dplyr, ggplot2, ggraph, igraph, incidence, leaflet, lubridate, magrittr, RColorBrewer, rlang, scales, spdep, stats, treemapify, utils
Suggests: checkmate, covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-27 15:15:10 UTC; juandanielumanacaro
Author: Juan D. Umana [aut, cre, cph] , Juan Montenegro-Torres [aut] , Julian Otero [aut] , Hugo Gruson [ctb]
Maintainer: Juan D. Umana <jd.umana10@uniandes.edu.co>
Repository: CRAN
Date/Publication: 2024-06-28 09:40:05 UTC

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New package CommEcol with initial version 1.8.1
Package: CommEcol
Title: Community Ecology Analyses
Version: 1.8.1
Date: 2024-06-18
Depends: vegan, rncl
Imports: ape, picante, adespatial, betapart, gmp
Description: Autosimilarity curves, standardization of spatial extent, dissimilarity indexes that overweight rare species, phylogenetic and functional (pairwise and multisample) dissimilarity indexes and nestedness for phylogenetic, functional and other diversity metrics. The methods for phylogenetic and functional nestedness is described in Melo, Cianciaruso and Almeida-Neto (2014) <doi:10.1111/2041-210X.12185>. This should be a complement to available packages, particularly 'vegan'.
License: GPL-2
NeedsCompilation: no
Maintainer: Adriano Sanches Melo <asm.adrimelo@gmail.com>
Author: Adriano Sanches Melo [aut, cre]
Repository: CRAN
LazyLoad: yes
Packaged: 2024-06-18 18:28:35 UTC; asmad
Date/Publication: 2024-06-28 09:50:02 UTC

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New package rapidsplithalf with initial version 0.2
Package: rapidsplithalf
Title: A Fast Split-Half Reliability Algorithm
Version: 0.2
Date: 2024-06-24
Description: Accurately estimates the reliability of cognitive tasks using a fast and flexible permutated split-half reliability algorithm that supports stratified splitting while maintaining equal split sizes. See Kahveci, Bathke, and Blechert (2022) <doi:10.31234/osf.io/ta59r> for details.
License: GPL (>= 2)
Depends: R(>= 4.0)
Imports: Rcpp (>= 1.0.5), doParallel, foreach
Suggests: knitr, rmarkdown
LinkingTo: Rcpp
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-06-26 16:17:45 UTC; b1066151
Author: Sercan Kahveci [aut, cre]
Maintainer: Sercan Kahveci <sercan.kahveci@plus.ac.at>
Repository: CRAN
Date/Publication: 2024-06-28 08:50:02 UTC

More information about rapidsplithalf at CRAN
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Thu, 27 Jun 2024

New package simpletex with initial version 1.0.3
Package: simpletex
Title: Mathematical Formulas and Character Recognition
Version: 1.0.3
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Date: 2024-06-26 12:29:14 UTC
Description: By calling the 'SimpleTex' <https://simpletex.cn/> open API implements text and mathematical formula recognition on the image, and the output formula can be used directly with 'Markdown' and 'LaTeX'.
License: MIT + file LICENSE
URL: https://gitlab.com/chuxinyuan/simpletex
BugReports: https://gitlab.com/chuxinyuan/simpletex/-/issues
Depends: R (>= 3.6)
Imports: glue, digest, httr, jsonlite
Suggests: testthat (>= 2.1.0), knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-26 12:33:33 UTC; cxy
Author: Xinyuan Chu [aut, cre]
Repository: CRAN
Date/Publication: 2024-06-27 14:30:02 UTC

More information about simpletex at CRAN
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New package scorematchingad with initial version 0.0.64
Package: scorematchingad
Title: Score Matching Estimation by Automatic Differentiation
Version: 0.0.64
Description: Hyvärinen's score matching (Hyvärinen, 2005) <https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful estimation technique when the normalising constant for a probability distribution is difficult to compute. This package implements score matching estimators using automatic differentiation in the 'CppAD' library <https://github.com/coin-or/CppAD> and is designed for quickly implementing score matching estimators for new models. Also available is general robustification (Windham, 1995) <https://www.jstor.org/stable/2346159>. Already in the package are estimators for directional distributions (Mardia, Kent and Laha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible Polynomially-Tilted Pairwise Interaction model for compositional data. The latter estimators perform well when there are zeros in the compositions (Scealy and Wood, 2023) <doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy, Hingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-1 [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: testthat, ks, movMF, cubature, simdd, numDeriv
Enhances: RcppEigen (>= 0.3.3.7), RcppXPtrUtils
Depends: R (>= 3.5.0)
Imports: MCMCpack, optimx, FixedPoint, Rdpack, Rcpp (>= 1.0.9), methods, stats, R6, utils, rlang, ellipsis
LinkingTo: Rcpp (>= 1.0.9), RcppEigen (>= 0.3.3.7)
NeedsCompilation: yes
Packaged: 2024-06-26 04:38:51 UTC; kassel
Author: Kassel Liam Hingee [aut, cre] , Janice Scealy [aut] , Bradley M. Bell [cph]
Maintainer: Kassel Liam Hingee <kassel.hingee@anu.edu.au>
Repository: CRAN
Date/Publication: 2024-06-27 14:40:03 UTC

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New package mlts with initial version 1.0.0
Package: mlts
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Version: 1.0.0
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM). The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference. Path models and formulas for user-defined models can be easily created with functions using 'knitr'. Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/munchfab/mlts
BugReports: https://github.com/munchfab/mlts/issues
Imports: cowplot, dplyr (>= 1.1.3), ggplot2, methods, mvtnorm, pdftools, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rmarkdown, rstan (>= 2.32.3), rstantools (>= 2.4.0), stats
Suggests: knitr, testthat (>= 3.0.0)
Biarch: true
Depends: R (>= 3.5.0)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2024-06-26 10:25:36 UTC; fabi
Author: Kenneth Koslowski [aut, cre, cph] , Fabian Muench [aut] , Tobias Koch [aut] , Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Repository: CRAN
Date/Publication: 2024-06-27 14:20:02 UTC

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New package LatentBMA with initial version 0.1.0
Package: LatentBMA
Title: Bayesian Model Averaging for Univariate Link Latent Gaussian Models
Version: 0.1.0
Author: Gregor Zens [aut, cre], Mark F.J. Steel [aut]
Maintainer: Gregor Zens <zens@iiasa.ac.at>
Description: Bayesian model averaging (BMA) algorithms for univariate link latent Gaussian models (ULLGMs). For detailed information, refer to Steel M.F.J. & Zens G. (2024) "Model Uncertainty in Latent Gaussian Models with Univariate Link Function" <doi:10.48550/arXiv.2406.17318>. The package supports various g-priors and a beta-binomial prior on the model space. It also includes auxiliary functions for visualizing and tabulating BMA results. Currently, it offers an out-of-the-box solution for model averaging of Poisson log-normal (PLN) and binomial logistic-normal (BiL) models. The codebase is designed to be easily extendable to other likelihoods, priors, and link functions.
Encoding: UTF-8
License: MIT + file LICENSE
Imports: ggplot2 (>= 3.5.1), knitr (>= 1.47), mnormt (>= 2.1.1), progress (>= 1.2.3), reshape2 (>= 1.4.4)
Suggests: rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-26 14:03:10 UTC; Gregor
Repository: CRAN
Date/Publication: 2024-06-27 14:40:26 UTC

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New package greenR with initial version 0.0.1.1
Package: greenR
Title: Green Index Quantification, Analysis and Visualization
Version: 0.0.1.1
Description: Quantification, analysis, and visualization of urban greenness within city networks using data from 'OpenStreetMap' <https://www.openstreetmap.org>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: DT, httr, magrittr, dplyr, ggplot2, osmdata, sf, htmltools, leaflet, shiny, tibble, SuperpixelImageSegmentation, OpenImageR, osrm, spatstat.geom, stats, units, duckdb, DBI, data.table, RColorBrewer, htmlwidgets, viridisLite, rstudioapi, jsonlite
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-26 14:29:23 UTC; smahajan
Author: Sachit Mahajan [aut, cre]
Maintainer: Sachit Mahajan <sachitmahajan90@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-27 14:40:08 UTC

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New package frailtypack with initial version 3.6.1
Package: frailtypack
Version: 3.6.1
Date: 2024-06-25
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Depends: R (>= 3.5.0), survival, boot, MASS, survC1, doBy
Imports: statmod, nlme, shiny, rootSolve, splines
LazyLoad: no
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested fra [...truncated...]
License: GPL (>= 2.0)
URL: https://virginie1rondeau.wixsite.com/virginierondeau/software-frailtypack https://frailtypack-pkg.shinyapps.io/shiny_frailtypack/
Suggests: knitr, testthat, rmarkdown, markdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2024-06-27 14:40:11 UTC
Packaged: 2024-06-25 12:17:58 UTC; Quent
NeedsCompilation: yes
Author: Virginie Rondeau [aut, cre] , Juan R. Gonzalez [aut], Yassin Mazroui [aut], Audrey Mauguen [aut], Amadou Diakite [aut], Alexandre Laurent [aut], Myriam Lopez [aut], Agnieszka Krol [aut], Casimir L. Sofeu [aut], Julien Dumerc [aut], Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>

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New package bayesCureRateModel with initial version 1.0
Package: bayesCureRateModel
Title: Bayesian Cure Rate Modeling for Time-to-Event Data
Version: 1.0
Date: 2024-06-26
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Description: A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2023) <doi:10.48550/arXiv.2310.06926>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of Gamma distributions. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.
License: GPL-2
URL: https://github.com/mqbssppe/Bayesian_cure_rate_model
Imports: Rcpp (>= 1.0.12),doParallel, foreach, mclust, coda, HDInterval, VGAM, calculus, flexsurv
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2024-06-26 11:12:12 UTC; panagiotis
Author: Panagiotis Papastamoulis [aut, cre] , Fotios Milienos [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-06-27 14:20:06 UTC

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New package geohabnet with initial version 2.1.3
Package: geohabnet
Title: Geographical Risk Analysis Based on Habitat Connectivity
Version: 2.1.3
Date: 2024-06-26
Description: The geohabnet package is designed to perform a geographically or spatially explicit risk analysis of habitat connectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067> proposed the concept of cropland connectivity as a risk factor for plant pathogen or pest invasions. As the functions in geohabnet were initially developed thinking on cropland connectivity, users are recommended to first be familiar with the concept by looking at the Xing et al paper. In a nutshell, a habitat connectivity analysis combines information from maps of host density, estimates the relative likelihood of pathogen movement between habitat locations in the area of interest, and applies network analysis to calculate the connectivity of habitat locations. The functions of geohabnet are built to conduct a habitat connectivity analysis relying on geographic parameters (spatial resolution and spatial extent), dispersal parameters (in two commonly used dispersal kernels: inverse power law and negative exponent [...truncated...]
License: GPL-3
Encoding: UTF-8
Imports: config (>= 0.3.1), geodata (>= 0.6.2), geosphere (>= 1.5.18), igraph (>= 2.0.3), terra (>= 1.7.29), easycsv (>= 1.0.8), yaml (>= 2.3.7), stats, stringr (>= 1.5.0), memoise (>= 2.0.1), graphics, rlang (>= 1.1.1), viridisLite (>= 0.4.2), beepr (>= 1.3), rnaturalearth (>= 0.3.3), tools, methods, future.apply (>= 1.11.0), future (>= 1.33.0), magrittr (>= 2.0.3), ggplot2 (>= 3.5.1), patchwork (>= 1.2.0)
Suggests: devtools, knitr, lintr (>= 3.0.2), mockthat (>= 0.2.8), pkgdown, rmarkdown, testthat (>= 3.1.7)
URL: https://garrettlab.github.io/HabitatConnectivity/, https://CRAN.R-project.org/package=geohabnet/, https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/, https://www.garrettlab.com/
BugReports: https://github.com/GarrettLab/HabitatConnectivity/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-26 19:05:04 UTC; kkeshav
Author: Krishna Keshav [aut, cre], Aaron Plex [aut] , Garrett Lab [ctb] , Karen Garrett [aut] , University of Florida [cph, fnd]
Maintainer: Krishna Keshav <kkeshav@ufl.edu>
Repository: CRAN
Date/Publication: 2024-06-27 11:50:02 UTC

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Wed, 26 Jun 2024

New package readme2vignette with initial version 0.1.0
Package: readme2vignette
Title: Convert README to Vignette During Package Installation
Version: 0.1.0
Description: Convert README.md to vignettes when installing packages without vignettes.
License: MIT + file LICENSE
URL: https://github.com/indenkun/readme2vignette
BugReports: https://github.com/indenkun/readme2vignette/issues
Encoding: UTF-8
Imports: desc, fs, glue, knitr, pkgbuild, remotes, rmarkdown, usethis, utils, whisker
NeedsCompilation: no
Packaged: 2024-06-26 06:57:06 UTC; kobayashi
Author: Mao Kobayashi [aut, cre]
Maintainer: Mao Kobayashi <kobamao.jp@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-26 13:00:02 UTC

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New package neodistr with initial version 0.1.1
Package: neodistr
Title: Neo-Normal Distribution
Version: 0.1.1
Maintainer: Achmad Syahrul Choir <madsyair@stis.ac.id>
Description: Provides functions for calculating the density, cumulative distribution, quantile, and random number of neo-normal distribution. It also interfaces with the 'brms' package, allowing the use of the neo-normal distribution as a custom family. This integration enables the application of various 'brms' formulas for neo-normal regression. The package implements the following distributions: Modified to be Stable as Normal from Burr (MSNBurr), Modified to be Stable as Normal from Burr-IIa (MSNBurr-IIa), Generalized of MSNBurr (GMSNBurr), and Jones-Faddy Skew-t. References: Choir, A. S. (2020).Unpublished Dissertation. Iriawan, N. (2000).Unpublished Dissertation. Jones, M. C. and Faddy,M. J. (2003).<doi:10.1111/1467-9868.00378>. Rigby, R. A., Stasinopoulos, M. D., Heller, G. Z., & Bastiani, F. D. (2019) <doi:10.1201/9780429298547>.
License: GPL-3
Depends: R (>= 3.6.0),shinythemes,plotly,brms
Imports: rstan , stats,Rmpfr,ggplot2,shiny
Suggests: kableExtra,knitr, testthat
URL: https://github.com/madsyair/neodistr
BugReports: https://github.com/madsyair/neodistr/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-25 12:34:26 UTC; madsyair
Author: Achmad Syahrul Choir [aut, cre] , Anisa' Faoziah [aut], Nur Iriawan [aut]
Repository: CRAN
Date/Publication: 2024-06-26 12:40:02 UTC

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New package gamlssx with initial version 1.0.1
Package: gamlssx
Title: Generalized Additive Extreme Value Models for Location, Scale and Shape
Version: 1.0.1
Date: 2024-06-25
Description: Fits generalized additive models for the location, scale and shape parameters of a generalized extreme value response distribution. The methodology is based on Rigby, R.A. and Stasinopoulos, D.M. (2005), <doi:10.1111/j.1467-9876.2005.00510.x> and implemented using functions from the 'gamlss' package <doi:10.32614/CRAN.package.gamlss>.
Imports: gamlss, gamlss.dist, nieve, stats
License: GPL (>= 3)
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.3.0)
Suggests: testthat (>= 3.0.0)
URL: https://paulnorthrop.github.io/gamlssx/, https://github.com/paulnorthrop/gamlssx
BugReports: https://github.com/paulnorthrop/gamlssx/issues
NeedsCompilation: no
Packaged: 2024-06-25 13:19:36 UTC; Paul
Author: Paul J. Northrop [aut, cre, cph], Jennifer Ji [aut]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2024-06-26 12:40:05 UTC

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New package frequentistSSDBinary with initial version 0.1.0
Package: frequentistSSDBinary
Title: Screened Selection Design with Binary Endpoints
Version: 0.1.0
Maintainer: Chia-Wei Hsu <Chia-Wei.Hsu@stjude.org>
Description: A study based on the screened selection design (SSD) is an exploratory phase II randomized trial with two or more arms but without concurrent control. The primary aim of the SSD trial is to pick a desirable treatment arm (e.g., in terms of the response rate) to recommend to the subsequent randomized phase IIb (with the concurrent control) or phase III. The proposed designs can “partially” control or provide the empirical type I error/false positive rate by an optimal algorithm (implemented by the optimal_2arm_binary() or optimal_3arm_binary() function) for each arm. All the design needed components (sample size, operating characteristics) are supported.
License: GPL-2
Encoding: UTF-8
Depends: mvtnorm, clinfun, ph2mult
NeedsCompilation: no
Packaged: 2024-06-26 03:27:31 UTC; chsu1
Author: Chia-Wei Hsu [aut, cre], Zongheng Cai [aut], Haitao Pan [aut]
Repository: CRAN
Date/Publication: 2024-06-26 13:00:06 UTC

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New package ewp with initial version 0.1.1
Package: ewp
Title: An Empirical Model for Underdispersed Count Data
Version: 0.1.1
Description: Count regression models for underdispersed small counts (lambda < 20) based on the three-parameter exponentially weighted Poisson distribution of Ridout & Besbeas (2004) <DOI:10.1191/1471082X04st064oa>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
LinkingTo: BH, Rcpp
Imports: Rcpp
Suggests: covr, DHARMa, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-06-25 15:01:44 UTC; philipp.boerschsupan
Author: Philipp Boersch-Supan [aut, cre] , James Clarke [aut]
Maintainer: Philipp Boersch-Supan <pboesu@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-26 12:50:02 UTC

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New package clinicalomicsdbR with initial version 1.0.5
Package: clinicalomicsdbR
Title: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing
Version: 1.0.5
Description: Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr2, R6, dplyr, utils, jsonlite
BugReports: https://github.com/bzhanglab/clinicalomicsdbR/issues
URL: https://github.com/bzhanglab/clinicalomicsdbR
NeedsCompilation: no
Packaged: 2024-06-25 14:56:04 UTC; zhanglab
Author: John Elizarraras [aut, cre, ctb]
Maintainer: John Elizarraras <john.elizarraras@bcm.edu>
Repository: CRAN
Date/Publication: 2024-06-26 12:50:05 UTC

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Tue, 25 Jun 2024

New package VsusP with initial version 1.0.0
Package: VsusP
Title: Variable Selection using Shrinkage Priors
Version: 1.0.0
Description: Bayesian variable selection using shrinkage priors to identify significant variables in high-dimensional datasets. The package includes methods for determining the number of significant variables through innovative clustering techniques of posterior distributions, specifically utilizing the 2-Means and Sequential 2-Means (S2M) approaches. The package aims to simplify the variable selection process with minimal tuning required in statistical analysis.
License: GPL (>= 3)
Encoding: UTF-8
Imports: bayesreg, stats
Suggests: covr, MASS, knitr, rmarkdown, tinytex, testthat (>= 3.0.0)
Maintainer: Nilson Chapagain <nilson.chapagain@gmail.com>
URL: https://github.com/nilson01/VsusP-variable-selection-using-shrinkage-priors
BugReports: https://github.com/nilson01/VsusP-variable-selection-using-shrinkage-priors/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-24 08:16:11 UTC; nilson
Author: Nilson Chapagain [aut, cre] , Debdeep Pati [aut]
Repository: CRAN
Date/Publication: 2024-06-25 14:10:02 UTC

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New package stgam with initial version 0.0.1.0
Package: stgam
Title: Spatially and Temporally Varying Coefficient Models Using Generalized Additive Models
Version: 0.0.1.0
Author: Lex Comber [aut, cre], Paul Harris [ctb], Chris Brunsdon [ctb]
Maintainer: Lex Comber <a.comber@leeds.ac.uk>
Description: A framework for specifying spatially, temporally and spatial-and-temporally varying coefficient models using Generalized Additive Models with Gaussian Process smooths. The smooths are parameterised with location and / or time attributes. Importantly the framework supports the investigation of the presence and nature of any space-time dependencies in the data, allows the user to evaluate different model forms (specifications) and to pick the most probable model or to combine multiple varying coefficient models using Bayesian Model Averaging. For more details see: Brunsdon et al (2023) <doi:10.4230/LIPIcs.GIScience.2023.17>, Comber et al (2023) <doi:10.4230/LIPIcs.GIScience.2023.22> and Comber et al (2024) <doi:10.1080/13658816.2023.2270285>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: cols4all, knitr, purrr, rmarkdown, sf, testthat (>= 3.0.0), tidyr
URL: https://github.com/lexcomber/stgam
BugReports: https://github.com/lexcomber/stgam/issues
Depends: R (>= 2.10),
LazyData: true
Imports: cowplot, doParallel, dplyr, foreach, ggplot2, glue, grDevices, magrittr, metR, mgcv, parallel, tidyselect
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-24 15:05:36 UTC; geoaco
Repository: CRAN
Date/Publication: 2024-06-25 14:20:02 UTC

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New package sreg with initial version 1.0.0
Package: sreg
Title: Stratified Randomized Experiments
Version: 1.0.0
Description: Estimate average treatment effects (ATEs) in stratified randomized experiments. 'sreg' is designed to accommodate scenarios with multiple treatments and cluster-level treatment assignments, and accommodates optimal linear covariate adjustment based on baseline observable characteristics. 'sreg' computes estimators and standard errors based on Bugni, Canay, Shaikh (2018) <doi:10.1080/01621459.2017.1375934>; Bugni, Canay, Shaikh, Tabord-Meehan (2024+) <doi:10.48550/arXiv.2204.08356>; and Jiang, Linton, Tang, Zhang (2023+) <doi:10.48550/arXiv.2201.13004>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, extraDistr, rlang, tidyr, cli
Suggests: haven, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 2.10)
VignetteBuilder: knitr
URL: https://github.com/jutrifonov/sreg
BugReports: https://github.com/jutrifonov/sreg/issues
NeedsCompilation: no
Packaged: 2024-06-24 18:46:10 UTC; trifonovjuri
Author: Juri Trifonov [aut, cre, cph], Yuehao Bai [aut], Azeem Shaikh [aut], Max Tabord-Meehan [aut]
Maintainer: Juri Trifonov <jutrifonov@uchicago.edu>
Repository: CRAN
Date/Publication: 2024-06-25 14:30:01 UTC

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New package SFSI with initial version 1.4
Package: SFSI
Title: Sparse Family and Selection Index
Version: 1.4
Date: 2024-06-19
Description: Here we provide tools for the estimation of coefficients in penalized regressions when the (co)variance matrix of predictors and the covariance vector between predictors and response, are provided. These methods are extended to the context of a Selection Index (commonly used for breeding value prediction). The approaches offer opportunities such as the integration of high-throughput traits in genetic evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2> and solutions for training set optimization in Genomic Prediction ('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.
URL: https://github.com/MarcooLopez/SFSI
LazyLoad: true
Depends: R (>= 3.6.0)
Imports: stats, scales, tensorEVD (>= 0.1.3), parallel, reshape2, viridis, igraph, stringr, ggplot2
Suggests: BGLR, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
License: GPL-3
NeedsCompilation: yes
Packaged: 2024-06-25 04:41:59 UTC; marco
Author: Marco Lopez-Cruz [aut, cre], Gustavo de los Campos [aut], Paulino Perez-Rodriguez [ctb]
Maintainer: Marco Lopez-Cruz <maraloc@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 14:50:09 UTC

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New package RiskMap with initial version 0.1.0
Package: RiskMap
Title: Geo-Statistical Modeling of Spatially Referenced Data
Version: 0.1.0
Description: Provides functions for geo-statistical analysis of both continuous and count data using maximum likelihood methods. The models implemented in the package use stationary Gaussian processes with Matern correlation function to carry out spatial prediction in a geographical area of interest. The underpinning theory of the methods implemented in the package are found in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://claudiofronterre.github.io/RiskMap/
Imports: sf, stats, methods, ggplot2, Matrix, maxLik, terra, xtable
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-06-24 19:38:38 UTC; giorgi
Author: Emanuele Giorgi [aut, cre] , Claudio Fronterre [ctb]
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2024-06-25 14:40:05 UTC

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New package metadeconfoundR with initial version 1.0.2
Package: metadeconfoundR
Title: Covariate-Sensitive Analysis of Cross-Sectional High-Dimensional Data
Version: 1.0.2
Maintainer: Till Birkner <metadeconf@till-birkner.de>
Description: Using non-parametric tests, naive associations between omics features and metadata in cross-sectional data-sets are detected. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests, as first described in Forslund, Chakaroun, Zimmermann-Kogadeeva, et al. (2021) <doi:10.1038/s41586-021-04177-9>. The generated output can be graphically summarized using the built-in plotting function.
License: GPL-2
Encoding: UTF-8
LazyData: true
URL: https://github.com/TillBirkner/metadeconfoundR
BugReports: https://github.com/TillBirkner/metadeconfoundR/issues
Imports: lmtest, foreach, parallel, doParallel, stats, futile.logger, lme4, ggplot2, reshape2, methods, rlang
Depends: R (>= 3.5.0), detectseparation
Suggests: pander, knitr, gridExtra, kableExtra
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-24 19:41:48 UTC; tbirkne
Author: Till Birkner [aut, cre] , Sofia Kirke Forslund-Startceva [ctb]
Repository: CRAN
Date/Publication: 2024-06-25 14:40:02 UTC

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New package ExactCox with initial version 0.1.0
Package: ExactCox
Title: Exact Test and Exact Confidence Interval for the Cox Model
Version: 0.1.0
Author: Yongwu Shao [aut, cre, cph]
Maintainer: Yongwu Shao <ywshao@gmail.com>
Description: Performs the exact test on whether there is a difference between two survival curves. Exact confidence interval for the hazard ratio can also be generated for the Cox model.
Imports: BiasedUrn
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-25 05:38:56 UTC; donghua
Repository: CRAN
Date/Publication: 2024-06-25 15:00:01 UTC

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New package CMGFM with initial version 1.1
Package: CMGFM
Title: Covariate-Augumented Generalized Factor Model
Version: 1.1
Date: 2024-06-21
Author: Wei Liu [aut, cre], Jiakun Jiang [aut], Dewei Xiang [aut], Xuancheng Zhou [aut]
Maintainer: Wei Liu <LiuWeideng@gmail.com>
Description: Covariate-augumented generalized factor model is designed to account for cross-modal heterogeneity, capture nonlinear dependencies among the data, incorporate additional information, and provide excellent interpretability while maintaining high computational efficiency.
BugReports: https://github.com/feiyoung/CMGFM/issues
License: GPL-3
Depends: irlba, R (>= 3.5.0)
Imports: MASS, stats, GFM, Rcpp (>= 1.0.10)
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-06-25 04:40:10 UTC; 10297
Repository: CRAN
Date/Publication: 2024-06-25 15:00:05 UTC

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New package autovi with initial version 0.4.0
Package: autovi
Title: Auto Visual Inference with Computer Vision Models
Version: 0.4.0
Description: Provides automated visual inference of residual plots using computer vision models, facilitating diagnostic checks for classical normal linear regression models.
License: MIT + file LICENSE
URL: https://tengmcing.github.io/autovi/, https://github.com/TengMCing/autovi/
BugReports: https://github.com/TengMCing/autovi/issues
Encoding: UTF-8
Imports: bandicoot, ggplot2, stats, tibble, tools, reticulate, utils, cassowaryr, cli
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), covr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-06-24 19:02:05 UTC; patrickli
Author: Weihao Li [aut, cre, cph]
Maintainer: Weihao Li <llreczx@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 14:30:05 UTC

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New package RPointCloud with initial version 0.6.2
Package: RPointCloud
Version: 0.6.2
Date: 2024-06-24
Title: Visualizing Topological Loops and Voids
Description: Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) <doi:10.1101/2024.05.16.593927>.
Depends: R (>= 3.5)
Imports: methods, graphics, stats, TDA, ClassDiscovery, Mercator, rgl, splines, circlize
Suggests: knitr, rmarkdown, Polychrome, igraph, ape, PCDimension
License: Artistic-2.0
URL: http://oompa.r-forge.r-project.org/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-24 15:20:25 UTC; KRC
Author: Kevin R. Coombes [aut, cre], Jake Reed [aut], RB McGee [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:41:08 UTC

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New package phylopairs with initial version 0.1.0
Package: phylopairs
Title: Comparative Analyses of Lineage-Pair Traits
Version: 0.1.0
Description: Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context. Lineage-pair traits are characters that are defined for pairs of lineages instead of individual taxa. Examples include the strength of reproductive isolation, range overlap, competition coefficient, diet niche similarity, and relative hybrid fitness. Users supply a lineage-pair dataset and a phylogeny. 'phylopairs' calculates a covariance matrix for the pairwise-defined data and provides built-in models to test for relationships among variables while taking this covariance into account. Bayesian sampling is run through built-in 'Stan' programs via the 'rstan' package. The various models and methods that this package makes available are described in Anderson et al. (In Review), Coyne and Orr (1989) <doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002) <doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007) <doi:10.1002/ece3.3093>.
License: GPL (>= 3)
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.5.0)
Imports: ape, loo, methods, phytools, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.4.0)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2024-06-24 15:29:55 UTC; Sean
Author: Sean A. S. Anderson [aut, cre]
Maintainer: Sean A. S. Anderson <sean.as.anderson@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:50:03 UTC

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New package mssearchr with initial version 0.1.1
Package: mssearchr
Title: Library Search Against Electron Ionization Mass Spectral Databases
Version: 0.1.1
Description: Perform library searches against electron ionization mass spectral databases using either the API provided by 'MS Search' software (<https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:nistlibs>) or custom implementations of the Identity and Similarity algorithms.
License: MIT + file LICENSE
URL: https://mass-spec.ru/projects/gcmsdata/mssearchr/eng/
BugReports: https://github.com/AndreySamokhin/mssearchr/issues
Depends: R (>= 3.5.0)
Imports: Rcpp
Suggests: testthat (>= 3.0.0)
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
LazyData: true
Packaged: 2024-06-24 15:11:58 UTC; Andrey
Author: Andrey Samokhin [aut, cre, cph]
Maintainer: Andrey Samokhin <andrey.s.samokhin@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:40:36 UTC

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New package FastRet with initial version 1.1.3
Package: FastRet
Title: Retention Time Prediction in Liquid Chromatography
Version: 1.1.3
Description: A framework for predicting retention times in liquid chromatography. Users can train custom models for specific chromatography columns, predict retention times using existing models, or adjust existing models to account for altered experimental conditions. The provided functionalities can be accessed either via the R console or via a graphical user interface. Related work: Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
License: GPL-3
URL: https://github.com/spang-lab/FastRet/, https://spang-lab.github.io/FastRet/
BugReports: https://github.com/spang-lab/FastRet/issues
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: bslib, caret, cluster, data.table, digest, DT, future, ggplot2, glmnet, htmltools, promises, rcdk, readxl, shiny (>= 1.8.1), shinybusy, shinyhelper, shinyjs, xgboost, xlsx
Suggests: cli, devtools, doParallel, httpgd, knitr, languageserver, lintr, pkgdown, pkgbuild, pkgload, rlang, rmarkdown, servr, tibble, testthat (>= 3.0.0), toscutil, usethis, withr
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-24 13:34:58 UTC; tobi
Author: Christian Amesoeder [aut, cph] , Marian Schoen [aut, cph], Tobias Schmidt [aut, cre, cph] , Fadi Fadil [ctb] , Katja Dettmer [ths, cph] , Peter Oefner [ths, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:20:34 UTC

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New package BRcal with initial version 0.0.4
Package: BRcal
Title: Boldness-Recalibration of Binary Events
Version: 0.0.4
Description: Boldness-recalibration maximally spreads out probability predictions while maintaining a user specified level of calibration, facilitated the brcal() function. Supporting functions to assess calibration via Bayesian and Frequentist approaches, Maximum Likelihood Estimator (MLE) recalibration, Linear in Log Odds (LLO)-adjust via any specified parameters, and visualize results are also provided. Methodological details can be found in Guthrie & Franck (2024) <doi:10.1080/00031305.2024.2339266>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.3)
LazyData: true
Imports: nloptr, fields, ggplot2
Suggests: knitr, rmarkdown, devtools, xfun, gridExtra, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/apguthrie/BRcal
BugReports: https://github.com/apguthrie/BRcal/issues
NeedsCompilation: no
Packaged: 2024-06-24 14:18:57 UTC; apgut
Author: Adeline P. Guthrie [aut, cre], Christopher T. Franck [aut]
Maintainer: Adeline P. Guthrie <apguthrie47@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:30:08 UTC

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New package babette with initial version 2.3.4
Package: babette
Title: Control 'BEAST2'
Version: 2.3.4
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.
License: GPL-3
VignetteBuilder: knitr
URL: https://docs.ropensci.org/babette/ (website), https://github.com/ropensci/babette
BugReports: https://github.com/ropensci/babette/issues
Depends: beautier (>= 2.6.12), beastier (>= 2.5), mauricer (>= 2.5.2), R (>= 3.5.0), tracerer
Imports: phangorn, rlang (>= 1.1.0), stringr, xml2
Suggests: ape, ggplot2, knitr, lintr, nLTT, rappdirs, rmarkdown, spelling, testthat (>= 2.1.0)
Language: en-US
Encoding: UTF-8
SystemRequirements: BEAST2 (https://www.beast2.org/)
NeedsCompilation: no
Packaged: 2024-06-24 09:17:09 UTC; richel
Author: Richel J.C. Bilderbeek [aut, cre] , Joelle Barido-Sottani [rev] , David Winter [rev] , Jason Griffiths [ctb] , Olivier Roy [ctb], Giovanni Laudanno [ctb]
Maintainer: Richel J.C. Bilderbeek <rjcbilderbeek@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-25 11:20:06 UTC

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New package bsynth with initial version 1.0
Package: bsynth
Title: Bayesian Synthetic Control
Version: 1.0
Description: Implements the Bayesian Synthetic Control method for causal inference in comparative case studies. This package provides tools for estimating treatment effects in settings with a single treated unit and multiple control units, allowing for uncertainty quantification and flexible modeling of time-varying effects. The methodology is based on the paper by Vives and Martinez (2022) <doi:10.48550/arXiv.2206.01779>.
License: Apache License 2.0
URL: https://github.com/google/bsynth, https://arxiv.org/abs/2206.01779
BugReports: https://github.com/google/bsynth/issues
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0)
Imports: R6, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), cubelyr, dplyr, ggplot2, glue, magrittr, methods, purrr, rstan (>= 2.18.1), rstantools (>= 2.1.1), scales, tibble, tidyr, vizdraws (>= 1.1), stats, rlang
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, roxygen2, gsynth, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-06-23 16:15:49 UTC; rstudio
Author: Ignacio Martinez [aut, cre] , Jaume [aut]
Maintainer: Ignacio Martinez <ignacio@martinez.fyi>
Repository: CRAN
Date/Publication: 2024-06-25 10:50:03 UTC

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Mon, 24 Jun 2024

New package treesitter.r with initial version 1.0.1
Package: treesitter.r
Title: 'R' Grammar for 'Tree-Sitter'
Version: 1.0.1
Description: Provides bindings to an 'R' grammar for 'Tree-sitter', to be used alongside the 'treesitter' package. 'Tree-sitter' builds concrete syntax trees for source files of any language, and can efficiently update those syntax trees as the source file is edited.
License: MIT + file LICENSE
URL: https://github.com/r-lib/tree-sitter-r
BugReports: https://github.com/r-lib/tree-sitter-r/issues
Depends: R (>= 4.3.0)
Suggests: testthat (>= 3.0.0), treesitter
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-06-21 20:50:21 UTC; davis
Author: Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd], Tree-sitter authors [cph]
Maintainer: Davis Vaughan <davis@posit.co>
Repository: CRAN
Date/Publication: 2024-06-24 15:30:02 UTC

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New package treesitter with initial version 0.1.0
Package: treesitter
Title: Bindings to 'Tree-Sitter'
Version: 0.1.0
Description: Provides bindings to 'Tree-sitter', an incremental parsing system for programming tools. 'Tree-sitter' builds concrete syntax trees for source files of any language, and can efficiently update those syntax trees as the source file is edited. It also includes a robust error recovery system that provides useful parse results even in the presence of syntax errors.
License: MIT + file LICENSE
URL: https://github.com/DavisVaughan/r-tree-sitter
BugReports: https://github.com/DavisVaughan/r-tree-sitter/issues
Depends: R (>= 4.3.0)
Imports: cli (>= 3.6.2), R6 (>= 2.5.1), rlang (>= 1.1.3), vctrs (>= 0.6.5)
Suggests: testthat (>= 3.0.0), treesitter.r
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-06-22 00:02:29 UTC; davis
Author: Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd], Tree-sitter authors [cph]
Maintainer: Davis Vaughan <davis@posit.co>
Repository: CRAN
Date/Publication: 2024-06-24 15:30:05 UTC

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New package rcausim with initial version 0.1.1
Package: rcausim
Title: Generate Causally-Simulated Data
Version: 0.1.1
Description: Generate causally-simulated data to serve as ground truth for evaluating methods in causal discovery and effect estimation. The package provides tools to assist in defining functions based on specified edges, and conversely, defining edges based on functions. It enables the generation of data according to these predefined functions and causal structures. This is particularly useful for researchers in fields such as artificial intelligence, statistics, biology, medicine, epidemiology, economics, and social sciences, who are developing a general or a domain-specific methods to discover causal structures and estimate causal effects. Data simulation adheres to principles of structural causal modeling. Detailed methodologies and examples are documented in our vignette, available at <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rcausim/blob/master/doc/causal_simulation_exemplar.html>.
Depends: R (>= 4.2)
Imports: dplyr, magrittr, purrr, tidyr, igraph
Suggests: broom, ggnetwork, ggpubr, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0), tidyverse
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-22 02:42:13 UTC; herdiantrisufriyana
Author: Herdiantri Sufriyana [aut, cre] , Emily Chia-Yu Su [aut]
Maintainer: Herdiantri Sufriyana <herdi@tmu.edu.tw>
Repository: CRAN
Date/Publication: 2024-06-24 15:30:09 UTC

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New package latent2likert with initial version 1.2.1
Package: latent2likert
Title: Converting Latent Variables into Likert Scale Responses
Version: 1.2.1
Description: Effectively simulates the discretization process inherent to Likert scales while minimizing distortion. It converts continuous latent variables into ordinal categories to generate Likert scale item responses. Particularly useful for accurately modeling and analyzing survey data that use Likert scales, especially when applying statistical techniques that require metric data.
License: MIT + file LICENSE
URL: https://lalovic.io/latent2likert/
BugReports: https://github.com/markolalovic/latent2likert/issues/
Depends: R (>= 3.5)
Imports: graphics, mvtnorm, sn, stats, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-22 15:11:25 UTC; markolalovic
Author: Marko Lalovic [aut, cre]
Maintainer: Marko Lalovic <marko@lalovic.io>
Repository: CRAN
Date/Publication: 2024-06-24 15:50:02 UTC

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New package geppe with initial version 1.0
Package: geppe
Title: Generalised Exponential Poisson and Poisson Exponential Distributions
Version: 1.0
Date: 2024-06-23
Author: Michail Tsagris [aut, cre], Sofia Piperaki [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: Rfast2, stats
Description: Maximum likelihood estimation, random values generation, density computation and other functions for the exponential-Poisson generalised exponential-Poisson and Poisson-exponential distributions. References include: Rodrigues G. C., Louzada F. and Ramos P. L. (2018). "Poisson-exponential distribution: different methods of estimation". Journal of Applied Statistics, 45(1): 128--144. <doi:10.1080/02664763.2016.1268571>. Louzada F., Ramos, P. L. and Ferreira, H. P. (2020). "Exponential-Poisson distribution: estimation and applications to rainfall and aircraft data with zero occurrence". Communications in Statistics--Simulation and Computation, 49(4): 1024--1043. <doi:10.1080/03610918.2018.1491988>. Barreto-Souza W. and Cribari-Neto F. (2009). "A generalization of the exponential-Poisson distribution". Statistics and Probability Letters, 79(24): 2493--2500. <doi:10.1016/j.spl.2009.09.003>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-06-23 11:22:38 UTC; mtsag
Repository: CRAN
Date/Publication: 2024-06-24 16:00:02 UTC

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New package dartR.sexlinked with initial version 1.0.5
Package: dartR.sexlinked
Title: Analysing SNP Data to Identify Sex-Linked Markers
Version: 1.0.5
Date: 2024-06-22
Author: Diana Robledo-Ruiz [aut, cre], Floriaan Devloo-Delva [aut], Bernd Gruber [aut], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]
Description: Identifies, filters and exports sex linked markers using 'SNP' (single nucleotide polymorphism) data. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want understand the applied rational to identify sexlinked markers and/or want to cite 'dartR.sexlinked', you find the information by typing citation('dartR.sexlinked') in the console.
License: GPL (>= 3)
URL: https://green-striped-gecko.github.io/dartR/
BugReports: https://groups.google.com/g/dartr?pli=1
Depends: adegenet (>= 2.0.0), dartR.base, dartR.data, R (>= 3.5)
Imports: doParallel (>= 1.0.17), ggplot2, methods, utils, foreach, patchwork
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-06-22 06:09:12 UTC; bernd
Maintainer: Diana Robledo-Ruiz <diana.robledoruiz1@monash.edu>
Repository: CRAN
Date/Publication: 2024-06-24 15:40:02 UTC

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New package customiser with initial version 0.1.0
Package: customiser
Title: Use R Markdown to Write your "Rprofile"
Version: 0.1.0
Description: A simple way to write ".Rprofile" code in an R Markdown file and have it knit to the correct location for your operating system.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: fs, rmarkdown, knitr, rlang, withr
URL: https://github.com/jameslairdsmith/customiser
BugReports: https://github.com/jameslairdsmith/customiser/issues
NeedsCompilation: no
Packaged: 2024-06-22 20:02:20 UTC; jameslaird-smith
Author: James Laird-Smith [aut, cre, cph]
Maintainer: James Laird-Smith <jameslairdsmith@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-24 15:50:06 UTC

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New package csquares with initial version 0.0.3
Package: csquares
Title: Concise Spatial Query and Representation System (c-Squares)
Version: 0.0.3
Author: Pepijn de Vries [aut, cre]
Description: Encode and decode c-squares, from and to simple feature (sf) or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly join or query spatial data.
Imports: dplyr, methods, purrr, rlang, sf, stars, stringr, tidyr
Suggests: ggplot2
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
NeedsCompilation: no
Packaged: 2024-06-23 00:13:10 UTC; vries171
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Repository: CRAN
Date/Publication: 2024-06-24 15:50:09 UTC

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New package qtkit with initial version 0.10.0
Package: qtkit
Title: Quantitative Text Kit
Version: 0.10.0
Description: Support package for the textbook "An Introduction to Quantitative Text Analysis for Linguists: Reproducible Research using R" (Francom, 2024) <doi:10.4324/9781003393764> (available only after August 12, 2024). Includes functions to acquire, clean, and analyze text data as well as functions to document and share the results of text analysis. The package is designed to be used in conjunction with the book, but can also be used as a standalone package for text analysis.
License: GPL (>= 3)
URL: https://qtalr.github.io/qtkit/, https://github.com/qtalr/qtkit
BugReports: https://github.com/qtalr/qtkit/issues
Depends: R (>= 3.6)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
Author: Jerid Francom [aut, cre, cph]
Maintainer: Jerid Francom <francojc@wfu.edu>
NeedsCompilation: no
Packaged: 2024-06-16 03:54:30 UTC; francojc
Repository: CRAN
Date/Publication: 2024-06-24 15:00:02 UTC

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